bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Spray Administration of Formalin-Killed Streptococcus agalactiae in Hybrid Red Tilapia
Authors: Noraini O. , Sabri M. Y. , Siti-Zahrah A. 
Published: June 2013

Abstract
An initial evaluation of spray vaccination was carried out with 60 hybrid Red Tilapia Oreochromis spp., divided into three groups that consisted of 10 fish per group with duplicates. The formalin-killed cells (FKCs) of Streptococcus agalactiae were administered once to group 1 by spray and once daily for five consecutive days to group 2. Group 3 remained as the untreated control group and was sprayed with normal saline. A booster was given twice to all the groups, once at the second week and again at the fourth week after the first vaccination. After this initial evaluation, a challenge study was conducted with 40 tilapia divided into two groups that consisted of 10 fish per group with duplicates. Group 1 was vaccinated with FKCs of S. agalactiae by a single spray administration while group 2 remained as the untreated control group. A booster was given twice using the same protocol as in the initial evaluation. After 6 weeks, fish from one of the duplicate tanks from each of groups 1 and 2 were challenged with pathogenic S. agalactiae by intraperitoneal (IP) injection, while fish in another tank were challenged through immersion. Based on the observations, serum immunoglobulin M (IgM) levels were significantly higher (P &lt; 0.05) in the challenged fish than in the either the preexposed fish or the control group 1 week after the initial exposure. However, no significant differences (P &gt; 0.05) were noted between challenged groups 1 and 2. In addition, no significant differences (P &gt; 0.05) were observed between the frequencies of exposure. The mucus IgM level, however, remained high after each booster until the end of the 8-week study period. Meanwhile, serum IgM levels decreased after the challenge. A higher percentage of survival was noted for fish challenged through immersion (80%) compared with IP injection (70%). These results suggested that single spray exposure was able to induce IgM, which gave moderate to high protection during the challenge study.
Received October 9, 2012; accepted February 22, 2013
GEE for Multinomial Responses Using a Local Odds Ratios Parameterization
Authors: Touloumis Anestis , Agresti Alan , Kateri Maria 
Published: June 2013

AbstractSummaryIn this article, we propose a generalized estimating equations (GEE) approach for correlated ordinal or nominal multinomial responses using a local odds ratios parameterization. Our motivation lies upon observing that: (i) modeling the dependence between correlated multinomial responses via the local odds ratios is meaningful both for ordinal and nominal response scales and (ii) ordinary GEE methods might not ensure the joint existence of the estimates of the marginal regression parameters and of the dependence structure. To avoid (ii), we treat the so‐called “working” association vector as a “nuisance” parameter vector that defines the local odds ratios structure at the marginalized contingency tables after tabulating the responses without a covariate adjustment at each time pair. To estimate and simultaneously approximate adequately possible underlying dependence structures, we employ the family of association models proposed by Goodman. In simulations, the parameter estimators with the proposed GEE method for a marginal cumulative probit model appear to be less biased and more efficient than those with the independence “working” model, especially for studies having time‐varying covariates and strong correlation.
Regional density of private dentists: empirical evidence from Austria
Authors: Gächter Martin , Schwazer Peter , Theurl Engelbert , Winner Hannes 
Published: June 2013

AbstractObjectivesWe investigated the determinants of disparities in the regional density of private dentists in Austria. Specifically, we focused on the relationship between the density of private dentists and their public counterparts, thereby controlling for other possible covariates of dentist density.MethodsDentist density was measured at the district level. We used panel data of dentist density from 121 Austrian districts over the years 2001–2008. We applied a Hausman–Taylor framework to cope with possible endogeneity and to control for cross‐district effects in the dentist density.ResultsA significant negative relationship was found between the density of private and public dentists, indicating a substitution effect between the two dentist groups. A significant positive spatial relationship also existed for private and public dentists in the neighboring regions. Dental capacities in public and private hospitals and dental laboratories run by the public health insurance system did not have a significant effect on private dentist density.ConclusionsAlthough a strong negative relationship existed between private and public dentists within the districts, one should not draw the conclusion that private dentists in Austria are close substitutes for public dentists. Such a conclusion would require further empirical analysis on the utilization patterns of dental services and their relationships with financing mechanisms.
Developmental changes in memory encoding: insights from event‐related potentials
Authors: Rollins Leslie , Riggins Tracy 
Published: June 2013

