bluuebunny/crossref_metadata_2025 huggingface dataset:
Lightweight Design for Thin-Walled Cylindrical Shell Based on Action Mechanism of Bamboo Node
Authors: Xing Denghai , Chen Wuyi , Xing Dengjiang , Yang Tuo
Published: November 2012

Lightweight design is needed for many engineering structures, but conventional design methods cannot always meet requirements. Natural organisms have developed many types of structures with excellent properties and ingenious construction, and they can provide many new design ideas. In this paper, a thin-walled cylindrical shell, one of the most common structures, is designed to resist buckling based on the study of bionics. First, the structure and function of bamboo node are described, and a statistical analysis of internode length-to-diameter ratio in bamboo is performed to investigate structural characteristics of bamboo node. Then, through buckling analysis of three relevant experimental models, the action mechanism of bamboo node is investigated, and two rules for application of this structure in engineering are proposed. Finally, a bionic design method is introduced, and a lightweight design for a thin-walled cylindrical shell based on this method is presented. A comparison between the bionic shell and a conventional one shows that the weight was reduced by as much as 20.5%.
A Closed-Form Solution for Minimizing the Cycle Time in Motion Programs With Constant Velocity Segments
Authors: Flocker Forrest W. , Bravo Ramiro H.
Published: November 2012

An important need for some dynamic systems is to design a periodic motion program that has a constant velocity segment for a specified time. A few examples of such systems are cam-follower systems used in continuous motion manufacturing, linear actuators, space-based scanners, and industrial robots. In this paper, the closed-form solution is given for a motion program that minimizes the cycle time subject to user-specified limits on positive and negative acceleration and jerk. The main benefit of minimizing cycle time is to maximize the throughput. Two motion programs that address the problem are presented and critically examined. For general applicability, the solution is presented in dimensionless form and an example is given to show its implementation to a typical problem. Conclusions regarding the profiles are drawn and given.
Optimization of gadolinium oxide growth deposited on Si by high pressure sputtering
Authors: Feijoo Pedro Carlos , Pampillón María Ángela , Andrés Enrique San
Published: November 2012

High κ gadolinium oxide thin layers were deposited on silicon by high-pressure sputtering (HPS). In order to optimize the properties for microelectronics applications, different deposition conditions were used. Ti (scavenger) and Pt (nonreactive) were e-beam evaporated to fabricate metal–insulator–semiconductor (MIS) devices. According to x-ray diffraction, x-ray photoelectron spectroscopy, and Fourier-transform infrared spectroscopy, polycrystalline stoichiometric Gd2O3 films were obtained by HPS. The growth rate decreases when increasing the deposition pressure. For relatively thick films (40 nm), a SiOx interface as well as the formation of a silicate layer (GdSiOx) is observed. For thinner films, in Ti gated devices the SiOx interface disappears but the silicate layer extends over the whole thickness of the gadolinium oxide film. These MIS devices present lower equivalent oxide thicknesses than Pt gated devices due to interface scavenging. The density of interfacial defects Dit is found to decrease with deposition pressure, showing a reduced plasma damage of the substrate surface for higher pressures. MIS with the dielectric deposited at higher pressures also present lower flatband voltage shifts ΔVFB in the CHF–VG hysteresis curves.
Atomic layer deposition of aluminum-doped zinc oxide films for the light harvesting enhancement of a nanostructured silicon solar cell
Authors: Chen Sheng-Hui , Chan Shih-Hao , Chen Chun-Ko , Tseng Shao-Ze , Hsu Chieh-Hsiang , Cho Wen-Hao
Published: November 2012

Anodic-aluminum-oxide (AAO) template lithography and atomic layer deposition (ALD) antireflection coating techniques have often been applied for the fabrication of wide-angle antireflection structures on silicon solar cells. In this study, an AAO template was fabricated as a mask to block the high density plasma dry etching from the crystalline silicon to form nanostructures on the surface of the crystalline silicon wafer. Then, a 55-nm-thick aluminum-doped zinc oxide (AZO) film was deposited on the silicon nanostructures using the ALD method. The results show that the application of a nanostructured AZO film can decrease the average reflectivity of the crystalline silicon to 0.83% in the wavelength range from 400 to 850 nm for an incident angle of 8°. The conversion efficiency of the nanostructured silicon solar cell can be enhanced from 6.93% to 8.37%.
Blistering of atomic layer deposition Al2O3 layers grown on silicon and its effect on metal–insulator–semiconductor structures
Authors: Beldarrain Oihane , Duch Marta , Zabala Miguel , Rafí Joan Marc , González Mireia Bargalló , Campabadal Francesca
Published: November 2012

