bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of Appropriate Cryopreservation Protocols for Epididymal Cat Spermatozoa
Authors: Buranaamnuay K 
Published: February 2015

ContentsEffects of Equex and glycerol additions and sample dilution step on frozen–thawed epididymal cat spermatozoa were investigated. The epididymal sperm pellets were resuspended in extenders using one‐ (groups III and IV) or two‐ (groups I, II, V and VI) step dilution. For one‐step dilution, the pellets were resuspended in plain egg yolk‐Tris medium (EYT) + 5% glycerol with (IV)/without (III) 0.5% Equex and cooled (4°C, 1 h). For two‐step dilution, the pellets were resuspended in EYT (I and V) and in EYT + 3% glycerol (II and VI), cooled and further diluted with EYT + 10% glycerol with (I)/without (V) 1% Equex and with EYT + 7% glycerol with (II)/without (VI) 1% Equex. Immediately after freeze–thawing, no differences (p > 0.05) were found in the motility, viability and membrane integrity (HOST) among the groups except the lowest HOST in IV (p = 0.005 to p = 0.04). The acrosome integrity (FITC) in group I was comparable to that in group II (p > 0.05) and was higher than the rest (p < 0.001 to p = 0.02). At 2 h after thawing, the motility, viability and HOST were comparable among the groups (p > 0.05) except the lower percentages of viability in III (p = 0.008 to p = 0.3) and of HOST in IV (p = 0.005 to p = 0.2). Two‐step dilutions with Equex (I, II) were more beneficial for the FITC at 2 h than without Equex (V) (p = 0.005 and p = 0.02) and than one‐step dilutions (III, IV) (p < 0.001 to p = 0.02). In conclusion, epididymal cat sperm quality after freeze–thawing could be improved when Equex was added and two‐step dilution was performed during freezing. The extenders prepared for the first step of dilution could be with (3%) or without (0%) glycerol.
Forced regressive deposits of a deglaciation sequence: Example from the Late Quaternary succession in the Lake Saint‐Jean basin (Québec, Canada)
Authors: Nutz Alexis , Ghienne Jean‐François , Schuster Mathieu , Dietrich Pierre , Roquin Claude , Hay Murray B. , Bouchette Frédéric , Cousineau Pierre A. 
Published: February 2015

AbstractDifferentiating between forced regressive deposits from deglacial periods in high latitude domains and forced regressive deposits from the onset of glacial periods in low latitude domains is fundamental for the accurate interpretation of glacial cycles within the geological record and then for the reconstruction of palaeogeography and palaeo‐climate. A forced regressive deglacial sequence is documented from the Lake Saint‐Jean basin (Québec, Canada). In this area, the Late Pleistocene to Holocene sediments have recorded the Laurentide ice sheet retreat accompanied by the invasion of marine waters (Laflamme Gulf) from ca 12·9 cal kyr bp. Subsequently, fluvio‐deltaic and coastal prograding wedges were deposited; they followed the base‐level fall due to glacio‐isostatic rebound. This succession, representing a transition from glacial to post‐glacial periods within a previously glaciated area, was investigated through recent mapping, preserved landforms, facies analysis, and new optical stimulated luminescence and radiocarbon dates. Three basin‐scale geological sections share a common lower part made of isolated ice‐contact fan deposits overlying bedrock. Throughout the entire basin, ice‐contact fans are capped by glacimarine muds. Above, fluvial and coastal prograding systems were deposited and evolved through four steps: (i) deltaic systems progressively increased in width; (ii) coastal influence on sedimentation increased; (iii) hydrographic drainage systems became more organised; and (iv) deltas graded from steep (Gilbert delta) to low‐angle foresets (mouth‐bar delta). Deposited during the base‐level fall from glacio‐isostatic rebound, the complete succession has been designated as a single falling stage system tract referred to as a deglacial falling stage system tract. It is representative of a deglaciation sequence in areas previously covered by ice during glacial periods (i.e. medium to high latitude domains). Diagnostic criteria are provided to identify such a deglacial falling stage system tract in the geological record, which may aid identification of previously unknown glacial cycles.
Extension of the Optimised Virtual Fields Method to Estimate Viscoelastic Material Parameters from 3D Dynamic Displacement Fields
Authors: Connesson N. , Clayton E. H. , Bayly P. V. , Pierron F. 
Published: February 2015