AbstractThe aim of the present study was to investigate developmental changes in encoding processes between 6‐year‐old children and adults using event‐related potentials (ERPs). Although episodic memory (‘EM’) effects have been reported in both children and adults at retrieval and subsequent memory effects have been established in adults, no previous ERP studies have examined subsequent memory effects in children. This represents a critical gap in the literature because encoding processes, and changes in neural correlates supporting encoding, partially account for age‐related improvements in children's memory performance. Results revealed that subsequent memory effects differed between children and adults temporally, directionally, and topographically. These findings lend support to the hypothesis that encoding processes and their neural correlates are an important source of change in memory development.A video abstract of this article can be viewed at http://youtu.be/sH83_qVimgc.
Soil nitrous oxide emissions following crop residue addition: a meta‐analysis
Authors: Chen Huaihai , Li Xuechao , Hu Feng , Shi Wei 
Published: June 2013

AbstractAnnual production of crop residues has reached nearly 4 billion metric tons globally. Retention of this large amount of residues on agricultural land can be beneficial to soil C sequestration. Such potential impacts, however, may be offset if residue retention substantially increases soil emissions of N2O, a potent greenhouse gas and ozone depletion substance. Residue effects on soil N2O emissions have gained considerable attention since early 1990s; yet, it is still a great challenge to predict the magnitude and direction of soil N2O emissions following residue amendment. Here, we used a meta‐analysis to assess residue impacts on soil N2O emissions in relation to soil and residue attributes, i.e., soil pH, soil texture, soil water content, residue C and N input, and residue C : N ratio. Residue effects were negatively associated with C : N ratios, but generally residue amendment could not reduce soil N2O emissions, even for C : N ratios well above ca. 30, the threshold for net N immobilization. Residue effects were also comparable to, if not greater than, those of synthetic N fertilizers. In addition, residue effects on soil N2O emissions were positively related to the amounts of residue C input as well as residue effects on soil CO2 respiration. Furthermore, most significant and stimulatory effects occurred at 60–90% soil water‐filled pore space and soil pH 7.1–7.8. Stimulatory effects were also present for all soil textures except sand or clay content ≤10%. However, inhibitory effects were found for soils with >90% water‐filled pore space. Altogether, our meta‐analysis suggests that crop residues played roles beyond N supply for N2O production. Perhaps, by stimulating microbial respiration, crop residues enhanced oxygen depletion and therefore promoted anaerobic conditions for denitrification and N2O production. Our meta‐analysis highlights the necessity to connect the quantity and quality of crop residues with soil properties for predicting soil N2O emissions.
Prosthetic Rehabilitation of a Cleidocranial Dysplasia Patient with Vertical Maxillofacial Deficiency: A Clinical Report
Authors: Noh Kwantae , Kwon Kung‐Rock , Ahn Hyowon , Paek Janghyun , Pae Ahran 
Published: June 2013

AbstractCleidocranial dysplasia (CCD) is a rare congenital disorder characterized by skeletal and dental anomalies. This clinical report describes the prosthodontic approach to treating a CCD patient who presented with decreased facial height and relative mandibular protrusion due to maxillary hypoplasia after orthodontic treatment. Functional and esthetic rehabilitation was achieved using telescopic detachable prostheses in the maxilla and osseointegrated implants and metal‐ceramic fixed dental prostheses in the mandible. These treatment approaches precluded the need for orthognathic surgical correction and presented a favorable prognosis during the 5‐year observation period.
The Effect of Different Restorative and Abutment Materials on Marginal and Internal Adaptation of Three‐Unit Cantilever Implant‐Supported Fixed Partial Dentures: An In Vitro Study
Authors: Kahramanoğlu Erkut , Kulak‐Özkan Yasemin 
Published: June 2013