In this work, a study of the influence of the processing conditions on the blistering of Al2O3 layers grown by atomic layer deposition (ALD) on silicon substrates is presented. The phenomenon occurs when the as-deposited layers are annealed at high temperature in a N2 atmosphere. The characterization of the blistering in terms of density and dimensions indicates that the higher the annealing temperature the higher the density but also the smaller the blister diameter, while the thicker the oxide the larger the blisters. The processing of the blistered layers to obtain Al-Al2O3-Si structures enhances the blistering phenomenon and at the same time affects the silicon surface underneath the blister. This has been evidenced by chemical etching of the deposited layers that have revealed in circular silicon voids of the size of the blister. The influence of the oxygen precursor used in the ALD process has also been investigated, showing that the blister size is reduced when using O3 instead of H2O. Finally, the use of a thin thermally grown SiO2 layer is shown to avoid blistering of Al2O3 films.
Low-temperature atomic layer deposition of Al2O3 on blown polyethylene films with plasma-treated surfaces
Authors: Beom Lee Gyeong , Sik Son Kyung , Won Park Suk , Hyung Shim Joon , Choi Byoung-Ho
Published: November 2012

In this study, a layer of Al2O3 was deposited on blown polyethylene films by atomic layer deposition (ALD) at low temperatures, and the surface characteristics of these Al2O3-coated blown polyethylene films were analyzed. In order to examine the effects of the plasma treatment of the surfaces of the blown polyethylene films on the properties of the films, both untreated and plasma-treated film samples were prepared under various processing conditions. The surface characteristics of the samples were determined by x-ray photoelectron spectroscopy, as well as by measuring their surface contact angles. It was confirmed that the surfaces of the plasma-treated samples contained a hydroxyl group, which helped the precursor and the polyethylene substrate to bind. ALD of Al2O3 was performed through sequential exposures to trimethylaluminum and H2O at 60 °C. The surface morphologies of the Al2O3-coated blown polyethylene films were observed using atomic force microscopy and scanning electron microscopy/energy-dispersive x-ray spectroscopy. Further, it was confirmed that after ALD, the surface of the plasma-treated film was covered with alumina grains more uniformly than was the case for the surface of the untreated polymer film. It was also confirmed via the focused ion beam technique that the layer Al2O3 conformed to the surface of the blown polyethylene film.
Assessing the combined performance of texture and morphological parameters in distinguishing breast tumors in ultrasound images
Authors: Alvarenga André Victor , Infantosi Antonio Fernando C. , Pereira Wagner C. A. , Azevedo Carolina M.
Published: November 2012

Purpose:

This work aims to investigate the combination of morphological and texture parameters in distinguishing between malignant and benign breast tumors in ultrasound images.

Methods:

Linear discriminant analysis was applied to sets of up to five parameters, and then the performances were assessed using the areaAz (± standard error) under the receiver operator characteristic curve, accuracy (Ac), sensitivity (Se), specificity (Sp), positive predictive value, and negative predictive value.

Results:

The most relevant individual parameter was the normalized residual value (nrv), calculated from the convex polygon technique. The best performance among all studied combinations was achieved by two morphological and three texture parameters (nrv, con, std, R, and asmi), which correctly distinguished nearly 85% of the breast tumors.

Conclusions:

This result indicates that the combination of morphological and texture parameters may be useful to assist physicians in the diagnostic process, especially if it is associated with an automatic classification tool.
A method for registration of single photon emission computed tomography (SPECT) and computed tomography (CT) images for liver stereotactic radiotherapy (SRT)
Authors: Gayou Olivier , Day Ellen , Mohammadi Seyed , Kirichenko Alexander
Published: November 2012

Purpose:

To describe a simple method of coregistration of nonanatomic liver SPECT and CT images acquired in separate sessions for three‐dimensional (3D)‐CRT planning utilizing dual radiolabeled and radiopaque body surface markers, and evaluate the accuracy of the registration on the patient surface.

Methods:

Ten patients treated for liver metastases or hepatocellular carcinoma with stereotactic body radiation therapy or 3D‐CRT were selected for this study to evaluate the SPECT/CT registration process. All patients were positioned in a custom‐molded vacuum bag on the flat table top. Nine radiopaque markers were taped to the abdominal surface in three axial planes at the level of the liver. Following CT imaging, the nine radiopaque markers were then labeled with radioactive tags, each containing 10μCi of 99mTc, and SPECT images were acquired. The metric used to evaluate the registration was the fiducial registration error (FRE), defined as the root mean square of the distance between pairs of homologous markers on the CT and SPECT images. The evaluation of the registration accuracy was performed in two steps: first the minimum number of markers necessary to obtain a robust registration was optimized; second the FRE was calculated on the remaining set of unused markers. Additionally, the deformation of the patientˈs abdominal surface between CT and SPECT acquisition sessions was evaluated using the distances between all possible unused marker pairs on the CT and SPECT images separately. The root mean square of the CT‐to‐SPECT difference between those distances was used to define the deformation index (DI). The registration method was evaluated on all ten patients in addition to an anthropomorphic phantom study.