AbstractIn vivo measurement of the mechanical properties of soft tissues is essential to provide necessary data in biomechanics and medicine (early cancer diagnosis, study of traumatic brain injuries, etc.). Imaging techniques such as magnetic resonance elastography can provide 3D displacement maps in the bulk and in vivo, from which, using inverse methods, it is then possible to identify some mechanical parameters of the tissues (stiffness, damping, etc.). The main difficulties in these inverse identification procedures consist in dealing with the pressure waves contained in the data and with the experimental noise perturbing the spatial derivatives required during the processing. The optimised virtual fields method (OVFM) (Comput. Mech. 34, 2004, 439), designed to be robust to noise, presents natural and rigorous solution to deal with these problems. The OVFM has been adapted to identify material parameter maps from magnetic resonance elastography data consisting of 3D displacement fields in harmonically loaded soft materials. In this work, the method has been developed to identify elastic and viscoelastic models.The OVFM sensitivity to spatial resolution and to noise has been studied by analysing 3D analytically simulated displacement data. This study evaluates and describes the OVFM identification performances: Different biases on the identified parameters are induced by the spatial resolution and experimental noise. The well‐known identification problems in the case of quasi‐incompressible materials also find a natural solution in the OVFM. Moreover, an a posteriori criterion to estimate the local identification quality is proposed. The identification results obtained on actual experiments are briefly presented.
A Bee Swarm Algorithm for Optimising Sensor Distributions for Impact Detection on a Composite Panel
Authors: Scott M. , Worden K. 
Published: February 2015

AbstractThis paper describes the development of a bee swarm algorithm for optimising the distribution of impact detection sensors on a composite plate. The algorithm was initially developed and tested on a travelling salesman problem, it was then adapted to solve the sensor placement problem using an artificial neural network to assess the fitness of sensor distributions. It performed well, managing to quickly find optimum distributions within a constrained set of neural network parameters. The algorithm was modified further, to optimise the neural network parameters alongside the sensor distributions and the range that the network parameters could take was substantially increased. This led to significant increases in accuracy. The algorithm showed itself to be a very effective tool in the sensor optimisation problem as well as demonstrating the benefits of thoroughly optimising the neural network parameters.
Exploring lava‐flow hazards at Pico Island, Azores Archipelago (Portugal)
Authors: Cappello Annalisa , Zanon Vittorio , Del Negro Ciro , Ferreira Teresa J. L. , Queiroz Maria G. P. S. 
Published: February 2015

AbstractPico, the youngest island of the Azores Archipelago (Portugal), is characterized by a central volcano and a 30‐km‐long fissure zone. Its eruption rate is the highest of the Azores islands, with more than 35 eruptions in the last 2000 years. Here, we estimate the lava‐flow hazard for Pico Island by combining the vent opening probability derived from the spatial distribution of eruptive fissures, the classes of expected eruptions inferred from the physical and chemical characteristics of historical eruptions, and the lava‐flow paths simulated by the MAGFLOW model. The most likely area to host new eruptions is along a WNW–ESE trend centred on the central volcano, with the highest hazard affecting the two main residential zones of Lajes do Pico and Madalena. Our analysis is the first attempt to assess the lava‐flow hazard for Pico Island, and may have important implications for decision‐making in territorial management and future land‐use planning.
Immunization after renal transplantation: current clinical practice
Authors: Struijk G.H. , Lammers A.J.J. , Brinkman R.J. , Lombarts M.J.M.H. , van Vugt M. , van der Pant K.A.M.I. , ten Berge I.J.M. , Bemelman F.J. 
Published: February 2015

