bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of
irvR
, a Novel Regulator of the
irvA
-Dependent Pathway Required for Genetic Competence and Dextran-Dependent Aggregation in
Streptococcus mutans
Authors: Niu Guoqing , Okinaga Toshinori , Zhu Lin , Banas Jeffrey , Qi Felicia , Merritt Justin 
Published: August 2008

ABSTRACT

Previous studies identified
irvA
as a normally repressed but highly inducible transcription regulator capable of repressing mutacin I gene expression in
Streptococcus mutans
. In this study, we aimed to identify and characterize the regulator(s) responsible for repressing the expression of
irvA
. An uncharacterized open reading frame (SMU.1398) located immediately adjacent to
irvA
and annotated as a putative transcription repressor was identified as a likely candidate. The results of mutation studies confirmed that the expression of
irvA
was greatly increased in the SMU.1398 background. Mutation of SMU.1398 (“
irvR
”) abolished genetic competence and reduced the expression of the late competence genes/operons
comEA
,
comY
, and
dprA
without affecting the expression of the known competence regulators
comC
,
comED
, or
comX
. In addition,
irvR
was found to be a potent negative regulator of dextran-dependent aggregation (DDAG) and
gbpC
expression. Each of these
irvR
mutant phenotypes could be rescued with a double mutation of
irvA
or complemented by introducing a wild-type copy of
irvR
on a shuttle vector. These data indicate that the repression of
irvA
is critically dependent upon
irvR
and that
irvA
repression is essential for the development of genetic competence and the proper control of DDAG in
S. mutans
.
Characterization of the
Caulobacter crescentus
Holdfast Polysaccharide Biosynthesis Pathway Reveals Significant Redundancy in the Initiating Glycosyltransferase and Polymerase Steps
Authors: Toh Evelyn , Kurtz Harry D. , Brun Yves V. 
Published: August 2008

ABSTRACT

Caulobacter crescentus
cells adhere to surfaces by using an extremely strong polar adhesin called the holdfast. The polysaccharide component of the holdfast is comprised in part of oligomers of
N
-acetylglucosamine. The genes involved in the export of the holdfast polysaccharide and the anchoring of the holdfast to the cell were previously discovered. In this study, we identified a cluster of polysaccharide biosynthesis genes (
hfsEFGH
) directly adjacent to the holdfast polysaccharide export genes. Sequence analysis indicated that these genes are involved in the biosynthesis of the minimum repeat unit of the holdfast polysaccharide. HfsE is predicted to be a UDP-sugar lipid-carrier transferase, the glycosyltransferase that catalyzes the first step in polysaccharide biosynthesis. HfsF is predicted to be a flippase, HfsG is a glycosyltransferase, and HfsH is similar to a polysaccharide (chitin) deacetylase. In-frame
hfsG
and
hfsH
deletion mutants resulted in severe deficiencies both in surface adhesion and in binding to the holdfast-specific lectin wheat germ agglutinin. In contrast,
hfsE
and
hfsF
mutants exhibited nearly wild-type levels of adhesion and holdfast synthesis. We identified three paralogs to
hfsE
, two of which are redundant to
hfsE
for holdfast synthesis. We also identified a redundant paralog to the
hfsC
gene, encoding the putative polysaccharide polymerase, and present evidence that the
hfsE
and
hfsC
paralogs, together with the
hfs
genes, are absolutely required for proper holdfast synthesis.
Regulation by Nucleoid-Associated Proteins at the
Escherichia coli nir
Operon Promoter
Authors: Browning Douglas F. , Cole Jeffrey A. , Busby Stephen J. W. 
Published: August 2008

