bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliable automatic alignment of tomographic projection data by passive auto‐focus
Authors: Kingston A. , Sakellariou A. , Varslot T. , Myers G. , Sheppard A. 
Published: August 2011

Purpose:The authors present a robust algorithm that removes the blurring and double‐edge artifacts in high‐resolution computed tomography (CT) images that are caused by misaligned scanner components. This alleviates the time‐consuming process of physically aligning hardware, which is of particular benefit if components are moved or swapped frequently.Methods:The proposed method uses the experimental data itself for calibration. A parameterized model of the scanner geometry is constructed and the parameters are varied until the sharpest 3D reconstruction is found. The concept is similar to passive auto‐focus algorithms of digital optical instruments. The parameters are used to remap the projection data from thephysical detector to a virtual aligned detector. This is followed by a standard reconstruction algorithm, namely the Feldkamp algorithm. Feldkamp et al. [J. Opt. Soc. Am. A 1, 612–619 (1984)].Results:An example implementation is given for a rabbit liver specimen that was collected with a circular trajectory. The optimal parameters were determined in less computation time than that for a full reconstruction. The example serves to demonstrate that (a) sharpness is an appropriate measure for projection alignment, (b) our parameterization is sufficient to characterize misalignments for cone‐beam CT, and (c) the procedure determines parameter values with sufficient precision to remove the associated artifacts.Conclusions:The algorithm is fully tested and implemented for regular use at The Australian National University micro‐CT facility for both circular and helical trajectories. It can in principle be applied to more general imaging geometries and modalities. It is as robust as manual alignment but more precise since we have quantified the effect of misalignment.
In Vitro
Activity of E1210, a Novel Antifungal, against Clinically Important Yeasts and Molds
Authors: Miyazaki Mamiko , Horii Takaaki , Hata Katsura , Watanabe Nao-aki , Nakamoto Kazutaka , Tanaka Keigo , Shirotori Syuji , Murai Norio , Inoue Satoshi , Matsukura Masayuki , Abe Shinya , Yoshimatsu Kentaro , Asada Makoto 
Published: August 2011

ABSTRACT

E1210 is a new antifungal compound with a novel mechanism of action and broad spectrum of antifungal activity. We investigated the
in vitro
antifungal activities of E1210 compared to those of fluconazole, itraconazole, voriconazole, amphotericin B, and micafungin against clinical fungal isolates. E1210 showed potent activities against most
Candida
spp. (MIC
90
of ≤0.008 to 0.06 μg/ml), except for
Candida krusei
(MICs of 2 to >32 μg/ml). E1210 showed equally potent activities against fluconazole-resistant and fluconazole-susceptible
Candida
strains. E1210 also had potent activities against various filamentous fungi, including
Aspergillus fumigatus
(MIC
90
of 0.13 μg/ml). E1210 was also active against
Fusarium solani
and some black molds. Of note, E1210 showed the greatest activities against
Pseudallescheria boydii
(MICs of 0.03 to 0.13 μg/ml),
Scedosporium prolificans
(MIC of 0.03 μg/ml), and
Paecilomyces lilacinus
(MICs of 0.06 μg/ml) among the compounds tested. The antifungal action of E1210 was fungistatic, but E1210 showed no trailing growth of
Candida albicans
, which has often been observed with fluconazole. In a cytotoxicity assay using human HK-2 cells, E1210 showed toxicity as low as that of fluconazole. Based on these results, E1210 is likely to be a promising antifungal agent for the treatment of invasive fungal infections.
Phase III Randomized, Double-Blind Study Comparing Single-Dose Intravenous Peramivir with Oral Oseltamivir in Patients with Seasonal Influenza Virus Infection
Authors: Kohno Shigeru , Yen Muh-Yong , Cheong Hee-Jin , Hirotsu Nobuo , Ishida Tadashi , Kadota Jun-ichi , Mizuguchi Masashi , Kida Hiroshi , Shimada Jingoro 
Published: August 2011