AbstractPurposePassive fit is generally assumed to be a significant prerequisite for long‐term implant success. The aim of this study was to evaluate the precision fit of three‐unit implant‐supported fixed partial dentures with different restorative and abutment materials on two implant systems: the Straumann and Astra Tech.Materials and MethodsTwo mandibular epoxy resin models (one for each implant system) were fabricated, and two implants were inserted at the first and second molar region. Poly(vinyl siloxane) impression material was used to make the dental impression. For each implant system, fifteen models were fabricated, and each group was divided into three subgroups (group 1: titanium abutment with metal framework, group 2: titanium abutment with zirconium framework, group 3: zirconium abutment with zirconium framework). The replica technique was used to examine the marginal and internal gap values. For each restoration, 20 measurements were performed, totaling 1200 measurements for all groups. Data were evaluated statistically using ANOVA and LSD post hoc test (p < 0.05).ResultsThe highest values at internal adaptation measurements were found at the occlusal surface for all groups. When the mean values of the marginal measurements were assessed, the lowest measurements were found in group 3 (51.416 μm), and the highest values were found in group 1 (79.394 μm). There were statistically significant differences between subgroups for marginal measurements (p < 0.05).ConclusionsAs included in our study, marginal measurement values were found to be 46 to 87 μm. The marginal discrepancy of the tested materials could be considered clinically acceptable.
Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage ΦAQ113
Authors: Zago Miriam , Scaltriti Erika , Rossetti Lia , Guffanti Alessandro , Armiento Angelarita , Fornasari Maria Emanuela , Grolli Stefano , Carminati Domenico , Brini Elena , Pavan Paolo , Felsani Armando , D'Urzo Annalisa , Moles Anna , Claude Jean-Baptiste , Grandori Rita , Ramoni Roberto , Giraffa Giorgio 
Published: June 2013

ABSTRACT

The complete genomic sequence of the dairy
Lactobacillus helveticus
bacteriophage ΦAQ113 was determined. Phage ΦAQ113 is a
Myoviridae
bacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related to
Lactobacillus gasseri
phage KC5a and
Lactobacillus johnsonii
phage Lj771 genomes. The phylogenetic similarities between
L. helveticus
phage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration of
L. helveticus
as a health-promoting organism.
Increased Water Activity Reduces the Thermal Resistance of Salmonella enterica in Peanut Butter
Authors: He Yingshu , Li Ye , Salazar Joelle K. , Yang Jingyun , Tortorello Mary Lou , Zhang Wei 
Published: June 2013

ABSTRACT

Increased water activity in peanut butter significantly (
P
< 0.05) reduced the heat resistance of desiccation-stressed
Salmonella enterica
serotypes treated at 90°C. The difference in thermal resistance was less notable when strains were treated at 126°C. Using scanning electron microscopy, we observed minor morphological changes of
S. enterica
cells resulting from desiccation and rehydration processes in peanut oil.
Mannitol and the Mannitol-Specific Enzyme IIB Subunit Activate Vibrio cholerae Biofilm Formation
Authors: Ymele-Leki Patrick , Houot Laetitia , Watnick Paula I. 
Published: June 2013

ABSTRACT

Vibrio cholerae
is a halophilic, Gram-negative rod found in marine environments. Strains that produce cholera toxin cause the diarrheal disease cholera.
V. cholerae
use a highly conserved, multicomponent signal transduction cascade known as the phosphoenolpyruvate phosphotransferase system (PTS) to regulate carbohydrate uptake and biofilm formation. Regulation of biofilm formation by the PTS is complex, involving many different regulatory pathways that incorporate distinct PTS components. The PTS consists of the general components enzyme I (EI) and histidine protein (HPr) and carbohydrate-specific enzymes II. Mannitol transport by
V. cholerae
requires the mannitol-specific EII (EII
Mtl
), which is expressed only in the presence of mannitol. Here we show that mannitol activates
V. cholerae
biofilm formation and transcription of the
vps
biofilm matrix exopolysaccharide synthesis genes. This regulation is dependent on mannitol transport. However, we show that, in the absence of mannitol, ectopic expression of the B subunit of EII
Mtl
is sufficient to activate biofilm accumulation. Mannitol, a common compatible solute and osmoprotectant of marine organisms, is a main photosynthetic product of many algae and is secreted by algal mats. We propose that the ability of
V. cholerae
to respond to environmental mannitol by forming a biofilm may play an important role in habitat selection.
Lytic Infection of Lactococcus lactis by Bacteriophages Tuc2009 and c2 Triggers Alternative Transcriptional Host Responses
Authors: Ainsworth Stuart , Zomer Aldert , Mahony Jennifer , van Sinderen Douwe 
Published: June 2013