ABSTRACT

The
Escherichia coli
K-12
nir
operon promoter can be fully activated by binding of the regulator of fumarate and nitrate reduction (FNR) to a site centered at position −41.5 upstream of the transcript start, and this activation is modulated by upstream binding of the integration host factor (IHF) and Fis (factor for inversion stimulation) proteins. Thus, transcription initiation is repressed by the binding of IHF and Fis to sites centered at position −88 (IHF I) and position −142 (Fis I) and activated by IHF binding to a site at position −115 (IHF II). Here, we have exploited mutational analysis and biochemistry to investigate the actions of IHF and Fis at these sites. We show that the effects of IHF and Fis are position dependent and that IHF II functions independently of IHF I and Fis I. Using in vitro assays, we report that IHF and Fis repress transcription initiation by interfering with RNA polymerase binding. Differences in the upstream IHF and Fis binding sites at the
nir
promoter in related enteric bacteria fix the level of
nir
operon expression under anaerobic growth conditions.
Molecular Phylogeny of the Salmonellae: Relationships among
Salmonella
Species and Subspecies Determined from Four Housekeeping Genes and Evidence of Lateral Gene Transfer Events
Authors: McQuiston J. R. , Herrera-Leon S. , Wertheim B. C. , Doyle J. , Fields P. I. , Tauxe R. V. , Logsdon J. M. 
Published: August 2008

ABSTRACT

The salmonellae are a diverse group of bacteria within the family
Enterobacteriaceae
that includes two species,
Salmonella enterica
and
Salmonella bongori
. In order to characterize the phylogenetic relationships of the species and subspecies of
Salmonella
, we analyzed four housekeeping genes,
gapA, phoP, mdh
and
recA
, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of
Salmonella enterica
and six isolates of
Salmonella bongori
were included in this study. We present a robust phylogeny of the
Salmonella
species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene
recA
, which has not previously been reported, was obtained.
Cytological distinction between high-risk and low-risk human papillomavirus infections in SurePath liquid-based cell preparations
Authors: Wong N K S , Ng F Y , Leung G 
Published: August 2008

Aims:To investigate the correlation of various diagnostic cytological features in SurePath liquid-based cell preparations with high-risk human papillomavirus (HPV) infection.Methods:Case–control study. SurePath specimens from 510 cases that had been tested for HPV DNA by Hybrid Capture 2 assay were retrieved and re-examined for 10 cytological features. Distribution of these features in high- and low-risk HPV types was compared and risk statistics were estimated. Effects of cervicitis on the manifestation of HPV cytological changes were adjusted by means of logistic regression.Results:Cytological features of nuclear hyperchromasia, multinucleation and atypical metaplastic cells were predominantly noted in high-risk HPV infection in the category of atypical squamous cells of undetermined significance/low-grade squamous intraepithelial lesion. The odds ratios of these three features were 6–12 times higher in high-risk than low-risk HPV infection.Conclusions:Some diagnostic cytological features can be used as markers in Pap smear screening for assessing the types of HPV infection.
MAGNETIC PROPERTIES OF Yb1-xGaxBa2Cu3O7-δ HIGH TC SUPERCONDUCTORS
Authors: POP IULIU , SBÂRCIOG CARMEN , POP OVIDIU 
Published: September 2008

The thermal variation of the static magnetic susceptibility, for the Yb 1-x Ga x Ba 2 Cu 3 O 7-δ, x = 0.00; 0.01; 0.02; 0.03; 0.06 oxidic high TC superconductors was investigated. In the paramagnetic region, the reciprocal magnetic susceptibility temperature dependence is nonlinear, obeying the hyperbolic Neel law, valid for the ferromagnetic collinear magnetic structure. The effective magnetic moment value determined from the Curie constant is a giant one, suggesting the existence of Cu 3+ and Yb 6+ valence states in high TC superconducting compounds. The structural X-ray investigation revealed a homogeneous orthorhombic crystalline structure in Yb 1-x Ga x Ba 2 Cu 3 O 7-δ superconducting compounds.
ELECTRIC FORCE LINES OF THE DOUBLE REISSNER–NORDSTROM EXACT SOLUTION
Authors: PAOLINO ARMANDO , PIZZI MARCO 
Published: September 2008

Recently Alekseev and Belinski have presented a new exact solution to the Einstein–Maxwell equation which describes two Reissner–Nordstrom (RN) sources in reciprocal equilibrium (no struts or strings); one source is a naked singularity, the other is a black hole: this is the only possible configuration for two separable objects, apart from the well-known extreme case (mi = ei). In the present paper, after a brief summary of this solution, we study in some detail the coordinate systems used and the main features of the gravitational and electric fields. In particular, we graph the plots of the electric force lines in three qualitatively different situations: equal-sign charges, opposite charges and the case of a naked singularity near a neutral black hole.
The Effect of Neuromuscular Electrical Stimulation of the Infraspinatus on Shoulder External Rotation Force Production after Rotator Cuff Repair Surgery
Authors: Reinold Michael M. , Macrina Leonard C. , Wilk Kevin E. , Dugas Jeffrey R. , Cain E. Lyle , Andrews James R. 
Published: August 2008