AbstractBackgroundThe use of potent immunosuppressive drugs and increased travel by renal transplant recipients (RTR) has augmented the risk for infectious complications. Immunizations and changes in lifestyle are protective. The Kidney Disease: Improving Global Outcomes (KDIGO) Transplant Work Group has developed guidelines on vaccination following solid organ transplantation. The degree of adherence to these guidelines is unknown, as is which barriers must be overcome to improve adherence.MethodsWe performed a cross‐sectional national survey among Dutch nephrologists to assess vaccination policy and adherence to the KDIGO guidelines. In addition, to investigate awareness and attitude of RTR regarding their risk of infection, we performed a cross‐sectional survey of RTR in our outpatient clinic.ResultsA total of 132 (63%) nephrologists completed the survey. Reported immunization rates were 90.8% for influenza and 27.3% for hepatitis B. However, pneumococcal, tetanus toxoid, and meningococcal immunization rates were low. Twenty‐seven percent of respondents were familiar with the guideline contents. The most frequent perceived barrier to guideline adherence was expectation of low effectiveness. A total of 403 RTR (62%) completed the survey. Sixty‐eight percent perceived more risk for complicated infection. A significant correlation was found between education level and variables concerning awareness and attitude toward risk of infection.ConclusionsOur results show that nephrologists' knowledge of and adherence to the recommendations regarding immunization after renal transplantation is suboptimal. Most Dutch RTR are aware of their increased risk and the possible seriousness of infectious complications. However, their behavior does not match their awareness. This disparity points to an important role for nephrologists in providing adequate counseling.
Methicillin-Resistant Staphylococcus aureus in Commercial Swine Herds Is Associated with Disinfectant and Zinc Usage
Authors: Slifierz Mackenzie Jonathan , Friendship Robert M. , Weese J. Scott 
Published: February 2015

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) originating from swine is concerning for public health, but an understanding of the emergence and persistence of MRSA in nursery herds is lacking. The aim of this study was to determine whether MRSA in nursery pigs is associated with particular herd-level parameters, including the use of antimicrobials, disinfectants, and heavy metals, which may be driving the selection and persistence of antimicrobial resistance. Nasal cultures for MRSA were completed for 390 pigs from 26 farms at the end of the suckling phase and again at 3 weeks postweaning. Herd-level information was collected, and a random subset of MRSA isolates was screened for resistance to zinc and quaternary ammonium compounds (QACs). Multivariate analysis revealed that in-feed concentrations of zinc (
P
< 0.001) and frequent disinfection of nursery pens (
P
< 0.001) are associated with MRSA shedding in nursery pigs. Furthermore, 62.5% (25/40) of MRSA isolates carried the zinc resistance gene
czrC
and demonstrated decreased susceptibility to zinc. All MRSA isolates carried at least 1 QAC resistance gene. The most common genotype was
qacG qacH smr
, which occurred in 32.5% (13/40) of isolates. Seven isolates (17.5%) demonstrated a significant tolerance to benzalkonium chloride, indicating a potential to survive commercial QAC exposure in the presence of organic matter. Overall, these findings indicate that high levels of in-feed zinc and QAC-based disinfectants are important drivers in the selection and persistence of MRSA in commercial swine herds, and these agents may be coselecting for other antimicrobial resistance genes.
The
fur
Gene as a New Phylogenetic Marker for Vibrionaceae Species Identification
Authors: Machado Henrique , Gram Lone 
Published: February 2015

