bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Enhanced Data Perturbation Approach for Small Data Sets
Authors: Muralidhar Krishnamurty , Sarathy Rathindra 
Published: August 2005

ABSTRACTAs modern organizations gather, analyze, and share large quantities of data, issues of privacy, and confidentiality are becoming increasingly important. Perturbation methods are used to protect confidentiality when confidential, numerical data are shared or disseminated for analysis. Unfortunately, existing perturbation methods are not suitable for protecting small data sets. With small data sets, existing perturbation methods result in reduced protection against disclosure risk due to sampling error. Sampling error may also produce different results from the analysis of perturbed data compared to the original data, reducing data utility. In this study, we develop an enhancement of an existing perturbation technique, General Additive Data Perturbation, that can be used to effectively mask both large and small data sets. The proposed enhancement minimizes the risk of disclosure while ensuring that the results of commonly performed statistical analyses are identical and equal for both the original and the perturbed data.
Bone reactions to longstanding functional load at implants: an experimental study in dogs
Authors: Berglundh T. , Abrahamsson I. , Lindhe J. 
Published: August 2005

AbstractObjectives: The aims of the present investigation were (i) to study marginal bone level alterations following implant installation, abutment connection and functional loading and (ii) to analyse bone tissue reactions to functional load.Material and Methods: Six beagle dogs, about 1‐year old, were used. All mandibular pre‐molars were extracted. Three months later four implants of the Astra Tech Implants® Dental System were installed in one side of the mandible and four standard fixtures of the Brånemark System® were placed in the contralateral side of the mandible. Abutment connection was performed 3 months later and a plaque control programme was initiated. Three months after abutment connection fixed partial dentures (FPDs) made in gold were cemented to the maxillary canines and pre‐molars. FPDs were also connected to the three posterior implants in each side of the mandible, while the mesial implant in each side was used as an unloaded control. Radiographs were obtained from all implant sites following implant installation, abutment connection and FPD placement. Ten months after the FPD placement the radiographic examination was repeated. The animals were sacrificed and biopsies from all implant sites were obtained and prepared for histological analysis.Results: The radiographic analysis revealed that largest amount of bone loss occurred following implant installation and abutment connection and that this loss was more pronounced at Brånemark than at Astra implants. The bone level alterations that were observed at implants exposed to 10 months of functional load in both implant systems were small and did not differ from control sites. The histological analysis revealed that implants exposed to functional load exhibited a higher degree of bone‐to‐implant contact than control implants in both implant systems.Conclusion: It is suggested that functional load at implants may enhance osseointegration and does not result in marginal bone loss.
Analysis of rat calvaria defects implanted with a platelet‐rich plasma preparation: histologic and histometric observations
Authors: Pryor Mary E. , Polimeni Giuseppe , Koo Ki‐Tae , Hartman Michael J. , Gross Howard , April Milton , Safadi Fayez F. , Wikesjö Ulf M. E. 
Published: August 2005

AbstractObjectives: It has been suggested that degranulating platelet α‐granules release growth factors having a potential to modulate bone formation. The objective of this study was to evaluate the osteoconductive potential of a platelet‐rich plasma (PRP) preparation.Methods: Thirty adult male Sprague–Dawley rats were used. The PRP preparation was obtained from 10 ml of whole blood drawn from one age‐matched donor rat. The preparation was processed by gradient density centrifugation and stored at −80°C until use. Using aseptic techniques, the PRP preparation soak loaded onto an absorbable collagen sponge (ACS) or ACS alone was surgically implanted into contralateral critical size 6‐mm calvaria osteotomies in 18 animals. Twelve animals received ACS versus sham surgery in contralateral defects. Animals were sacrificed at 4 and 8 weeks when biopsies were collected for histologic and histometric analysis.Results: The animals were maintained without adverse events. Bone formation was highly variable in sites receiving PRP and control treatments. Defect bone fill at 4 weeks averaged (±SD) 28.8±27.4% (PRP/ACS) versus 39.1±24.4% (ACS; p=0.2626) and 62.0±20.0% (ACS) versus 71.6±32.2% (sham surgery; p=0.1088), and at 8 weeks 81.0±12.9% (PRP/ACS) versus 64.5±28.1% (ACS; p=0.2626) and 75.6±34.1% (ACS) versus 74.1±24.2% (sham surgery; p=0.7353). Remnants of the ACS biomaterial were observed at both 4 and 8 weeks in sites implanted with PRP/ACS or ACS.Conclusions: The results suggest that the PRP preparation has a limited potential to promote local bone formation.
Autogenous bone chips: influence of a new piezoelectric device (Piezosurgery®) on chip morphology, cell viability and differentiation
Authors: Chiriac G. , Herten M. , Schwarz F. , Rothamel D. , Becker J. 
Published: August 2005