Results:

The minimum number of markers above which the registration was not improved by more than 1 mm was 4. The FRE, calculated over the 5 remaining markers, was 6.1 mm for the patient population and 1.8 mm for the phantom study. The DI was 5.0 mm on average over all 10 patients and correlated well with the FRE. The DI was 1.6 mm for the phantom study, which represented the imaging systems’ resolution and the ability to place the CT and SPECT markers at the exact same location.

Conclusions:

It is feasible to use radiolabeled and radiopaque dual body surface markers for registration of SPECT and CT images acquired in separate sessions allowing conformal avoidance of SPECT‐defined functional normal liver. Point‐based rigid registration accuracy on the patient surface of 6.1 mm can be achieved using 4 dual body surface markers. The main contribution to the registration error is the deformation of the abdominal surface, arising from the inability to setup the patient in the exact same position at different times on two different imaging systems, and to properly account for breathing artifacts on the CT and SPECT images.
Carpal tunnel syndrome diagnosis by a self‐normalization process and ultrasound compound imaging
Authors: Liao Yin‐Yin , Wu Chin‐Chou , Kuo Tai‐Tzung , Chen Jiann‐Perng , Hsu Yen‐Wei , Yeh Chih‐Kuang
Published: November 2012

Purpose:

Carpal tunnel syndrome (CTS) is the common entrapment neuropathy that occurs due to compression of the median nerve at the wrist. Ultrasound images have been used to highlight anatomical variants of the median nerve, and CTS is thought to be associated to enlargement of the cross‐sectional area (CSA) of the median nerve. However, there remains controversy regarding the most appropriate cutoff values of the computer measurements including the CSA, flattening ratio, and palmar bowing of median nerve, especially given that they can be influenced by image artifacts and factors that differ between individual patients. This study proposed a modified ultrasound compound imaging technique by moving fingers to reduce image artifacts, and the estimates of the normalized CSA [i.e., CSA at the wrist (CSAw) to CSA at the midforearm] with the aim of reducing discrepancies in CSA estimates and improving the ability of CTS discrimination.

Methods:

The subjects were examined with their arms supine and while they were making repetitive movements of their fingers (from an open palm into a clenched fist) within 3 s. By a commercial ultrasound scanner with a 10‐MHz linear array transducer, a total of 70 images were acquired in each subject. The frame rate of ultrasound system was 25 fps. Nine frames in the acquisition sequence that had produced partial speckle decorrelation were incoherently added to form a compound image, and the inplane motion of them was corrected using the multilevel block‐sum pyramid algorithm. The manual contours outlined by ten experimenters and three physicians were used to test the performance in determining the boundary of the median nerve. The receiver operating characteristic (ROC) curve was used to evaluate the usefulness of the estimates in distinguishing healthy volunteers from CTS patients.

Results:

The manual contours of the median nerve in the compound images had an average area overlap exceeding 90% and relatively small area errors. The areas under the ROC curve obtained using the CSAw estimates for the original and compound images were 0.60 ± 0.09 (mean ± standard error) and 0.80 ± 0.05, respectively; that using normalized CSA estimates for the original and compound images were 0.76 ± 0.04 and 0.89 ± 0.04, respectively. The results show that variations in the CSAw values of compound images for healthy overweight and obese subjects can adversely influence CTS diagnosis, but that this can be overcome using the normalized CSA estimate of compound images.

Conclusions:

Compound imaging provides images of superior quality for determining the location of the median nerve boundary. Using the normalized CSA estimate would assist in eliminating problems associated with variability between populations, since the subject becomes his or her own internal control, thereby improving the ultrasound‐based diagnosis of CTS.
Dose‐response curve of EBT, EBT2, and EBT3 radiochromic films to synchrotron‐produced monochromatic x‐ray beams
Authors: Brown Thomas A. D. , Hogstrom Kenneth R. , Alvarez Diane , Matthews Kenneth L. , Ham Kyungmin , Dugas Joseph P.
Published: November 2012

Purpose:

This work investigates the dose‐response curves of GAFCHROMIC® EBT, EBT2, and EBT3 radiochromic films using synchrotron‐produced monochromatic x‐ray beams. EBT2 film is being utilized for dose verification in photoactivated Auger electron therapy at the Louisiana State University Center for Advanced Microstructures and Devices (CAMD) synchrotron facility.