ABSTRACT

Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family
Vibrionaceae
, where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of
Vibrio
species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an
in silico
approach based on genomes from 103
Vibrionaceae
strains, we demonstrate here the high resolution of the
fur
gene in the identification of
Vibrionaceae
species and its usefulness as a phylogenetic marker. The
fur
gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermore, we developed a
fur
PCR sequencing-based method that allowed identification of
Vibrio
species. The discovery of the phylogenetic power of the
fur
gene and the development of a PCR method that can be used in amplification and sequencing of the gene are of general interest whether for use alone or together with the previously suggested loci in an MLSA.
Efficacies of Nisin A and Nisin V Semipurified Preparations Alone and in Combination with Plant Essential Oils for Controlling Listeria monocytogenes
Authors: Field Des , Daly Karen , O'Connor Paula M. , Cotter Paul D. , Hill Colin , Ross R. Paul 
Published: February 2015

ABSTRACT

The food-borne pathogenic bacterium
Listeria
is known for relatively low morbidity and high mortality rates, reaching up to 25 to 30%.
Listeria
is a hardy organism, and its control in foods represents a significant challenge. Many naturally occurring compounds, including the bacteriocin nisin and a number of plant essential oils, have been widely studied and are reported to be effective as antimicrobial agents against spoilage and pathogenic microorganisms. The aim of this study was to investigate the ability of semipurified preparations (SPP) containing either nisin A or an enhanced bioengineered derivative, nisin V, alone and in combination with low concentrations of the essential oils thymol, carvacrol, and
trans
-cinnamaldehyde, to control
Listeria monocytogenes
in both laboratory media and model food systems. Combinations of nisin V-containing SPP (25 μg/ml) with thymol (0.02%), carvacrol (0.02%), or cinnamaldehyde (0.02%) produced a significantly longer lag phase than any of the essential oil-nisin A combinations. In addition, the log reduction in cell counts achieved by the nisin V-carvacrol or nisin V-cinnamaldehyde combinations was twice that of the equivalent nisin A-essential oil treatment. Significantly, this enhanced activity was validated in model food systems against
L. monocytogenes
strains of food origin. We conclude that the fermentate form of nisin V in combination with carvacrol and cinnamaldehyde offers significant advantages as a novel, natural, and effective means to enhance food safety by inhibiting food-borne pathogens such as
L. monocytogenes
.
Targeting Enterococcus faecalis Biofilms with Phage Therapy
Authors: Khalifa Leron , Brosh Yair , Gelman Daniel , Coppenhagen-Glazer Shunit , Beyth Shaul , Poradosu-Cohen Ronit , Que Yok-Ai , Beyth Nurit , Hazan Ronen 
Published: February 2015

ABSTRACT

Phage therapy has been proven to be more effective, in some cases, than conventional antibiotics, especially regarding multidrug-resistant biofilm infections. The objective here was to isolate an anti-
Enterococcus faecalis
bacteriophage and to evaluate its efficacy against planktonic and biofilm cultures.
E. faecalis
is an important pathogen found in many infections, including endocarditis and persistent infections associated with root canal treatment failure. The difficulty in
E. faecalis
treatment has been attributed to the lack of anti-infective strategies to eradicate its biofilm and to the frequent emergence of multidrug-resistant strains. To this end, an anti-
E. faecalis
and
E. faecium
phage, termed EFDG1, was isolated from sewage effluents. The phage was visualized by electron microscopy. EFDG1 coding sequences and phylogeny were determined by whole genome sequencing (GenBank accession number
KP339049
), revealing it belongs to the
Spounavirinae
subfamily of the
Myoviridae
phages, which includes promising candidates for therapy against Gram-positive pathogens. This analysis also showed that the EFDG1 genome does not contain apparent harmful genes. EFDG1 antibacterial efficacy was evaluated
in vitro
against planktonic and biofilm cultures, showing effective lytic activity against various
E. faecalis
and
E. faecium
isolates, regardless of their antibiotic resistance profile. In addition, EFDG1 efficiently prevented
ex vivo
E. faecalis
root canal infection. These findings suggest that phage therapy using EFDG1 might be efficacious to prevent
E. faecalis
infection after root canal treatment.
Sulfur Isotope Fractionation during the Evolutionary Adaptation of a Sulfate-Reducing Bacterium
Authors: Pellerin André , Anderson-Trocmé Luke , Whyte Lyle G. , Zane Grant M. , Wall Judy D. , Wing Boswell A. 
Published: February 2015

