bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase Asymmetries in Normophonic Speakers: Visual Judgments and Objective Findings
Authors: Bonilha Heather Shaw , Deliyski Dimitar D. , Gerlach Terri Treman 
Published: October 2008

Purpose
To ascertain the amount of phase asymmetry of the vocal fold vibration in normophonic speakers via visualization techniques and compare findings for habitual and pressed phonations.

Method
Fifty-two normophonic speakers underwent stroboscopy and high-speed videoendoscopy (HSV). The HSV images were further processed into 4 visual displays: HSV playbacks, digital kymography (DKG) playbacks, mucosal wave kymography playbacks, and static kymographic images of the medial line from the DKG playback. Two types of phase asymmetries, left-right and anterior-posterior, were rated on a scale from 1 to 5. Objective measures of left-right phase asymmetry were obtained.

Results
The majority of normophonic speakers (81%) were noted to display anterior-posterior asymmetry; however, 66% of those were characterized as mild. Seventy-nine percent of participants were noted to display left-right asymmetry; however, 72% of those were mild. A moderate relationship between the objective measures and subjective ratings was found.

Conclusions
Most normophonic speakers exhibit mild left-right and anterior-posterior asymmetries for both habitual and pressed phonations. Asymmetries were noted more often during habitual than pressed phonations, and when visualized by HSV and kymography than stroboscopy. Differences between objective measures and visual judgments support the need to quantify vocal fold vibratory features.
Study of the In Vitro Activities of Rifaximin and Comparator Agents against 536 Anaerobic Intestinal Bacteria from the Perspective of Potential Utility in Pathology Involving Bowel Flora
Authors: Finegold S. M. , Molitoris D. , Väisänen M.-L. 
Published: October 2008

ABSTRACT
Rifaximin, ampicillin-sulbactam, neomycin, nitazoxanide, teicoplanin, and vancomycin were tested against 536 strains of anaerobic bacteria. The overall MIC of rifaximin at which 50% of strains were inhibited was 0.25 μg/ml. Ninety percent of the strains tested were inhibited by 256 μg/ml of rifaximin or less, an activity equivalent to those of teicoplanin and vancomycin but less than those of nitazoxanide and ampicillin-sulbactam.
In Vitro Model of Mycobacterial Growth Arrest Using Nitric Oxide with Limited Air
Authors: Hussain Syed , Malik Muhammad , Shi Lanbo , Gennaro Maria Laura , Drlica Karl 
Published: October 2008

ABSTRACT

An in vitro model of mycobacterial growth arrest was developed using
Mycobacterium bovis
BCG. When an exponentially growing culture was transferred to an evacuated tube, growth continued; treatment with a source of nitric oxide (diethylenetriamine-nitric oxide adduct [DETA-NO] at 50 μM) halted growth immediately, and aeration restored growth. When the period of growth arrest exceeded 4 h, a time lag occurred before aeration could restore growth. The lag time was maximal (24 h) after 16 h of growth arrest. These time lags indicated that one transition period was required for cells to achieve full arrest of growth and another for them to recover fully from growth arrest. DETA-NO-induced growth arrest failed to protect from the lethal effects of anaerobic shock, which caused rapid lysis of both growing and growth-arrested cells. While growth arrest had little effect on the lethal action of rifampin, it eliminated isoniazid lethality. Growth arrest reduced but did not eliminate fluoroquinolone lethality. Two fluoroquinolones, moxifloxacin and gatifloxacin, were equally lethal to exponentially growing cells, but moxifloxacin was more active during growth arrest. This difference is attributed to the fluoroquinolone C-7 ring structure, the only difference between the compounds. Collectively these data characterize a new system for halting mycobacterial growth that may be useful for evaluating new antituberculosis agents.
In Vitro Activity of Tomopenem (CS-023/RO4908463) against Anaerobic Bacteria
Authors: Tanaka Kaori , Mikamo Hiroshige , Nakao Kenichi , Ichiishi Taku , Goto Takatsugu , Yamagishi Yuka , Watanabe Kunitomo 
Published: October 2008

ABSTRACT

The antianaerobic activity of tomopenem, a new longer-half-life parenteral carbapenem, was compared with other carbapenems. Tomopenem showed broad activity against 63 reference species. The activity of tomopenem against 293 clinical isolates was potent (MIC
90
, 0.06 to 4 μg/ml) and comparable to those of meropenem and doripenem and more potent than that of panipenem.
Microanalysis of β-Lactam Antibiotics and Vancomycin in Plasma for Pharmacokinetic Studies in Neonates
Authors: Ahsman Maurice J. , Wildschut Enno D. , Tibboel Dick , Mathot Ron A. 
Published: October 2008