Methods:

Monochromatic beams of 25, 30, and 35 keV were generated on the tomography beamline at CAMD. Ion chamber depth‐dose measurements were used to determine the dose delivered to films irradiated at depths from 0.7 to 8.5 cm in a 10 × 10 × 10‐cm3 polymethylmethacrylate phantom. AAPM TG‐61 protocol was applied to convert measured ionization into dose. Films were digitized using an Epson 1680 Professional flatbed scanner and analyzed using the net optical density (NOD) derived from the red channel. A dose‐response curve was obtained at 35 keV for EBT film, and at 25, 30, and 35 keV for EBT2 and EBT3 films. Calibrations of films for 4 MV x‐rays were obtained for comparison using a radiotherapy accelerator at Mary Bird Perkins Cancer Center.

Results:

The sensitivity (NOD per unit dose) of EBT film at 35 keV relative to that for 4‐MV x‐rays was 0.73 and 0.76 for doses 50 and 100 cGy, respectively. The sensitivity of EBT2 film at 25, 30, and 35 keV relative to that for 4‐MV x‐rays varied from 1.09–1.07, 1.23–1.17, and 1.27–1.19 for doses 50–200 cGy, respectively. For EBT3 film the relative sensitivity was within 3% of unity for all three monochromatic x‐ray beams.

Conclusions:

EBT and EBT2 film sensitivity showed strong energy dependence over an energy range of 25 keV–4 MV, although this dependence becomes weaker for larger doses. EBT3 film shows weak energy dependence, indicating that it would be a better dosimeter for kV x‐ray beams where beam hardening effects can result in large changes in the effective energy.
Lack of the Phosphatase PTPN22 Increases Adhesion of Murine Regulatory T Cells to Improve Their Immunosuppressive Function
Authors: Brownlie Rebecca J. , Miosge Lisa A. , Vassilakos Demetrios , Svensson Lena M. , Cope Andrew , Zamoyska Rose
Published: November 2012

Loss of the phosphatase PTPN22 enhances the functions of both effector and regulatory T cells.
Remodeling a Tissue: Subtraction Adds Insight
Authors: Axelrod Jeffrey D.
Published: November 2012

Imaging, modeling, and genetics reveal the roles of an atypical myosin in morphogenesis.
Science Signaling
Podcast: 27 November 2012
Authors: Zamoyska Rose , VanHook Annalisa M.
Published: November 2012

A phosphatase implicated in autoiummunity modulates the activities of both effector and regulatory T cells.
Double Delivery During Plant Fertilization
Authors: Hines Pamela J.
Published: November 2012

The cysteine-rich proteins of
Arabidopsis
egg and central cells enable fusion with just one sperm each.
Help for Starving Cells
Authors: Kiberstis Paula A.
Published: November 2012

A metabolite is identified that may help cancer cells coordinate their mode of energy generation with nutrient conditions.
Bcl10 Does Double Duty
Authors: VanHook Annalisa M.
Published: November 2012

A protein that promotes NF-κB signaling during the immune response is also required for phagocytosis independently of NF-κB.
In Vitro
Interaction of Voriconazole and Anidulafungin against Triazole-Resistant Aspergillus fumigatus
Authors: Seyedmousavi Seyedmojtaba , Meletiadis Joseph , Melchers Willem J. G. , Rijs Antonius J. M. M. , Mouton Johan W. , Verweij Paul E.
Published: November 2012

Voriconazole is the recommended drug of first choice to treat infections caused by
Aspergillus fumigatus
. The efficacy of voriconazole might be hampered by the emergence of azole resistance. However, the combination of voriconazole with anidulafungin could improve therapeutic outcomes in azole-resistant invasive aspergillosis (IA). The
in vitro
interaction between voriconazole and anidulafungin was determined against voriconazole-susceptible and voriconazole-resistant (substitutions in the
cyp51A
gene, including single point [M220I and G54W] and tandem repeat [34-bp tandem repeat in the promoter region of the
cyp51A
gene in combination with substitutions at codon L98 and 46-bp tandem repeat in the promoter region of the
cyp51A
gene in combination with mutation at codons Y121 and T289] mutations) clinical
A. fumigatus
isolates using a checkerboard microdilution method with spectrophotometric analysis and a viability-based XTT {2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2H-tetrazolium hydroxide} assay within 2 h of exposure after 24 and 48 h of incubation at 35°C to 37°C. Fractional inhibitory concentration (FIC) indexes (FICis) were determined using different MIC endpoints and Bliss independence analysis performed based on the response surface calculation of the no-drug interaction. Significant synergistic interactions obtained based on measuring the FIC index were dependent on the MIC endpoint, in which FICs were inversely related to voriconazole and anidulafungin MICs and were influenced by the CYP51A genotype. A statistically significant difference was observed between FIC indexes of isolates harboring tandem repeat mutations and wild-type controls (
P
= 0.006 by one-way analysis of variance [ANOVA]), indicating that synergy is decreased in azole-resistant strains. Our results indicated that a combination of voriconazole and anidulafungin might be effective against infections caused by both azole-susceptible and azole-resistant
A. fumigatus
isolates, but the combination could possibly be less effective in voriconazole-resistant strains with high MICs. Studies
in vivo
and
in vitro-in vivo
correlation investigations are required to validate the potential synergy of voriconazole and anidulafungin.
R164H and V240H Replacements by Site-Directed Mutagenesis of TEM-149 Extended-Spectrum β-Lactamase: Kinetic Analysis of TEM-149
H240
and TEM-149
H164-H240
Laboratory Mutants
Authors: Perilli Mariagrazia , Celenza Giuseppe , Mercuri Paola Sandra , Galleni Moreno , Pellegrini Cristina , Segatore Bernardetta , Amicosante Gianfranco
Published: November 2012