ABSTRACT

Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in
Desulfovibrio vulgaris
Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm.
PeBL1, a Novel Protein Elicitor from Brevibacillus laterosporus Strain A60, Activates Defense Responses and Systemic Resistance in Nicotiana benthamiana
Authors: Wang Haoqian , Yang Xiufen , Guo Lihua , Zeng Hongmei , Qiu Dewen 
Published: February 2015

ABSTRACT

We report the identification, characterization, and gene cloning of a novel protein elicitor (PeBL1) secreted from
Brevibacillus laterosporus
strain A60. Through a purification process consisting of ion-exchange chromatography and high-performance liquid chromatography (HPLC), we isolated a protein that was identified by electrospray ionization quadrupole time of flight tandem mass spectrometry (ESI–Q-TOF–MS-MS). The 351-bp PeBL1 gene produces a 12,833-Da protein with 116 amino acids that contains a 30-residue signal peptide. The PeBL1 protein was expressed in
Escherichia coli
. The recombinant protein can induce a typical hypersensitive response (HR) and systemic resistance in
Nicotiana benthamiana
, like the endogenous protein. PeBL1-treated
N. benthamiana
exhibited strong resistance to the infection of tobacco mosaic virus-green fluorescent protein (TMV-GFP) and
Pseudomonas syringae
pv. tabaci compared to control
N. benthamiana
. In addition, PeBL1 triggered a cascade of events that resulted in defense responses in plants, including reactive oxygen species (ROS) production, extracellular-medium alkalization, phenolic-compound deposition, and expression of several defense-related genes. Real-time quantitative-PCR analysis indicated that the known defense-related genes
PR-1
,
PR-5
,
PDF1.2
,
NPR1
, and
PAL
were upregulated to varying degrees by PeBL1. This research not only provides insights into the mechanism by which beneficial bacteria activate plant systemic resistance, but also sheds new light on a novel strategy for biocontrol using strain A60.
Diverse Nitrogen Sources in Seminal Fluid Act in Synergy To Induce Filamentous Growth of Candida albicans
Authors: Alvarez Francisco J. , Ryman Kicki , Hooijmaijers Cornelis , Bulone Vincent , Ljungdahl Per O. 
Published: February 2015

ABSTRACT

The pathogenic fungus
Candida albicans
is the leading cause of vulvovaginal candidiasis (VVC). VVC represents a major quality-of-life issue for women during their reproductive years, a stage of life where the vaginal epithelium is subject to periodic hormonally induced changes associated with menstruation and concomitant exposure to serum as well as potential intermittent contact with seminal fluid. Seminal fluid potently triggers
Candida albicans
to switch from yeastlike to filamentous modes of growth, a developmental response tightly linked to virulence. Conversely, vaginal fluid inhibits filamentation. Here, we used artificial formulations of seminal and vaginal fluids that faithfully mimic genuine fluids to assess the contribution of individual components within these fluids to filamentation. The high levels of albumin, amino acids, and
N
-acetylglucosamine in seminal fluid act synergistically as potent inducers of filamentous growth, even at atmospheric levels of CO
2
and reduced temperatures (30°C). Using a simplified
in vitro
model that mimics the natural introduction of seminal fluid into the vulvovaginal environment, a pulse of artificial seminal fluid (ASF) was found to exert an enduring potential to overcome the inhibitory efficacy of artificial vaginal fluid (AVF) on filamentation. These findings suggest that a transient but substantial change in the nutrient levels within the vulvovaginal environment during unprotected coitus can induce resident
C. albicans
cells to engage developmental programs associated with virulent growth.