ABSTRACT
Rational dosing of antibiotics in neonates should be based on pharmacokinetic (PK) parameters assessed in specific populations. PK studies of neonates are hampered by the limited total plasma volume, which restricts the sample volume and sampling frequency. Available drug assay methods require large sample volumes and are labor-intensive or time-consuming. The objective of this study was to develop a rapid ultra-performance liquid chromatographic method with tandem mass spectrometry detection for simultaneous quantification of amoxicillin, meropenem, cefazolin, cefotaxime, deacetylcefotaxime, ceftriaxone, and vancomycin in 50 μl of plasma. Cleanup consisted of protein precipitation with cold acetonitrile (1:4) and solvent evaporation before reversed-phase chromatographic separation and detection using electrospray ionization tandem mass spectrometry. Standard curves were prepared over a large dynamic range with adequate limits of quantitation. Intra- and interrun accuracy and precision were within 100% ± 15% and 15%, respectively, with acceptable matrix effects. Coefficients of variation for matrix effects and recovery were <10% over six batches of plasma. Stability in plasma and aqueous stocks was generally sufficient, but stability of meropenem and ceftriaxone in extracts could limit autosampler capacity. The instrument run time was approximately 3.50 min per sample. Method applicability was demonstrated with plasma samples from an extracorporeal membrane oxygenation-treated neonate. Different β-lactam antibiotics can be added to this method with additional ion transitions. Using ultra-performance liquid chromatography mass spectrometry, this method allows simple and reliable quantification of multiple antibiotics in 50 μl of plasma for PK studies of neonates.
In Vitro Activities of a Novel Nanoemulsion against
Burkholderia
and Other Multidrug-Resistant Cystic Fibrosis-Associated Bacterial Species
Authors: LiPuma John J. , Rathinavelu Sivaprakash , Foster Bridget K. , Keoleian Jordan C. , Makidon Paul E. , Kalikin Linda M. , Baker James R. 
Published: October 2008

ABSTRACT

Respiratory tract infection, most often involving opportunistic bacterial species with broad-spectrum antibiotic resistance, is the primary cause of death in persons with cystic fibrosis (CF). Species within the
Burkholderia cepacia
complex are especially problematic in this patient population. We investigated a novel surfactant-stabilized oil-in-water nanoemulsion (NB-401) for activity against 150 bacterial isolates recovered primarily from CF respiratory tract specimens. These specimens included 75
Burkholderia
isolates and 75 isolates belonging to other CF-relevant species including
Pseudomonas
,
Achromobacter
,
Pandoraea
,
Ralstonia
,
Stenotrophomonas
, and
Acinetobacter
. Nearly one-third of the isolates were multidrug resistant, and 20 (13%) were panresistant based on standard antibiotic testing. All isolates belonging to the same species were genotyped to ensure that each isolate was a distinct strain. The MIC
90
of NB-401 was 125 μg/ml. We found no decrease in activity against multidrug-resistant or panresistant strains. MBC testing showed no evidence of tolerance to NB-401. We investigated the activity of NB-401 against a subset of strains grown as a biofilm and against planktonic strains in the presence of CF sputum. Although the activity of NB-401 was decreased under both conditions, the nanoemulsion remained bactericidal for all strains tested. These results support NB-401's potential role as a novel antimicrobial agent for the treatment of infection due to CF-related opportunistic pathogens.
Plasmid-Mediated 16S rRNA Methylases in Aminoglycoside-Resistant
Enterobacteriaceae
Isolates in Shanghai, China
Authors: Wu Qiong , Zhang Yibo , Han Lizhong , Sun Jingyong , Ni Yuxing 
Published: October 2008

ABSTRACT

High-level resistance to aminoglycosides produced by 16S rRNA methylases in
Enterobacteriaceae
isolates was investigated. The prevalences of
armA
in
Escherichia coli
,
Klebsiella pneumoniae
, and
Enterobacter cloacae
were 0.6%, 3.0%, and 10%, respectively.
rmtB
was more prevalent than
armA
. Pulsed-field gel electrophoresis patterns indicated that
armA
and
rmtB
have spread horizontally and clonally.
Characterization of
tet
(32) Genes from the Oral Metagenome
Authors: Warburton Philip , Roberts Adam P. , Allan Elaine , Seville Lorna , Lancaster Holli , Mullany Peter 
Published: October 2008