AbstractAim: The aim of the present study was to investigate the influence of a new piezoelectric device, designed for harvesting autogenous bone chips from intra‐oral sites, on chip morphology, cell viability and differentiation.Methods: A total of 69 samples of cortical bone chips were randomly gained by either (1) a piezoelectric device (PS), or (2) conventional rotating drills (RD). Shape and size of the bone chips were compared by means of morphometrical analysis. Outgrowing osteoblasts were identified by means of alkaline phosphatase activity (AP), immunhistochemical staining for osteocalcin (OC) synthesis and reverse transcriptase‐polymerase chain reaction phenotyping.Results: In 88.9% of the RD and 87.9% of the PS specimens, an outgrowth of adherent cells nearby the bone chips was observed after 6–19 days. Confluence of cells was reached after 4 weeks. Positive staining for AP and OC identified the cells as osteoblasts. The morphometrical analysis revealed a statistically significant more voluminous size of the particles collected with PS than RD.Conclusion: Within the limits of the present study, it may be concluded that both the harvesting methods are not different from each other concerning their detrimental effect on viability and differentiation of cells growing out of autogenous bone chips derived from intra‐oral cortical sites.
Open flap debridement with or without intentional cementum removal: a 4‐month follow‐up
Authors: Wilson Sallum Antonio , Vasconcelos Alves Renato , Flávio Teixeira Damis Lúcio , Fernanda Roesler Bertolini Patricia , Humberto Nociti Francisco , Antonio Sallum Enilson 
Published: August 2005

AbstractObjectives: The aim of this study was to investigate the influence of cementum removal on periodontal repair.Material and Methods: Forty subjects with chronic periodontitis and presenting, at least, two proximal sites in anterior teeth (upper or lower) with probing depth 5 mm were selected. After oral hygiene instructions and ultrasonic supragingival instrumentation, the subjects were randomly assigned for one of the following groups: CIC, scaled with Gracey curettes; CIUS, scaled with ultrasonic device; CDC, calculus deattachment with Gracey curettes and brushing with saline solution; and CDUS, calculus deattachment with ultrasonic device and brushing with saline solution. Full‐thickness flaps were reflected and the instrumentation was performed with a clinical microscope. Probing depth (PD), relative gingival margin level (RGML) and relative attachment level (RAL) were registered at five experimental periods: baseline and 30, 60, 90 and 120 days postoperative.Results: All the approaches were able to markedly reduce the PD values from the baseline to the other evaluation periods (p<0.0001). The increase in RGML values was statistically significant only for the CDUS group. There were no statistically significant differences between the baseline and postoperative values in all groups for the RAL changes. The changes in RAL were statistically significant only among the groups CDC and CDUS (p<0.0001).Conclusion: The conventional scaling and root planing and the calculus deattachment were effective in reducing the probing depth values, regardless of the instrumentation method.
Effects of phase I periodontal treatment on gingival crevicular fluid levels of matrix metalloproteinase‐3 and tissue inhibitor of metalloproteinase‐1
Authors: Tüter Gülay , Kurtiş Bülent , Serdar Muhittin , Yücel Ayşegül , Ayhan Eylem , Karaduman Burcu , Özcan Gönen 
Published: August 2005

AbstractObjectives: The aim of this study was to evaluate the effects of phase I periodontal treatment on gingival crevicular fluid (GCF) levels of matrix metalloproteinase (MMP)‐3 and tissue inhibitors of metalloproteinase (TIMP)‐1.Methods: Plaque index, gingival index, pocket depth and clinical attachment loss were recorded and GCF samples were collected from 20 chronic periodontitis (CP) patients and 20 periodontally healthy controls (C) before treatment. CP patients received phase I periodontal treatment and all clinical parameters were recorded and GCF samples were collected once more after treatment. Assays were performed by an enzyme‐linked immunosorbent assay.Results: All of the clinical parameters improved significantly after the therapy (p<0.05). Baseline GCF levels of MMP‐3 were significantly higher than C and that level was reduced significantly by treatment compared with baseline levels (p<0.05). Baseline GCF levels of TIMP‐1 were lower than post‐treatment levels and C (p<0.05). GCF levels of TIMP‐1 increased significantly by treatment compared with baseline levels (p<0.05).Conclusion: This study shows that the clinical improvements after phase I periodontal therapy are accompanied by reduction in MMP‐3 and increasing in TIMP‐1 GCF levels.
WATER‐ABSORPTION CHARACTERISTICS OF VARIOUS PEARL MILLET CULTIVARS AND SORGHUM GROWN IN NORTHERN NIGERIA
Authors: BADAU M.H. , NKAMA I. , JIDEANI I.A. 
Published: August 2005