Two laboratory mutant forms, TEM-149
H240
and TEM-149
H164-H240
, of the TEM-149 extended-spectrum β-lactamase enzyme were constructed by site-directed mutagenesis. TEM-149
H240
and TEM-149
H164-H240
were similar in kinetic behavior, except with respect to benzylpenicillin and ceftazidime. Molecular modeling of the two mutant enzymes demonstrated the role of histidine at position 240 in the reduction of the affinity of the enzyme for ceftazidime.
Population Pharmacokinetic and Pharmacodynamic Properties of Intramuscular Quinine in Tanzanian Children with Severe Falciparum Malaria
Authors: Hendriksen Ilse C. E. , Maiga Deogratius , Lemnge Martha M. , Mtove George , Gesase Samwel , Reyburn Hugh , Lindegardh Niklas , Day Nicholas P. J. , von Seidlein Lorenz , Dondorp Arjen M. , Tarning Joel , White Nicholas J.
Published: November 2012

Although artesunate is clearly superior, parenteral quinine is still used widely for the treatment of severe malaria. A loading-dose regimen has been recommended for 30 years but is still often not used. A population pharmacokinetic study was conducted with 75 Tanzanian children aged 4 months to 8 years with severe malaria who received quinine intramuscularly; 69 patients received a loading dose of 20 mg quinine dihydrochloride (salt)/kg of body weight. Twenty-one patients had plasma quinine concentrations detectable at baseline. A zero-order absorption model with one-compartment disposition pharmacokinetics described the data adequately. Body weight was the only significant covariate and was implemented as an allometric function on clearance and volume parameters. Population pharmacokinetic parameter estimates (and percent relative standard errors [%RSE]) of elimination clearance, central volume of distribution, and duration of zero-order absorption were 0.977 liters/h (6.50%), 16.7 liters (6.39%), and 1.42 h (21.5%), respectively, for a typical patient weighing 11 kg. Quinine exposure was reduced at lower body weights after standard weight-based dosing; there was 18% less exposure over 24 h in patients weighing 5 kg than in those weighing 25 kg. Maximum plasma concentrations after the loading dose were unaffected by body weight. There was no evidence of dose-related drug toxicity with the loading dosing regimen. Intramuscular quinine is rapidly and reliably absorbed in children with severe falciparum malaria. Based on these pharmacokinetic data, a loading dose of 20 mg salt/kg is recommended, provided that no loading dose was administered within 24 h and no routine dose was administered within 12 h of admission. (This study has been registered with Current Controlled Trials under registration number ISRCTN 50258054.)
Contribution of Structural Domains to the Activity of Ribonuclease 7 against Uropathogenic Bacteria
Authors: Wang Huanyu , Schwaderer Andrew L. , Kline Jennifer , Spencer John David , Kline David , Hains David S.
Published: November 2012

Ribonuclease 7 (RNase 7) is a 14.5-kDa peptide that possesses potent antimicrobial properties against Gram-negative and Gram-positive bacteria and is expressed in a variety of epithelial tissues. Little is known about its mechanisms of action and the determinants of its antimicrobial properties. The objective of this study was to identify the intrinsic functional domains of RNase 7 that influence its activity against uropathogenic bacteria. A series of RNase 7 fragments were generated that contained different components of its secondary motifs starting from both the N terminus and the C terminus of RNase 7. We determined the antimicrobial properties of each fragment against both Gram-positive
Staphylococcus saprophyticus
and Gram-negative
Escherichia coli
and
Proteus mirabilis
. RNase 7 fragments displayed significant differences in their antimicrobial activity profiles. Compared to N-terminal fragments, C-terminal fragments showed uniformly decreased activity against Gram-negative
E. coli
and
P. mirabilis
and Gram-positive
S. saprophyticus
. Fragments that lack β-sheets 1, 3, and 4 also demonstrated significantly decreased activities. We have also identified one fragment with at least 4-fold increased potency against both
E. coli
and
Staphylococcus
compared to full-length peptide. We identified distinct regions of the peptide that are independently responsible for Gram-negative and Gram-positive activity. Our results suggest that distinct mechanisms are responsible for RNase 7's antimicrobial activity against various uropathogens.
HIV-1 Subtype Is an Independent Predictor of Reverse Transcriptase Mutation K65R in HIV-1 Patients Treated with Combination Antiretroviral Therapy Including Tenofovir
Authors: Theys K. , Vercauteren J. , Snoeck J. , Zazzi M. , Camacho R. J. , Torti C. , Schülter E. , Clotet B. , Sönnerborg A. , De Luca A. , Grossman Z. , Struck D. , Vandamme A.-M. , Abecasis A. B.
Published: November 2012