ABSTRACTAntiviral medications with activity against influenza viruses are important in controlling influenza. We compared intravenous peramivir, a potent neuraminidase inhibitor, with oseltamivir in patients with seasonal influenza virus infection. In a multinational, multicenter, double-blind, double-dummy randomized controlled study, patients aged ≥20 years with influenza A or B virus infection were randomly assigned to receive either a single intravenous infusion of peramivir (300 or 600 mg) or oral administration of oseltamivir (75 mg twice a day [b.i.d.] for 5 days). To demonstrate the noninferiority of peramivir in reducing the time to alleviation of influenza symptoms with hazard model analysis and a noninferiority margin of 0.170, we planned to recruit 1,050 patients in South Korea, Japan, and Taiwan. A total of 1,091 patients (364 receiving 300 mg and 362 receiving 600 mg of peramivir; 365 receiving oseltamivir) were included in the intent-to-treat infected population. The median durations of influenza symptoms were 78.0, 81.0, and 81.8 h in the groups treated with 300 mg of peramivir, 600 mg of peramivir, and oseltamivir, respectively. The hazard ratios of the 300- and 600-mg-peramivir groups compared to the oseltamivir group were 0.946 (97.5% confidence interval [CI], 0.793, 1.129) and 0.970 (97.5% CI, 0.814, 1.157), respectively. Both peramivir groups were noninferior to the oseltamivir group (97.5% CI, <1.170). The overall incidence of adverse drug reactions was significantly lower in the 300-mg-peramivir group, but the incidence of severe reactions in either peramivir group was not different from that in the oseltamivir group. Thus, a single intravenous dose of peramivir may be an alternative to a 5-day oral dose of oseltamivir for patients with seasonal influenza virus infection.
Once-Daily Amikacin Dosing in Burn Patients Treated with Continuous Venovenous Hemofiltration
Authors: Akers Kevin S. , Cota Jason M. , Frei Christopher R. , Chung Kevin K. , Mende Katrin , Murray Clinton K. 
Published: August 2011

ABSTRACT

Amikacin clearance can be increased in burn injury, which is often complicated by renal insufficiency. Little is known about the impact of renal replacement therapies, such as continuous venovenous hemofiltration (CVVH), on amikacin pharmacokinetics. We retrospectively examined the clinical pharmacokinetics, bacteriology, and clinical outcomes of 60 burn patients given 15 mg/kg of body weight of amikacin in single daily doses. Twelve were treated with concurrent CVVH therapy, and 48 were not. The pharmacodynamic target of ≥10 for the maximum concentration of drug in serum divided by the MIC (
C
max
/MIC) was achieved in only 8.5% of patients, with a small reduction of
C
max
in patients receiving CVVH and no difference in amikacin clearance. Mortality and burn size were greater in patients who received CVVH. Overall, 172 Gram-negative isolates were recovered from the blood cultures of 39 patients, with amikacin MIC data available for 82 isolates from 24 patients. A 10,000-patient Monte Carlo simulation was conducted incorporating pharmacokinetic and MIC data from these patients. The cumulative fraction of response (CFR) was similar in CVVH and non-CVVH patients. The CFR rates were not significantly improved by a theoretical 20 mg/kg amikacin dose. Overall, CVVH did not appear to have a major impact on amikacin serum concentrations. The low pharmacodynamic target attainment appears to be primarily due to higher amikacin MICs rather than more rapid clearance of amikacin related to CVVH therapy.
Impairment of Swimming Motility by Antidiarrheic Lactobacillus acidophilus Strain LB Retards Internalization of Salmonella enterica Serovar Typhimurium within Human Enterocyte-Like Cells
Authors: Liévin-Le Moal Vanessa , Amsellem Raymonde , Servin Alain L. 
Published: August 2011

ABSTRACT

We report that both culture and the cell-free culture supernatant (CFCS) of
Lactobacillus acidophilus
strain LB (Lactéol Boucard) have the ability (i) to delay the appearance of
Salmonella enterica
serovar Typhimurium strain SL1344-induced mobilization of F-actin and, subsequently, (ii) to retard cell entry by
S
. Typhimurium SL1344. Time-lapse imaging and Western immunoblotting showed that
S
. Typhimurium SL1344 swimming motility, as represented by cell tracks of various types, was rapidly but temporarily blocked without affecting the expression of FliC flagellar propeller protein. We show that the product(s) secreted by
L. acidophilus
LB that supports the inhibitory activity is heat stable and of low molecular weight. The product(s) caused rapid depolarization of the
S
. Typhimurium SL1344 cytoplasmic membrane without affecting bacterial viability. We identified inhibition of swimming motility as a newly discovered mechanism by which the secreted product(s) of
L. acidophilus
strain LB retards the internalization of the diarrhea-associated pathogen
S. enterica
serovar Typhimurium within cultured human enterocyte-like cells.
Nonconcordance with Surgical Site Infection Prevention Guidelines and Rates of Surgical Site Infections for General Surgical, Neurological, and Orthopedic Procedures
Authors: Young Barnaby , Ng Tat Ming , Teng Christine , Ang Brenda , Tai Hwei Yee , Lye David C. 
Published: August 2011