Background Muscle weakness, particularly of shoulder external rotation, is common after rotator cuff repair surgery. Neuromuscular electrical stimulation has been shown to be an effective adjunct in the enhancement of muscle recruitment. Hypothesis Shoulder external rotation peak force can be enhanced by neuromuscular electrical stimulation after rotator cuff repair surgery. Study Design Controlled laboratory study. Methods Thirty-nine patients (20 men, 19 women) who had undergone rotator cuff repair surgery were tested a mean of 10.5 days after surgery. Testing consisted of placing patients supine with the shoulder in 45° of abduction, neutral rotation, and 15° of horizontal adduction. Neuromuscular electrical stimulation was applied to the infraspinatus muscle belly and inferior to the spine of the scapula. Placement was confirmed by palpating the muscle during a resisted isometric contraction of the external rotators. Patients performed 3 isometric shoulder external rotation contractions with and without neuromuscular electrical stimulation, each with a 5-second hold against a handheld dynamometer. Neuromuscular electrical stimulation was applied at maximal intensity within comfort at 50 pulses per second, symmetrical waveform, and a 1-second ramp time. The 3 trials under each condition were recorded, and an average was taken. The order of testing was randomized for each patient tested. A paired samples t test was used to determine significant differences between conditions ( P < .05). Each group was also divided based on age, rotator cuff tear size, number of days postoperative, and neuromuscular electrical stimulation intensity. Analysis of variance Models were used to determine the influence of these variables on external rotation force production ( P < .05). Results Peak force production was significantly greater ( P < .001) when tested with neuromuscular electrical stimulation (3.75 kg) as opposed to without neuromuscular electrical stimulation (3.08 kg) for all groups tested. There was no significant difference based on the size of the tear, age of the patient, number of days after surgery, or level of neuromuscular electrical stimulation intensity. Conclusion Peak shoulder external rotation force was significantly increased by 22% when tested with neuromuscular electrical stimulation after rotator cuff repair surgery. Neuromuscular electrical stimulation significantly increased force production regardless of the age of the patient, size of the tear, intensity of the current, or the number of days postoperative. Clinical Relevance Neuromuscular electrical stimulation may be used concomitantly with exercises to enhance the amount of force production and potentially minimize the inhibition of the rotator cuff after repair surgery.
Systematic Review of Single-Bundle Anterior Cruciate Ligament Reconstruction Outcomes
Authors: Lewis Paul B. , Parameswaran A. Dushi , Rue John-Paul H. , Bernard R. Bach 
Published: August 2008

Background There is increasing interest in comparing the efficacy of single-bundle versus double-bundle anterior cruciate ligament reconstruction. Challenging this comparison, however, has been the lack of an established consensus on the success of single-bundle reconstruction. Hypothesis The current outcomes of single-bundle reconstruction can be clarified from a large unbiased body of evidence for future comparisons with double-bundle reconstructions. Study Design Systematic review. Methods A systematic review of 11 randomized, controlled trials comparing patellar tendon and hamstring tendon grafting is reported. The respective outcomes of each group were combined to assist the orthopaedic surgeon in assessing the current success of single-bundle reconstruction. The primary factors assessed were tibial subluxation and side-to-side differences in laxity. Secondary outcomes included concomitant injuries and treatments, complications, graft failure, range of motion, and radiographic evidence of degenerative changes. Results In this review of 1024 single-bundle anterior cruciate ligament reconstructions, 495 concomitant meniscal tears, 95 chondral injuries, and 2 posterior cruciate ligament tears were noted. The complication rate was 6%, and graft failure 4%. Reported pivot-shift test results were negative in 81 % of cases; reported Lachman tests were negative in 59% cases; and KT-1000 arthrometer side-to-side differences were ≤5 mm in 86% of cases. Flexion and extension deficits were reported in 9 of 11 studies through mean range of motion or deficit ranges. Radiographic changes of articular surface abnormalities were observed in 7% of the knees at follow-up investigation. Conclusion Systematic review of a significant body of unbiased outcome data on single-bundle anterior cruciate ligament reconstruction demonstrates it to be a safe, consistent surgical procedure affording reliable results. Clinical Relevance These results may be used to assist orthopaedic surgeons in evaluating the benefit and practicality of pursuing new anterior cruciate ligament reconstruction techniques over standard single-bundle anterior cruciate ligament reconstruction.
Low Cost Polymer Composites with Rural Resources
Authors: Mishra S.C. 
Published: August 2008