ABSTRACT Ten pearl millet cultivars and one sorghum cultivar were evaluated for physical properties and chemical composition. Water‐absorption characteristics of these grains were also determined using Peleg's equation. Results indicated wide variations in thousand‐kernel weight and volume, grain hardness, percent floaters, in addition to considerable variations in protein, fat and crude fiber. Peleg's equation gave a reasonable fit to experimental data. Peleg constants K1 were obtained for the pearl millet cultivars. Temperature dependence of the reciprocal of the Peleg constant K1 was determined using an Arrhenius equation. Activation energies were in the range of 1.405–6.572 kJ/mol. A linear relationship was proposed to describe the relationship between the rate of absorbed water per unit change in temperature and activation energy.
The Bacteriophage P1hotGene Product Can Substitute for theEscherichia coliDNA Polymerase III θ Subunit
Authors: Chikova Anna K. , Schaaper Roel M. 
Published: August 2005

ABSTRACTThe θ subunit (holEgene product) ofEscherichia coliDNA polymerase (Pol) III holoenzyme is a tightly bound component of the polymerase core. Within the core (α-ε-θ), the α and ε subunits carry the DNA polymerase and 3′ proofreading functions, respectively, while the precise function of θ is unclear.holEhomologs are present in genomes of other enterobacteriae, suggestive of a conserved function. Putative homologs have also been found in the genomes of bacteriophage P1 and of certain conjugative plasmids. The presence of these homologs is of interest, because these genomes are fully dependent on the host replication machinery and contribute few, if any, replication factors themselves. To study the role of these θ homologs, we have constructed anE. colistrain in whichholEis replaced by the P1 homolog,hot. We show thathotis capable of substituting forholEwhen it is assayed for its antimutagenic action on the proofreading-impaireddnaQ49mutator, which carries a temperature-sensitive ε subunit. The ability ofhotto substitute forholEwas also observed with other, although not all,dnaQmutator alleles tested. The data suggest that the P1hotgene product can substitute for the θ subunit and is likely incorporated in the Pol III complex. We also show that overexpression of either θ or Hot further suppresses thednaQ49mutator phenotype. This suggests that the complexing ofdnaQ49-ε with θ is rate limiting for its ability to proofread DNA replication errors. The possible role ofhotfor bacteriophage P1 is discussed.
Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains ofMycoplasma hyopneumoniaeand a Strain ofMycoplasma synoviae
Authors: Vasconcelos Ana Tereza R. , Ferreira Henrique B. , Bizarro Cristiano V. , Bonatto Sandro L. , Carvalho Marcos O. , Pinto Paulo M. , Almeida Darcy F. , Almeida Luiz G. P. , Almeida Rosana , Alves-Filho Leonardo , Assunção Enedina N. , Azevedo Vasco A. C. , Bogo Maurício R. , Brigido Marcelo M. , Brocchi Marcelo , Burity Helio A. , Camargo Anamaria A. , Camargo Sandro S. , Carepo Marta S. , Carraro Dirce M. , de Mattos Cascardo Júlio C. , Castro Luiza A. , Cavalcanti Gisele , Chemale Gustavo , Collevatti Rosane G. , Cunha Cristina W. , Dallagiovanna Bruno , Dambrós Bibiana P. , Dellagostin Odir A. , Falcão Clarissa , Fantinatti-Garboggini Fabiana , Felipe Maria S. S. , Fiorentin Laurimar , Franco Gloria R. , Freitas Nara S. A. , Frías Diego , Grangeiro Thalles B. , Grisard Edmundo C. , Guimarães Claudia T. , Hungria Mariangela , Jardim Sílvia N. , Krieger Marco A. , Laurino Jomar P. , Lima Lucymara F. A. , Lopes Maryellen I. , Loreto Élgion L. S. , Madeira Humberto M. F. , Manfio Gilson P. , Maranhão Andrea Q. , Martinkovics Christyanne T. , Medeiros Sílvia R. B. , Moreira Miguel A. M. , Neiva Márcia , Ramalho-Neto Cicero E. , Nicolás Marisa F. , Oliveira Sergio C. , Paixão Roger F. C. , Pedrosa Fábio O. , Pena Sérgio D. J. , Pereira Maristela , Pereira-Ferrari Lilian , Piffer Itamar , Pinto Luciano S. , Potrich Deise P. , Salim Anna C. M. , Santos Fabrício R. , Schmitt Renata , Schneider Maria P. C. , Schrank Augusto , Schrank Irene S. , Schuck Adriana F. , Seuanez Hector N. , Silva Denise W. , Silva Rosane , Silva Sérgio C. , Soares Célia M. A. , Souza Kelly R. L. , Souza Rangel C. , Staats Charley C. , Steffens Maria B. R. , Teixeira Santuza M. R. , Urmenyi Turan P. , Vainstein Marilene H. , Zuccherato Luciana W. , Simpson Andrew J. G. , Zaha Arnaldo 
Published: August 2005