ABSTRACT

Surgical site infection (SSI) is a common and preventable complication of surgery, but the relative importance of individual measures recommended by guidelines has not been determined. Elective general surgical, neurological, and orthopedic procedures requiring antibiotic prophylaxis from a 3-month period were retrospectively studied to determine concordance with SSI prevention guidelines and to identify factors which predicted the development of SSIs. A total of 216 surgeries were reviewed, with 18 SSIs (8.3%). A mean of 1.4 antibiotic prophylaxis errors per surgery were identified, with correct antibiotic type identified for 64%, antibiotic timing for 83%, supplemental antibiotic dosing for 34%, and antibiotic duration of less than 24 h for 44%. Normothermia was present in 79% of surgeries, and normoglycemia was present in 17%. Univariate analysis of the SSI rate identified four significant factors. Antibiotic prophylaxis for less than 24 h postoperatively (odds ratio [OR], 0.213; 95% confidence interval [95% CI]0.060 to 0.757) and neurosurgery (OR, 0.118; 95% CI, 0.15 to 0.903) correlated with a reduced risk of SSI. The mean number of prophylaxis errors (OR, 1.6; 95% CI, 1.02 to 2.4) and a duration of surgical drainage for more than 3 days (OR, 2.679; 95% CI, 1.009 to 7.113) predicted SSI. By multivariate analysis, errors in individual antibiotic prophylaxis measures were not significantly associated with SSI; however, the presence of more than two errors was significant (OR, 4.030; 95% CI, 1.018 to 15.96). A strong correlation was identified between the degree of concordance to SSI prevention guidelines and the SSI rate (
P
= 0.001, Mantel-Haenszel linear-by-linear association chi-square test).
In Vitro
and
In Vivo
Activities of Novel, Semisynthetic Thiopeptide Inhibitors of Bacterial Elongation Factor Tu
Authors: Leeds J. A. , LaMarche M. J. , Brewer J. T. , Bushell S. M. , Deng G. , Dewhurst J. M. , Dzink-Fox J. , Gangl E. , Jain A. , Lee L. , Lilly M. , Manni K. , Mullin S. , Neckermann G. , Osborne C. , Palestrant D. , Patane M. A. , Raimondi A. , Ranjitkar S. , Rann E. M. , Sachdeva M. , Shao J. , Tiamfook S. , Whitehead L. , Yu D. 
Published: August 2011

ABSTRACT

Recently, we identified aminothiazole derivatives of GE2270 A. These novel semisynthetic congeners, like GE2270 A, target the essential bacterial protein elongation factor Tu (EF-Tu). Medicinal chemistry optimization of lead molecules led to the identification of preclinical development candidates 1 and 2. These cycloalklycarboxylic acid derivatives show activity against difficult to treat Gram-positive pathogens and demonstrate increased aqueous solubility compared to GE2270 A. We describe here the
in vitro
and
in vivo
activities of compounds 1 and 2 compared to marketed antibiotics. Compounds 1 and 2 were potent against clinical isolates of methicillin-resistant
Staphylococcus aureus
and vancomycin-resistant enterococci (MIC
90
≤ 0.25 μg/ml) but weaker against the streptococci (MIC
90
≥ 4 μg/ml). Like GE2270 A, the derivatives inhibited bacterial protein synthesis and selected for spontaneous loss of susceptibility via mutations in the
tuf
gene, encoding EF-Tu. The mutants were not cross-resistant to other antibiotic classes. In a mouse systemic infection model, compounds 1 and 2 protected mice from lethal
S. aureus
infections with 50% effective doses (ED
50
) of 5.2 and 4.3 mg/kg, respectively. Similarly, compounds 1 and 2 protected mice from lethal systemic
E. faecalis
infections with ED
50
of 0.56 and 0.23 mg/kg, respectively. In summary, compounds 1 and 2 are active
in vitro
and
in vivo
activity against difficult-to-treat Gram-positive bacterial infections and represent a promising new class of antibacterials for use in human therapy.
Characterization of the Retrocyclin Analogue RC-101 as a Preventative of Staphylococcus aureus Nasal Colonization
Authors: Lamers Ryan P. , Eade Colleen R. , Waring Alan J. , Cole Amy L. , Cole Alexander M. 
Published: August 2011