The natural fiber composites can be very cost-effective materials, especially for the building and construction industry (e.g., panels, false ceilings, partition boards, etc.), packaging, automobile, and storage devices, etc. They can also be a potential candidate for partial replacement of high cost glass/Kevlar fibers to make polymer composites used for low cost applications. From the point of view of wood substitution, natural fiber composite boards could offer an excellent eco-friendly solution, considering ever-depleting forest reserves and corresponding premiums on wood. Composites based on locally available resources are poised to penetrate the market. Any value-added application avenues for these fiber composites would directly contribute to the economic benefit of their growers. With increasing emphasis on fuel efficiency, natural fiber-based composites are finding wider application in the transport industries. Hence, the value-added application of natural fiber-based composites made from rural industries will ensure the international market has cheaper substitution materials. Keeping the above in view, this research work has been undertaken to process polymer composites using naturally available resources such as bamboo strips, coconut leaf sticks, etc. The strength property relationships of these composites are evaluated, after subjection to different environments. This study will enable the manufacturer to select these materials for suitable applications.
Mechanical and Physical Properties of Wood-Plastic Composite Panels
Authors: Chaharmahali Majid , Mirbagheri Jamal , Tajvidi Mehdi , Najafi Saeed Kazemi , Mirbagheri Yaser 
Published: August 2008

In this research wood-plastic composite (WPC) panels were produced from high density polyethylene, MDF, and particle-board waste at 60, 70, and 80 wt% fiber loadings using the dry blend/hot press method. Physical and mechanical properties of the panels were studied and compared with conventional MDF and particle-board panels. The results indicated that the studied properties of the composites were strongly affected by the kind and proportion of the wood fiber and polymer. Maximum values of the flexural modulus of the WPC panels were reached at 70% fiber content. The flexural strength and impact strength of the WPC panels declined when fiber content increased from 60 to 80%. The flexural modulus of the WPC panels was lower than that of the virgin MDF panels but the flexural modulus of the composites with 70% fibers was close to that of particle-board panels. Flexural strength of MDF panels was noticeably higher than those of wood-plastic composites whereas the flexural modulus of particle-board panels was comparable to that of the wood-plastic composites at 80% fiber content. Furthermore, water uptake of wood-plastic samples increased with the increase in fiber content; however, it was relatively low compared with virgin MDF and particle-board panels.
Compatibility of Embryonic Stem Cells with Biomaterials
Authors: Handschel Jörg , Berr Karin , Depprich Rita , Naujoks Christian , Kübler Norbert R. , Meyer Ulrich , Ommerborn Michelle , Lammers Lydia 
Published: August 2008

Periodontal bone defects and atrophy of the jaws in an aging population are of special concern. Tissue engineering using embryonic stem cells (ESCs) and biomaterials may offer new therapeutic options. The purpose of this study is to evaluate the compatibility of ESCs with biomaterials and the influence of biomaterials on the osteogenic gene expression profile. Therefore, ESCs are cultured with various biomaterials. The cytocompatibility of murine ESCs is measured regarding the proliferation of the cells on the materials by CyQUANT ® assay, the morphology by scanning electron microscopy, and the influence on the gene expression by real time PCR. The results show that insoluble collagenous bone matrix, followed by β-tricalciumphosphate, is most suitable for bone tissue engineering regarding cell proliferation, and phenotype. The gene expression analysis indicates that biomaterials do influence the gene expression of ESCs. Our results provide new insight into the cytocompatibility of ESCs on different scaffolds.
Mineral phases and element composition of the copper hyperaccumulator lichen Lecanora polytropa
Authors: Purvis O. W. , Pawlik-Skowrońska B. , Cressey G. , Jones G. C. , Kearsley A. , Spratt J. 
Published: September 2008