ABSTRACT

Here we present an entire temporal transcriptional profile of
Lactococcus lactis
subsp.
cremoris
UC509.9 undergoing lytic infection with two distinct bacteriophages, Tuc2009 and c2. Furthermore, corresponding high-resolution whole-phage genome tiling arrays of both bacteriophages were performed throughout lytic infection. Whole-genome microarrays performed at various time points postinfection demonstrated a rather modest impact on host transcription. The majority of changes in the host transcriptome occur during late infection stages; few changes in host gene transcription occur during the immediate and early infection stages. Alterations in the
L. lactis
UC509.9 transcriptome during lytic infection appear to be phage specific, with relatively few differentially transcribed genes shared between cells infected with Tuc2009 and those infected with c2. Despite the apparent lack of a coordinated general phage response, three themes common to both infections were noted: alternative transcription of genes involved in catabolic flux and energy production, differential transcription of genes involved in cell wall modification, and differential transcription of genes involved in the conversion of ribonucleotides to deoxyribonucleotides. The transcriptional profiles of both bacteriophages during lytic infection generally correlated with the findings of previous studies and allowed the confirmation of previously predicted promoter sequences. In addition, the host transcriptional response to lysogenization with Tuc2009 was monitored along with tiling array analysis of Tuc2009 in the lysogenic state. Analysis identified 44 host genes with altered transcription during lysogeny, 36 of which displayed levels of transcription significantly reduced from those for uninfected cells.
Extracellular Electron Transfer to Fe(III) Oxides by the Hyperthermophilic Archaeon Geoglobus ahangari via a Direct Contact Mechanism
Authors: Manzella Michael P. , Reguera Gemma , Kashefi Kazem 
Published: June 2013

ABSTRACT

The microbial reduction of Fe(III) plays an important role in the geochemistry of hydrothermal systems, yet it is poorly understood at the mechanistic level. Here we show that the obligate Fe(III)-reducing archaeon
Geoglobus ahangari
uses a direct-contact mechanism for the reduction of Fe(III) oxides to magnetite at 85°C. Alleviating the need to directly contact the mineral with the addition of a chelator or the electron shuttle anthraquinone-2,6-disulfonate (AQDS) stimulated Fe(III) reduction. In contrast, entrapment of the oxides within alginate beads to prevent cell contact with the electron acceptor prevented Fe(III) reduction and cell growth unless AQDS was provided. Furthermore, filtered culture supernatant fluids had no effect on Fe(III) reduction, ruling out the secretion of an endogenous mediator too large to permeate the alginate beads. Consistent with a direct contact mechanism, electron micrographs showed cells in intimate association with the Fe(III) mineral particles, which once dissolved revealed abundant curled appendages. The cells also produced several heme-containing proteins. Some of them were detected among proteins sheared from the cell's outer surface and were required for the reduction of insoluble Fe(III) oxides but not for the reduction of the soluble electron acceptor Fe(III) citrate. The results thus support a mechanism in which the cells directly attach and transfer electrons to the Fe(III) oxides using redox-active proteins exposed on the cell surface. This strategy confers on
G. ahangari
a competitive advantage for accessing and reducing Fe(III) oxides under the extreme physical and chemical conditions of hot ecosystems.
Fungus-Specific Sirtuin HstD Coordinates Secondary Metabolism and Development through Control of LaeA
Authors: Kawauchi Moriyuki , Nishiura Mika , Iwashita Kazuhiro 
Published: June 2013