ABSTRACTNasal colonization ofStaphylococcus aureusis a risk factor for pathogenic autoinfection, particularly in postoperative patients and the immunocompromised. As such, standardized preoperative nasal decolonization ofS. aureushas become a major consideration for the prevention of nosocomial infection. However, only a few treatment options for nasal decolonization are currently available, with resistance to these approaches already a concern. Here we have identified the macrocyclic θ-defensin analogue RC-101 as a promising anti-S. aureusagent for nasal decolonization. RC-101 exhibits bactericidal effects againstS. aureuswith the use ofin vitroepithelium-free systems, while also preventing the pathogen's proliferation and attachment in anex vivohuman nasal epithelial cell adhesion model and an organotypic model of human airway epithelia. Peptide concentrations as low as 2.5 μM elicited significant reductions inS. aureusgrowth in epithelium-free systems, with 10 μM concentrations being completely bactericidal for all strains tested, including USA300. Inex vivonasal colonization models, RC-101 significantly reduced adherence, survival, and proliferation ofS. aureuson human nasal epithelia. Reductions inS. aureusviability were evident in these assays, with as little as 1 μg of peptide per tissue, while 10 μg of RC-101 completely prevented adhesion of all strains tested. Furthermore, RC-101 did not exhibit cellular toxicity to human nasal epithelia at concentrations up to 200 μM, nor did it induce a proinflammatory response in these cells. Collectively, the findings of this study identify RC-101 as a potential preventative ofS. aureusnasal colonization.
Dissemination of an NDM-2-Producing Acinetobacter baumannii Clone in an Israeli Rehabilitation Center
Authors: Espinal P. , Fugazza G. , López Y. , Kasma M. , Lerman Y. , Malhotra-Kumar S. , Goossens H. , Carmeli Y. , Vila J. 
Published: August 2011

ABSTRACT

New Delhi metallo-β-lactamase (NDM-1) was initially identified in various
Enterobacteriaceae
and recently in
Acinetobacter baumannii
. This study described the clonal dissemination of an NDM-2-producing
A. baumannii
isolate in an Israeli rehabilitation ward and the genetic surroundings of the gene. The
bla
NDM-2
gene was surrounded by the
ble
and
trpF
genes downstream and two copies of the IS
Aba125
on both sides. These are the first NDM-producing
A. baumannii
strains in Israel from patients with no previous travel or hospitalization on the Indian subcontinent.
The MUT056399 Inhibitor of FabI Is a New Antistaphylococcal Compound
Authors: Escaich S. , Prouvensier L. , Saccomani M. , Durant L. , Oxoby M. , Gerusz V. , Moreau F. , Vongsouthi V. , Maher Kirsty , Morrissey Ian , Soulama-Mouze C. 
Published: August 2011

ABSTRACT

MUT056399 is a highly potent new inhibitor of the FabI enzyme of both
Staphylococcus aureus
and
Escherichia coli. In vitro
, MUT056399 was very active against
S. aureus
strains, including methicillin-susceptible
S. aureus
(MSSA), methicillin-resistant
S. aureus
(MRSA), linezolid-resistant, and multidrug-resistant strains, with MIC
90
s between 0.03 and 0.12 μg/ml. MUT056399 was also active against coagulase-negative staphylococci, with MIC
90
s between 0.12 and 4 μg/ml. The antibacterial spectrum is consistent with specific FabI inhibition with no activity against bacteria using FabK but activity against FabI-containing Gram-negative bacilli.
In vitro
, resistant clones of
S. aureus
were obtained at a low frequency. All of the resistant clones analyzed were found to contain mutations in the
fabI
gene.
In vivo
, MUT056399, administered subcutaneously, protected mice from a lethal systemic infection induced by MSSA, MRSA, and vancomycin-intermediate
S. aureus
strains (50% effective doses ranging from 19.3 mg/kg/day to 49.6 mg/kg/day). In the nonneutropenic murine thigh infection model, the same treatment with MUT056399 reduced the bacterial multiplication of MSSA and MRSA in the thighs of immunocompetent mice. These properties support MUT056399 as a very promising candidate for a novel drug to treat severe staphylococcal infections.
Influence of Pore Structure on the Effectiveness of a Biogenic Carbonate Surface Treatment for Limestone Conservation
Authors: De Muynck Willem , Leuridan Stijn , Van Loo Denis , Verbeken Kim , Cnudde Veerle , De Belie Nele , Verstraete Willy 
Published: August 2011