ABSTRACT

tet
(32) was identified in three bacterial isolates and in metagenomic DNA from the human oral cavity. The regions immediately flanking the gene were found to have similarities to the mobile elements Tn
B1230
from
Butyrivibrio fibrisolvens
, ATE-3 from
Arcanobacterium pyogenes
, and CTn
5
from
Clostridium difficile
.
Correlating Echinocandin MIC and Kinetic Inhibition of
fks1
Mutant Glucan Synthases for
Candida albicans
: Implications for Interpretive Breakpoints
Authors: Garcia-Effron Guillermo , Park Steven , Perlin David S. 
Published: October 2008

ABSTRACT

A detailed kinetic characterization of echinocandin inhibition was performed for mutant 1,3-β-
d
-glucan synthase enzymes from clinical isolates of
Candida albicans
with nine different
FKS1
mutations resulting in high MICs. Among 14 mutant Fks1p enzymes studied, the kinetic parameters 50% inhibitory concentration and
K

i

increased 50-fold to several thousandfold relative to those for the wild type. Enzymes with mutations at Ser645 (S645P, S645Y, and S645F) within hot spot 1 showed the most prominent decrease in sensitivity, while those with mutations at the N- and C-terminal ends of hot spot 1 generally retained greater sensitivity to all three drugs. Kinetic inhibitions by caspofungin, micafungin, and anidulafungin were comparable among the
fks1
mutant enzymes, although absolute values did vary with specific mutations. Amino acid substitutions in Fks1p did not alter
K

m

values, although some mutations decreased the
V
max
. Given the association of
FKS1
mutations with clinical resistance, an evaluation of the kinetic parameters for the inhibition of mutant 1,3-β-
d
-glucan synthase as a function of the MIC enabled an independent evaluation of the recently adopted susceptibility breakpoint for echinocandin drugs. Overall, a breakpoint MIC of ≥2 μg/ml for caspofungin captured nearly 100% of
fks1 C. albicans
strains when a kinetic inhibition rise threshold of ≤50-fold for the
K

i

was used as a measure of susceptibility. A similar MIC breakpoint for micafungin and anidulafungin was less inclusive, and a projected MIC of ≥0.5 μg/ml was required for >95% coverage of clinical isolates. However, when MIC determinations were performed in the presence of 50% serum, all
fks1
mutants showed MIC values of ≥2 μg/ml for the three echinocandin drugs. The 1,3-β-
d
-glucan synthase kinetic inhibition data support the proposed susceptibility breakpoint for caspofungin in
C. albicans
, but a lower susceptibility breakpoint (≤0.5 μg/ml) may be more appropriate for anidulafungin and micafungin. Overall, the data indicate that MIC testing with caspofungin may serve as a surrogate marker for resistance among the class of echinocandin drugs.
Clinical Outcomes, Safety, and Pharmacokinetics of OPT-80 in a Phase 2 Trial with Patients withClostridium difficileInfection
Authors: Louie T. , Miller M. , Donskey C. , Mullane K. , Goldstein E. J. C. 
Published: October 2008

ABSTRACTOPT-80, a novel, minimally absorbed macrocycle, is a candidate treatment option forClostridium difficileinfection (CDI) based on cure without recurrence of CDI in the hamster challenge model, good in vitro activity againstC. difficile, and relative sparing of commensal gram-negative anaerobes. In this open-label, dose-ranging clinical trial, 48 evaluable subjects were randomized to receive either 50, 100, or 200 mg of OPT-80 orally every 12 h for 10 days as treatment for mild to moderately severe CDI. OPT-80 was well tolerated by all subjects. Plasma concentrations were below the lower limit of quantitation in almost one-half of patients and typically ≤20 ng/ml across the dose range; the mean fecal concentrations exceeded the MIC at which 90% of the isolates tested are inhibited by 2,000- to 10,000-fold with increasing dosages. Resolution of diarrhea within 10 days was achieved in 10/14 patients (71%), 12/15 patients (80%), and 15/16 patients (94%), and the median time to resolution of diarrhea was reduced from 5.5 to 3.0 days with increasing dosages. Across all groups, the clinical cure rate, which was defined as resolution of diarrheal disease without the need for further treatment, was 41/45 patients (91%). Recurrence of CDI at ∼1 month after treatment was observed in two (5%) patients, one each in the 100-mg and 400-mg groups. The apparent high clinical response, good tolerance, low recurrence rate, and more-complete and rapid symptom control with the highest dosage support the selection of the 200-mg twice-daily dose for further clinical development of OPT-80 for treatment of CDI.
Four Superoxide Dismutases Contribute to
Bacillus anthracis
Virulence and Provide Spores with Redundant Protection from Oxidative Stress
Authors: Cybulski Robert J. , Sanz Patrick , Alem Farhang , Stibitz Scott , Bull Robert L. , O'Brien Alison D. 
Published: October 2008