Subtype-dependent selection of HIV-1 reverse transcriptase resistance mutation K65R was previously observed in cell culture and small clinical investigations. We compared K65R prevalence across subtypes A, B, C, F, G, and CRF02_AG separately in a cohort of 3,076 patients on combination therapy including tenofovir. K65R selection was significantly higher in HIV-1 subtype C. This could not be explained by clinical and demographic factors in multivariate analysis, suggesting subtype sequence-specific K65R pathways.
A Time-to-Event Pharmacodynamic Model Describing Treatment Response in Patients with Pulmonary Tuberculosis Using Days to Positivity in Automated Liquid Mycobacterial Culture
Authors: Chigutsa Emmanuel , Patel Kashyap , Denti Paolo , Visser Marianne , Maartens Gary , Kirkpatrick Carl M. J. , McIlleron Helen , Karlsson Mats O.
Published: November 2012

Days to positivity in automated liquid mycobacterial culture have been shown to correlate with mycobacterial load and have been proposed as a useful biomarker for treatment responses in tuberculosis. However, there is currently no quantitative method or model to analyze the change in days to positivity with time on treatment. The objectives of this study were to describe the decline in numbers of mycobacteria in sputum collected once weekly for 8 weeks from patients on treatment for tuberculosis using days to positivity in liquid culture. One hundred forty-four patients with smear-positive pulmonary tuberculosis were recruited from a tuberculosis clinic in Cape Town, South Africa. A nonlinear mixed-effects repeated-time-to-event modeling approach was used to analyze the time-to-positivity data. A biexponential model described the decline in the estimated number of bacteria in patients' sputum samples, while a logistic model with a lag time described the growth of the bacteria in liquid culture. At baseline, the estimated number of rapidly killed bacteria is typically 41 times higher than that of those that are killed slowly. The time to kill half of the rapidly killed bacteria was about 1.8 days, while it was 39 days for slowly killed bacteria. Patients with lung cavitation had higher bacterial loads than patients without lung cavitation. The model successfully described the increase in days to positivity as treatment progressed, differentiating between bacteria that are killed rapidly and those that are killed slowly. Our model can be used to analyze similar data from studies testing new drug regimens.
Inhaled Microparticles Containing Clofazimine Are Efficacious in Treatment of Experimental Tuberculosis in Mice
Authors: Verma Rahul Kumar , Germishuizen Willem A. , Motheo M. Portia , Agrawal Atul Kumar , Singh Amit Kumar , Mohan Mradul , Gupta Pushpa , Gupta Umesh Datta , Cholo Moloko , Anderson Ronald , Fourie P. Bernard , Misra Amit
Published: November 2012

Inhalable clofazimine-containing dry powder microparticles (CFM-DPI) and native clofazimine (CFM) were evaluated for activity against
Mycobacterium tuberculosis
in human monocyte-derived macrophage cultures and in mice infected with a low-dose aerosol. Both formulations resulted in 99% killing at 2.5 μg/ml
in vitro
. In mice, 480 μg and 720 μg CFM-DPI inhaled twice per week over 4 weeks reduced numbers of CFU in the lung by as much as log
10
2.6; 500 μg oral CFM achieved a log
10
0.7 reduction.
Rifaximin Resistance in Escherichia coli Associated with Inflammatory Bowel Disease Correlates with Prior Rifaximin Use, Mutations in
rpoB
, and Activity of Phe-Arg-β-Naphthylamide-Inhibitable Efflux Pumps
Authors: Kothary Vishesh , Scherl Ellen J. , Bosworth Brian , Jiang Zhi-Dong , DuPont Herbert L. , Harel Josee , Simpson Kenneth W. , Dogan Belgin
Published: November 2012