ABSTRACT
A ureolytic biodeposition treatment was applied to five types of limestone in order to investigate the effect of pore structure on the protective performance of a biogenic carbonate surface treatment. Protective performance was assessed by means of transport and degradation processes, and the penetration depth of the treatment was visualized by microtomography. Pore size governs bacterial adsorption and hence the location and amount of carbonate precipitated. This study indicated that in macroporous stone, biogenic carbonate formation occurred to a larger extent and at greater depths than in microporous stone. As a consequence, the biodeposition treatment exhibited the greatest protective performance on macroporous stone. While precipitation was limited to the outer surface of microporous stone, biogenic carbonate formation occurred at depths of greater than 2 mm for Savonnières and Euville. For Savonnières, the presence of biogenic carbonate resulted in a 20-fold decreased rate of water absorption, which resulted in increased resistance to sodium sulfate attack and to freezing and thawing. While untreated samples were completely degraded after 15 cycles of salt attack, no damage was observed in biodeposition-treated Savonnières. From this study, it is clear that biodeposition is very effective and more feasible for macroporous stones than for microporous stones.
Abundance and Distribution of Synechococcus spp. and Cyanophages in the Chesapeake Bay
Authors: Wang Kui , Wommack K. Eric , Chen Feng 
Published: August 2011

ABSTRACT

Despite the increasing knowledge of
Synechococcus
spp. and their co-occurring cyanophages in oceanic and coastal water, little is known about their abundance, distribution, and interactions in the Chesapeake Bay estuarine ecosystem. A 5-year interannual survey shows that
Synechococcus
spp. and their phages are persistent and abundant members of Chesapeake Bay microbial communities.
Synechococcus
blooms (10
6
cells ml
−1
) were often observed in summer throughout the Bay, contributing 20 to 40% of total phytoplankton chlorophyll
a
. The distribution of phycoerythrin-containing (PE-rich)
Synechococcus
cells appeared to mostly correlate with the salinity gradient, with higher abundances at higher salinities. Cyanophages infectious to
Synechococcus
were also abundant (up to 6 × 10
5
viruses ml
−1
by the most probable number assay) during summer months in the Bay. The covariation in abundance of
Synechococcus
spp. and cyanophages was evident, although the latitude of observed positive correlation varied in different years, mirroring the changing environmental conditions and therefore the host-virus interactions. The impacts of cyanophages on host
Synechococcus
populations also varied spatially and temporally. Higher phage-related
Synechococcus
mortality was observed in drought years. Virus-mediated host mortality and subsequent liberation of dissolved organic matter (DOM) may substantially influence oceanic biogeochemical processing through the microbial loop as well as the microbial carbon pump. These observations emphasize the influence of environmental gradients on natural
Synechococcus
spp. and their phage population dynamics in the estuarine ecosystem.
Relevance of Bifidobacterium animalis subsp. lactis Plasminogen Binding Activity in the Human Gastrointestinal Microenvironment
Authors: Candela Marco , Turroni Silvia , Centanni Manuela , Fiori Jessica , Bergmann Simone , Hammerschmidt Sven , Brigidi Patrizia 
Published: August 2011

ABSTRACT

Human plasmin(ogen) is regarded as a component of the molecular cross talk between the probiotic species
Bifidobacterium animalis
subsp.
lactis
and the human host. However, up to now, only
in vitro
studies have been reported. Here, we demonstrate that the probiotic strain
B. animalis
subsp.
lactis
BI07 is capable of recruiting plasmin(ogen) present at physiological concentrations in crude extracts from human feces. Our results provide evidence that supports the significance of the
B. lactis
-plasmin(ogen) interaction in the human gastrointestinal tract.
Association of Antibiotic Resistance in Agricultural Escherichia coli Isolates with Attachment to Quartz
Authors: Liu Ping , Soupir Michelle L. , Zwonitzer Martha , Huss Bridgette , Jarboe Laura R. 
Published: August 2011

ABSTRACT

Surface water can be contaminated by bacteria from various sources, including manure from agricultural facilities. Attachment of these bacteria to soil and organic particles contributes to their transport through the environment, though the mechanism of attachment is unknown. As bacterial attachment to human tissues is known to be correlated with antibiotic resistance, we have investigated here the relationship between bacterial attachment to environmental particles and antibiotic resistance in agricultural isolates. We evaluated 203
Escherichia coli
isolates collected from swine facilities for attachment to quartz, resistance to 13 antibiotics, and the presence of genes encoding 13 attachment factors. The genes encoding type I, EcpA, P pili, and Ag43 were detected, though none was significantly related to attachment. Quartz attachment was positively and significantly (
P
< 0.0038) related to combined resistance to amoxicillin/streptomycin/tetracycline/sulfamethazine/tylosin/chlortetracycline and negatively and significantly (
P
< 0.0038) related to combined resistance to nalidixic acid/kanamycin/neomycin. These results provide clear evidence for a link between antibiotic resistance and attachment to quartz in agricultural isolates. We propose that this may be due to encoding by the responsible genes on a mobile genetic element. Further exploration of the relationship between antibiotic resistance and attachment to environmental particles will improve the understanding and modeling of environmental transport processes, with the goal of preventing human exposure to antibiotic-resistant or virulent microorganisms.