AbstractMineral phases and element localization were investigated in the vivid turquoise-coloured lichen, Lecanora polytropa, sampled from a psammite boulder in a wall supporting mine spoil at the abandoned copper mine, Riddarhyttan Kopparverke, southern Sweden. Normally pale yellowish (usnic acid), the lichen is turquoise coloured internally with bluish inclusions. X-ray mapping shows that Cu occurs on and within the lichen and does not coincide with P or S, suggesting that it is indeed associated with carbon or other elements not detected (or reported) using X-ray mapping. Scanning electron microscopy in back-scatter mode confirmed that the greatest Cu concentrations occur in the form of crystalline aggregates in coloured inclusions below the major internal turquoise layer with smaller Cu contents. X-ray diffraction with a position-sensitive detector (XRD-PSD) confirmed coloured crystalline aggregates consisted of the copper oxalate, moolooite. The study confirms the value of XRD-PSD as a non-destructive tool to characterize small (~50 μm) metal oxalate inclusions obtained from within lichen samples.
Kinetics of high-pressure mineral phase transformations using in situ time-resolved X-ray diffraction in the Paris-Edinburgh cell: a practical guide for data acquisition and treatment
Authors: Perrillat J. P. 
Published: September 2008

AbstractSynchrotron X-ray diffraction (XRD) is a powerful technique to study in situ and in real-time the structural and kinetic processes of pressure-induced phase transformations. This paper presents the experimental set-up developed at beamline ID27 of the ESRF to perform time-resolved angle dispersive XRD in the Paris-Edinburgh cell. It provides a practical guide for the acquisition of isobaric-isothermal kinetic data and the construction of transformation-time plots. The interpretation of experimental data in terms of reaction mechanisms and transformation rates is supported by an overview of the kinetic theory of solid-solid transformations, with each step of data processing illustrated by experimental results of relevance to the geosciences. Reaction kinetics may be affected by several factors such as the sample microstructure, impurities or differential stress. Further high-pressure kinetic studies should investigate the influence of such processes, in order to acquire kinetic information more akin to natural or technological processes.
Rhesus macaque rhadinovirus-associated non-Hodgkin lymphoma: animal model for KSHV-associated malignancies
Authors: Orzechowska Beata U. , Powers Michael F. , Sprague Jerald , Li He , Yen Bonnie , Searles Robert P. , Axthelm Michael K. , Wong Scott W. 
Published: August 2008

AbstractRhesus macaque rhadinovirus (RRV) is closely related to Kaposi sarcoma-associated herpesvirus (KSHV) and is associated with the development of B-cell hyperplasia and persistent lymphadenopathy resembling multicentric Castleman disease in rhesus macaques (RMs) coinfected with simian immunodeficiency virus (SIV). Here we investigated whether RMs experimentally infected with SIV and RRV can develop other disease manifestations observed in HIV- and KSHV-infected patients. As reported earlier, inoculation of SIV-infected RMs with RRV results in persistent RRV infection, whereas immunocompetent animals infected with RRV exhibit viremia 2 weeks after infection, followed by a period of no virus detection until they are subsequently made immunodeficient by SIV infection. A subset of animals developed abnormal cellular proliferations characterized as extranodal lymphoma and a proliferative mesenchymal lesion. In situ hybridization and immunohistochemistry analysis indicate RRV is present in both malignancies, and DNA microarray analysis detected viral interleukin-6 (vIL-6) and viral FLICE-like inhibitory protein (vFLIP) transcripts. Reverse-transcriptase polymerase chain reaction analysis confirmed vIL-6 and vFLIP expression, and that of RRV open reading frames 72 and 73, homologs of KSHV open reading frames shown to be expressed in primary effusion lymphoma. These data support the utility of the RRV-/SIV-infected RM as an excellent animal model to investigate KSHV-like pathogenesis.