Escherichia coli
is implicated in the pathogenesis of inflammatory bowel disease (IBD). Rifaximin, a nonabsorbable derivative of rifampin effective against
E. coli
, improves symptoms in mild-to-moderate IBD. However, rifaximin resistance can develop in a single step
in vitro
. We examined the prevalence and mechanisms of rifaximin resistance in 62 strains of
E. coli
isolated from the ileal mucosa of 50 patients (19 with ileal Crohn's disease [L1+L3], 6 with colonic Crohn's disease [L2], 13 with ulcerative colitis [UC], 4 with symptomatic non-IBD diagnoses [NI], and 8 healthy [H]). Resistance (MIC > 1,024 mg/liter) was present in 12/48 IBD-associated ileal
E. coli
strains. Resistance correlated with prior rifaximin treatment (
P
< 0.00000001) but not with the presence of ileal inflammation (
P
= 0.73) or
E. coli
phylogroup. Mutations in a 1,057-bp region of
rpoB
, which encodes the bacterial target of rifaximin, were identified in 10/12 resistant strains versus 0/50 sensitive strains (
P
< 0.000000001) and consisted of seven amino acid substitutions. The efflux pump inhibitor Phe-Arg-β-naphthylamide (PAβN) lowered the MIC of 9/12 resistant strains 8- to 128-fold. Resistance was stable in the absence of rifaximin in 10/12 resistant strains after 30 passages. We conclude that IBD-associated ileal
E. coli
frequently manifest resistance to rifaximin that correlates with prior rifaximin use, amino acid substitutions in
rpoB
, and activity of PAβN-inhibitable efflux pumps, but not with the presence of ileal inflammation or
E. coli
phylogroup. These findings have significant implications for treatment trials targeting IBD-associated
E. coli
.
Anaerobic Coculture of Microalgae with Thermosipho globiformans and Methanocaldococcus jannaschii at 68°C Enhances Generation of
n
-Alkane-Rich Biofuels after Pyrolysis
Authors: Yamane Kunio , Matsuyama Shigeru , Igarashi Kensuke , Utsumi Motoo , Shiraiwa Yoshihiro , Kuwabara Tomohiko
Published: November 2012

We tested different alga-bacterium-archaeon consortia to investigate the production of oil-like mixtures, expecting that
n
-alkane-rich biofuels might be synthesized after pyrolysis.
Thermosipho globiformans
and
Methanocaldococcus jannaschii
were cocultured at 68°C with microalgae for 9 days under two anaerobic conditions, followed by pyrolysis at 300°C for 4 days.
Arthrospira platensis
(
Cyanobacteria
),
Dunaliella tertiolecta
(
Chlorophyta
),
Emiliania huxleyi
(
Haptophyta
), and
Euglena gracilis
(
Euglenophyta
) served as microalgal raw materials.
D. tertiolecta
,
E. huxleyi
, and
E. gracilis
cocultured with the bacterium and archaeon inhibited their growth and CH
4
production.
E. huxleyi
had the strongest inhibitory effect. Biofuel generation was enhanced by reducing impurities containing alkanenitriles during pyrolysis. The composition and amounts of
n
-alkanes produced by pyrolysis were closely related to the lipid contents and composition of the microalgae. Pyrolysis of
A. platensis
and
D. tertiolecta
containing mainly phospholipids and glycolipids generated short-carbon-chain
n
-alkanes (
n
-tridecane to
n
-nonadecane) and considerable amounts of isoprenoids.
E. gracilis
also produced mainly short
n
-alkanes. In contrast,
E. huxleyi
containing long-chain (31 and 33 carbon atoms) alkenes and very long-chain (37 to 39 carbon atoms) alkenones, in addition to phospholipids and glycolipids, generated a high yield of
n
-alkanes of various lengths (
n
-tridecane to
n
-pentatriacontane). The gas chromatography-mass spectrometry (GC-MS) profiles of these
n
-alkanes were similar to those of native petroleum crude oils despite containing a considerable amount of
n
-hentriacontane. The ratio of phytane to
n
-octadecane was also similar to that of native crude oils.
Bacterial and Archaeal Diversity in Sediments of West Lake Bonney, McMurdo Dry Valleys, Antarctica
Authors: Tang Chao , Madigan Michael T. , Lanoil Brian
Published: November 2012

Bacterial and archaeal diversity was examined in a sediment core from Lake Bonney, Antarctica. Members of the
Archaea
showed both low abundance and diversity, whereas bacterial diversity was moderately high and some phyla were fairly abundant, even in geologically old samples. Microbial diversity correlated with sample texture and differed in silty and coarse samples.
FLX Pyrosequencing Analysis of the Effects of the Brown-Algal Fermentable Polysaccharides Alginate and Laminaran on Rat Cecal Microbiotas
Authors: An Choa , Kuda Takashi , Yazaki Takahiro , Takahashi Hajime , Kimura Bon
Published: November 2012