ABSTRACT

The
Bacillus anthracis
genome encodes four superoxide dismutases (SODs), enzymes capable of detoxifying oxygen radicals. That two of these SODs, SOD15 and SODA1, are present in the outermost layers of the
B. anthracis
spore is indicated by previous proteomic analyses of the exosporium. Given the requirement that spores must survive interactions with reactive oxygen species generated by cells such as macrophages during infection, we hypothesized that SOD15 and SODA1 protect the spore from oxidative stress and contribute to the pathogenicity of
B. anthracis
. To test these theories, we constructed a double-knockout (Δ
sod15
Δ
sodA1
) mutant of
B. anthracis
Sterne strain 34F2 and assessed its lethality in an A/J mouse intranasal infection model. The 50% lethal dose of the Δ
sod15
Δ
sodA1
strain was similar to that of the wild type (34F2), but surprisingly, measurable whole-spore SOD activity was greater than that in 34F2. A quadruple-knockout strain (Δ
sod15
Δ
sodA1
Δ
sodC
Δ
sodA2
) was then generated, and as anticipated, spore-associated SOD activity was diminished. Moreover, the quadruple-knockout strain, compared to the wild type, was attenuated more than 40-fold upon intranasal challenge of mice. Spore resistance to exogenously generated oxidative stress and to macrophage-mediated killing correlated with virulence in A/J mice. Allelic exchange that restored
sod15
and
sodA1
to their wild-type state restored wild-type characteristics. We conclude that SOD molecules within the spore afford
B. anthracis
protection against oxidative stress and enhance the pathogenicity of
B. anthracis
in the lung. We also surmise that the presence of four SOD alleles within the genome provides functional redundancy for this key enzyme.
SarZ Promotes the Expression of Virulence Factors and Represses Biofilm Formation by Modulating SarA and
agr
in
Staphylococcus aureus
Authors: Tamber Sandeep , Cheung Ambrose L. 
Published: October 2008

ABSTRACT

Staphylococcus aureus
is a remarkably adaptable organism capable of multiple modes of growth in the human host, as a part of the normal flora, as a pathogen, or as a biofilm. Many of the regulatory pathways governing these modes of growth are centered on the activities of two regulatory molecules, the DNA binding protein SarA and the regulatory RNAIII effector molecule of the
agr
system. Here, we describe the modulation of these regulators and their downstream target genes by SarZ, a member of the SarA/MarR family of transcriptional regulators. Transcriptional and phenotypic analyses of a
sarZ
mutant demonstrated that the decreased transcription of
mgrA
and the
agr
RNAIII molecule was accompanied by increased transcription of
spa
(protein A) and downregulation of
hla
(alpha-hemolysin) and
sspA
(V8 protease) transcripts when compared to its isogenic parent. The decrease in protease activity was also associated with an increase in SarA expression. Consistent with an increase in SarA levels, the
sarZ
mutant displayed an enhanced ability to form biofilms. Together, our results indicate that SarZ may be an important regulator governing the dissemination phase of
S. aureus
infections, as it promotes toxin expression while repressing factors required for biofilm formation.
Interleukin-23 Orchestrates Mucosal Responses to
Salmonella enterica
Serotype Typhimurium in the Intestine
Authors: Godinez Ivan , Raffatellu Manuela , Chu Hiutung , Paixão Tatiane A. , Haneda Takeshi , Santos Renato L. , Bevins Charles L. , Tsolis Renée M. , Bäumler Andreas J. 
Published: October 2008

ABSTRACT

Salmonella enterica
serotype Typhimurium causes an acute inflammatory reaction in the ceca of streptomycin-pretreated mice that involves T-cell-dependent induction of gamma interferon (IFN-γ), interleukin-22 (IL-22), and IL-17 expression (genes
Ifn-γ
,
Il-22
, and
Il-17
, respectively). We investigated here the role of IL-23 in initiating these inflammatory responses using the streptomycin-pretreated mouse model. Compared to wild-type mice, the expression of IL-17 was abrogated, IL-22 expression was markedly reduced, but IFN-γ expression was normal in the ceca of IL-23p19-deficient mice during serotype Typhimurium infection. IL-23p19-deficient mice also exhibited a markedly reduced expression of regenerating islet-derived 3 gamma, keratinocyte-derived cytokine, and reduced neutrophil recruitment into the cecal mucosa during infection. Analysis of CD3
+
lymphocytes in the intestinal mucosa by flow cytometry revealed that αβ T cells were the predominant cell type expressing the IL-23 receptor in naive mice. However, a marked increase in the number of IL-23 receptor-expressing γδ T cells was observed in the lamina propria during serotype Typhimurium infection. Compared to wild-type mice, γδ T-cell-receptor-deficient mice exhibited blunted expression of IL-17 during serotype Typhimurium infection, while IFN-γ expression was normal. These data suggested that γδ T cells are a significant source, but not the sole source, of IL-17 in the acutely inflamed cecal mucosa of mice. Collectively, our results point to IL-23 as an important player in initiating a T-cell-dependent amplification of inflammatory responses in the intestinal mucosa during serotype Typhimurium infection.
Cytotoxic Necrotizing Factor Type 1-Neutralizing Monoclonal Antibody NG8 Recognizes Three Amino Acids in a C-Terminal Region of the Toxin and Reduces Toxin Binding to HEp-2 Cells
Authors: Grande Kerian K. , Meysick Karen C. , Rasmussen Susan B. , O'Brien Alison D. 
Published: October 2008