ABSTRACTThis work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogenMycoplasma hyopneumoniaeand a strain of the avian pathogenMycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in theM. hyopneumoniaestrains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed betweenM. synoviaeandMycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences fromM. gallisepticumtoM. synoviae.
Localization of SpoVAD to the Inner Membrane of Spores of
Bacillus subtilis
Authors: Vepachedu Venkata Ramana , Setlow Peter 
Published: August 2005

ABSTRACT

The products of the hexacistronic
spoVA
operon of
Bacillus subtilis
may be involved in the transport of dipicolinic acid into the forespore during sporulation and its release during spore germination. The major hydrophilic coding region of
B. subtilis spoVAD
was cloned, the protein was expressed in
Escherichia coli
as a His tag fusion protein, and a rabbit antiserum was raised against the purified protein. Western blot analyses of fractions from
B. subtilis
spores showed that SpoVAD is an integral inner membrane protein present at levels >50-fold higher than those of the spore's nutrient germinant receptors that are also present in the inner membrane. SpoVAD also persisted in outgrowing spores.
Biochemical Characterization of RssA-RssB, a Two-Component Signal Transduction System Regulating Swarming Behavior in
Serratia marcescens
Authors: Wei Jun-Rong , Tsai Yu-Huan , Soo Po-Chi , Horng Yu-Tze , Hsieh Shang-Chen , Ho Shen-Wu , Lai Hsin-Chih 
Published: August 2005

ABSTRACT

Our previous study had identified a pair of potential two-component signal transduction proteins, RssA-RssB, involved in the regulation of
Serratia marcescens
swarming. When mutated, both
rssA
and
rssB
mutants showed precocious swarming phenotypes on LB swarming agar, whereby swarming not only occurred at 37°C but also initiated on a surface of higher agar concentration and more rapidly than did the parent strain at 30°C. In this study, we further show that the predicted sensor kinase RssA and the response regulator RssB bear characteristics of components of the phosphorelay signaling system. In vitro phosphorylation and site-directed mutagenesis assays showed that phosphorylated RssA transfers the phosphate group to RssB and that histidine 248 and aspartate 51 are essential amino acid residues involved in the phosphotransfer reactions in RssA and RssB, respectively. Accordingly, while wild-type
rssA
could, the mutated
rssA
(H248A) in
trans
could not complement the precocious swarming phenotype of the
rssA
mutant. Although RssA-RssB regulates expressions of
shlA
and
ygfF
of
S. marcescens
(

ygfF
Sm

), in vitro DNA-binding assays showed that the phosphorylated RssB did not bind directly to the promoter regions of these two genes but bound to its own
rssB
promoter. Subsequent assays located the RssB binding site within a 63-bp
rssB
promoter DNA region and confirmed a direct negative autoregulation of the RssA-RssB signaling pathway. These results suggest that when activated, RssA-RssB acts as a negative regulator for controlling the initiation of
S. marcescens
swarming.
Regulation of
finP
Transcription by DNA Adenine Methylation in the Virulence Plasmid of
Salmonella enterica
Authors: Camacho Eva M. , Serna Ana , Madrid Cristina , Marqués Silvia , Fernández Raúl , de la Cruz Fernando , Juárez Antonio , Casadesús Josep 
Published: August 2005