ABSTRACT

The sirtuins are members of the NAD
+
-dependent histone deacetylase family that contribute to various cellular functions that affect aging, disease, and cancer development in metazoans. However, the physiological roles of the fungus-specific sirtuin family are still poorly understood. Here, we determined a novel function of the fungus-specific sirtuin HstD/
Aspergillus oryzae
Hst4 (AoHst4), which is a homolog of Hst4 in
A. oryzae
yeast. The deletion of all histone deacetylases in
A. oryzae
demonstrated that the fungus-specific sirtuin HstD/AoHst4 is required for the coordination of fungal development and secondary metabolite production. We also show that the expression of the
laeA
gene, which is the most studied fungus-specific coordinator for the regulation of secondary metabolism and fungal development, was induced in a Δ
hstD
strain. Genetic interaction analysis of
hstD
/
Aohst4
and
laeA
clearly indicated that HstD/AoHst4 works upstream of LaeA to coordinate secondary metabolism and fungal development. The
hstD/Aohst4
and
laeA
genes are fungus specific but conserved in the vast family of filamentous fungi. Thus, we conclude that the fungus-specific sirtuin HstD/AoHst4 coordinates fungal development and secondary metabolism via the regulation of LaeA in filamentous fungi.
ADF/Cofilin Is Not Essential but Is Critically Important for Actin Activities during Phagocytosis in Tetrahymena thermophila
Authors: Shiozaki Nanami , Nakano Kentaro , Kushida Yasuharu , Noguchi Taro Q. P. , Uyeda Taro Q. P. , Wloga Dorota , Dave Drashti , Vasudevan Krishna Kumar , Gaertig Jacek , Numata Osamu 
Published: June 2013

ABSTRACTADF/cofilin is a highly conserved actin-modulating protein. Reorganization of the actin cytoskeletonin vivothrough severing and depolymerizing of F-actin by this protein is essential for various cellular events, such as endocytosis, phagocytosis, cytokinesis, and cell migration. We show that in the ciliateTetrahymena thermophila, the ADF/cofilin homologue Adf73p associates with actin on nascent food vacuoles. Overexpression of Adf73p disrupted the proper localization of actin and inhibited the formation of food vacuoles.In vitro, recombinant Adf73p promoted the depolymerization of filaments made ofT. thermophilaactin (Act1p). Knockout cells lacking theADF73gene are viable but grow extremely slowly and have a severely decreased rate of food vacuole formation. Knockout cells have abnormal aggregates of actin in the cytoplasm. Surprisingly, unlike the case in animals and yeasts, inTetrahymena, ADF/cofilin is not required for cytokinesis. Thus, theTetrahymenamodel shows promise for future studies of the role of ADF/cofilinin vivo.
Importance and Determinants of Induction of Cold-Induced DEAD RNA Helicase in the Hyperthermophilic Archaeon Thermococcus kodakarensis
Authors: Nagaoka Eriko , Hidese Ryota , Imanaka Tadayuki , Fujiwara Shinsuke 
Published: June 2013

ABSTRACT

Thermococcus kodakarensis
, which grows optimally at 85°C, expresses cold stress-inducible DEAD box RNA helicase (
Tk-deaD
) when shifted to 60°C. A DDA1 deletion (Δ
Tk-deaD
) mutant exhibited decreased cell growth, and cells underwent lysis at 60°C in nutrient broth in the absence of elemental sulfur. In contrast, cells in medium containing elemental sulfur at 60°C did not undergo lysis, suggesting that
Tk-deaD
is necessary for cell growth in sulfur-free medium. To identify the element responsible for the cold response, a pTKR expression probe plasmid was constructed using thermostable catalase from
Pyrobaculum calidifontis
as a reporter. The plasmid pTKRD, which contained the transcription factor B recognition element, TATA region, and Shine-Dalgarno (SD) region, including the initiation codon of the
Tk-deaD
gene, exhibited cold inducibility. We also constructed a series of deletion and chimeric constructs with the glutamate dehydrogenase (
gdh
) promoter, whose expression is constitutive independent of culture temperatures and catalase expression. Reporter assay experiments indicated that the regulatory element is located in the region between the SD region and the initiation codon (ATG). Nucleotide sequences in the upstream regions of
Tk-deaD
and
gdh
were compared and revealed a five-adenosine (AAAAA) sequence between SD and ATG of
Tk-deaD
that was not present in
gdh
. Replacement of the repeated adenosine sequence with other sequences revealed that the AAAAA sequence is important for cold induction. This sequence-specific mechanism is unique and is one that has not been identified in other known cold-inducible genes.