ABSTRACT

Cytotoxic necrotizing factor type 1 (CNF1) and CNF2 are toxins of pathogenic
Escherichia coli
that share 85% identity over 1,014 amino acids. Although both of these toxins modify GTPases, CNF1 is a more potent inducer of multinucleation in HEp-2 cells, binds more efficiently to HEp-2 cells, and, despite the conservation of amino acids (C866 and H881) required for enzymatic activity of the toxins, deamidates RhoA and Cdc42 better than CNF2. Here we exploited the differences between CNF1 and CNF2 to define the epitope on CNF1 to which the CNF1-specific neutralizing monoclonal antibody (MAb) (MAb NG8) binds and to determine the mechanism by which MAb NG8 neutralizes CNF1 activity on HEp-2 cells. For these purposes, we generated a panel of 21 site-directed mutants in which amino acids in CNF1 were exchanged for the amino acids in CNF2 between amino acids 546 and 869 and vice versa. This region of CNF1 not only is recognized by MAb NG8 but also is involved in binding of this toxin to HEp-2 cells. All the mutants retained the capacity to induce multinucleation of HEp-2 cells. However, the CNF1 double mutant with D591E and F593L mutations (CNF1
D591E F593L
) and the CNF1
H661Q
single mutant displayed drastically reduced reactivity with MAb NG8. A reverse chimeric triple mutant, CNF1
E591D L593F Q661H
, imparted MAb NG8 reactivity to CNF2. MAb NG8 neutralized CNF2
E591D L593F Q661H
activity in a dose-dependent manner and reduced the binding of this chimeric toxin to HEp-2 cells. Taken together, these results pinpoint three amino acids in CNF1 that are key amino acids for recognition by neutralizing MAb NG8 and further help define a region in CNF1 that is critical for full toxin binding to HEp-2 cells.
Loss of Allergen 1 Confers a Hypervirulent Phenotype That Resembles Mucoid Switch Variants of
Cryptococcus neoformans
Authors: Jain Neena , Li Li , Hsueh Ye-Ping , Guerrero Abraham , Heitman Joseph , Goldman David L. , Fries Bettina C. 
Published: October 2008

ABSTRACT

Microbial survival in a host is usually dependent on the ability of a pathogen to undergo changes that promote escape from host defense mechanisms. The human-pathogenic fungus
Cryptococcus neoformans
undergoes phenotypic switching in vivo that promotes persistence in tissue. By microarray and real-time PCR analyses, the allergen 1 gene (
ALL1
) was found to be downregulated in the hypervirulent mucoid switch variant, both during logarithmic growth and during intracellular growth in macrophages. The
ALL1
gene encodes a small cytoplasmic protein that is involved in capsule formation. Growth of an
all1
Δ gene deletion mutant was normal. Similar to cells of the mucoid switch variant,
all1
Δ cells produced a larger polysaccharide capsule than cells of the smooth parent and the complemented strain produced, and the enlarged capsule inhibited macrophage phagocytosis. The mutant exhibited a modest defect in capsule induction compared to all of the other variants. In animal models the phenotype of the
all1
Δ mutant mimicked the hypervirulent phenotype of the mucoid switch variant, which is characterized by decreased host survival and elevated intracranial pressure. Decreased survival is likely the result of both an ineffective cell-mediated immune response and impaired phagocytosis by macrophages. Consequently, we concluded that, unlike loss of most virulence-associated genes, where loss of gene function results in attenuated virulence, loss of the
ALL1
gene enhances virulence by altering the host-pathogen interaction and thereby impairing clearance. Our data identified the first cryptococcal gene associated with elevated intracranial pressure and support the hypothesis that an environmental opportunistic pathogen has modified its virulence in vivo by epigenetic downregulation of gene function.