ABSTRACT

DNA adenine methylase (Dam
−
) mutants of
Salmonella enterica
serovar Typhimurium contain reduced levels of FinP RNA encoded on the virulence plasmid. Dam methylation appears to regulate
finP
transcription, rather than FinP RNA stability or turnover. The
finP
promoter includes canonical −10 and −35 modules and depends on the σ
70
factor. Regulation of
finP
transcription by Dam methylation does not require DNA sequences upstream from the −35 module, indicating that Dam acts at the promoter itself or downstream. Unexpectedly, a GATC site overlapping with the −10 module is likewise dispensable for Dam-mediated regulation. These observations indicate that Dam methylation regulates
finP
transcription indirectly and suggest the involvement of a host factor(s) responsive to the Dam methylation state of the cell. We provide evidence that one such factor is the nucleoid protein H-NS, which acts as a repressor of
finP
transcription in a Dam
−
background. H-NS also restrains transcription of the overlapping
traJ
gene, albeit in a Dam-independent fashion. Hence, the decreased FinP RNA content found in Dam
−
hosts of
S. enterica
appears to result from H-NS-mediated repression of
finP
transcription.
Phylogenetic Analysis of
Pasteuria penetrans
by Use of Multiple Genetic Loci
Authors: Charles Lauren , Carbone Ignazio , Davies Keith G. , Bird David , Burke Mark , Kerry Brian R. , Opperman Charles H. 
Published: August 2005

ABSTRACT

Pasteuria penetrans
is a gram-positive, endospore-forming eubacterium that apparently is a member of the
Bacillus-Clostridium
clade. It is an obligate parasite of root knot nematodes (
Meloidogyne
spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. Root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. Consequently,
P. penetrans
has long been recognized as a potential biocontrol agent for root knot nematodes, but the fastidious life cycle and the obligate nature of parasitism have inhibited progress on mass culture and deployment. We are currently sequencing the genome of the
Pasteuria
bacterium and have performed amino acid level analyses of 33 bacterial species (including
P. penetrans
) using concatenation of 40 housekeeping genes, with and without insertions/deletions (indels) removed, and using each gene individually. By application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data sets,
P. penetrans
was found to cluster tightly, with a high level of confidence, in the
Bacillus
class of the gram-positive, low-G+C-content eubacteria. Strikingly, our analyses identified
P. penetrans
as ancestral to
Bacillus
spp. Additionally, all analyses revealed that
P. penetrans
is surprisingly more closely related to the saprophytic extremophile
Bacillus haladurans
and
Bacillus subtilis
than to the pathogenic species
Bacillus anthracis
and
Bacillus cereus
. Collectively, these findings strongly imply that
P. penetrans
is an ancient member of the
Bacillus
group. We suggest that
P. penetrans
may have evolved from an ancient symbiotic bacterial associate of nematodes, possibly as the root knot nematode evolved to be a highly specialized parasite of plants.
Rickettsial
metK
-Encoded Methionine Adenosyltransferase Expression in an
Escherichia coli metK
Deletion Strain
Authors: Driskell Lonnie O. , Tucker Aimee M. , Winkler Herbert H. , Wood David O. 
Published: August 2005

ABSTRACT

The obligate intracellular bacterium
Rickettsia prowazekii
has recently been shown to transport the essential metabolite
S
-adenosylmethionine (SAM). The existence of such a transporter would suggest that the
metK
gene, coding for the enzyme that synthesizes SAM, is unnecessary for rickettsial growth. Genome sequencing has revealed that this is the case for the
metK
genes of the spotted fever group and the Madrid E strain of
R. prowazekii
, which contain recognizable inactivating mutations. However, several strains of the typhus group rickettsiae possess
metK
genes lacking obvious mutations. In order to determine if these genes code for a product that retains MAT function, an
Escherichia coli metK
deletion mutant was constructed in which individual rickettsial
metK
genes were tested for the ability to complement the methionine adenosyltransferase deficiency. Both the
R. prowazekii
Breinl and
R. typhi
Wilmington
metK
genes complemented at a level comparable to that of an
E. coli metK
control, demonstrating that the typhus group rickettsiae have the capability of synthesizing as well as transporting SAM. However, the appearance of mutations that affect the function of the
metK
gene products (a stop codon in the Madrid E strain and a 6-bp deletion in the Breinl strain) provides experimental support for the hypothesis that these typhus group genes, like the more degenerate spotted fever group orthologs, are in the process of gene degradation.