Edible brown algae are used as major food material in Far East Asian countries, particularly in South Korea and Japan. They contain fermentable dietary fibers, alginic acid (uronic acid polymer) and laminaran (β-1,3-glucan), that are fermented into organic acids by intestinal bacteria. To clarify the effect of edible algae on the intestinal environment, the cecal microbiotas of rats fed diets containing no dietary fiber (control) or 2% (wt/wt) sodium alginate or laminaran for 2 weeks were analyzed using FLX amplicon pyrosequencing with bar-coded primers targeting the bacterial 16S rRNA gene. The most abundant phylum in all groups was
Firmicutes
. Specifically,
Allobaculum
was dominant in all diet groups. In addition,
Bacteroides capillosus
(37.1%) was abundant in the alginate group, while
Clostridium ramosum
(3.14%) and
Parabacteroides distasonis
(1.36%) were only detected in the laminaran group. Furthermore, rats fed alginate showed simplified microbiota phylotypes compared with others. With respect to cecal chemical compounds, laminaran increased cecal organic acid levels, particularly propionic acid. Alginate increased total cecal organic acids. Cecal putrefactive compounds, such as indole, H
2
S, and phenol, were decreased by both alginate and laminaran. These results indicate that edible brown algae can alter the intestinal environment, with fermentation by intestinal microbiota.
Recombinant Bacillus subtilis That Grows on Untreated Plant Biomass
Authors: Anderson Timothy D. , Miller J. Izaak , Fierobe Henri-Pierre , Clubb Robert T.
Published: November 2012

Lignocellulosic biomass is a promising feedstock to produce biofuels and other valuable biocommodities. A major obstacle to its commercialization is the high cost of degrading biomass into fermentable sugars, which is typically achieved using cellulolytic enzymes from
Trichoderma reesei
. Here, we explore the use of microbes to break down biomass.
Bacillus subtilis
was engineered to display a multicellulase-containing minicellulosome. The complex contains a miniscaffoldin protein that is covalently attached to the cell wall and three noncovalently associated cellulase enzymes derived from
Clostridium cellulolyticum
(Cel48F, Cel9E, and Cel5A). The minicellulosome spontaneously assembles, thus increasing the practicality of the cells. The recombinant bacteria are highly cellulolytic and grew in minimal medium containing industrially relevant forms of biomass as the primary nutrient source (corn stover, hatched straw, and switch grass). Notably, growth did not require dilute acid pretreatment of the biomass and the cells achieved densities approaching those of cells cultured with glucose. An analysis of the sugars released from acid-pretreated corn stover indicates that the cells have stable cellulolytic activity that enables them to break down 62.3% ± 2.6% of the biomass. When supplemented with beta-glucosidase, the cells liberated 21% and 33% of the total available glucose and xylose in the biomass, respectively. As the cells display only three types of enzymes, increasing the number of displayed enzymes should lead to even more potent cellulolytic microbes. This work has important implications for the efficient conversion of lignocellulose to value-added biocommodities.
Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production
Authors: Varman Arul M. , Xiao Yi , Pakrasi Himadri B. , Tang Yinjie J.
Published: November 2012

Global warming and decreasing fossil fuel reserves have prompted great interest in the synthesis of advanced biofuels from renewable resources. In an effort to address these concerns, we performed metabolic engineering of the cyanobacterium
Synechocystis
sp. strain PCC 6803 to develop a strain that can synthesize isobutanol under both autotrophic and mixotrophic conditions. With the expression of two heterologous genes from the Ehrlich pathway, the engineered strain can accumulate 90 mg/liter of isobutanol from 50 mM bicarbonate in a gas-tight shaking flask. The strain does not require any inducer (i.e., isopropyl β-
d
-1-thiogalactopyranoside [IPTG]) or antibiotics to maintain its isobutanol production. In the presence of glucose, isobutanol synthesis is only moderately promoted (titer = 114 mg/liter). Based on isotopomer analysis, we found that, compared to the wild-type strain, the mutant significantly reduced its glucose utilization and mainly employed autotrophic metabolism for biomass growth and isobutanol production. Since isobutanol is toxic to the cells and may also be degraded photochemically by hydroxyl radicals during the cultivation process, we employed
in situ
removal of the isobutanol using oleyl alcohol as a solvent trap. This resulted in a final net concentration of 298 mg/liter of isobutanol under mixotrophic culture conditions.
Relevance of Fucose-Rich Extracellular Polysaccharides Produced by Rhizobium sullae Strains Nodulating Hedysarum coronarium L. Legumes
Authors: Gharzouli Razika , Carpï¿½nï¿½ Marie-Anne , Couderc Franï¿½ois , Benguedouar Ammar , Poinsot Vï¿½rï¿½na
Published: November 2012

Specific and complex interactions between soil bacteria, known as rhizobia, and their leguminous host plants result in the development of root nodules. This process implies a complex dialogue between the partners. Rhizobia synthesize different classes of polysaccharides: exopolysaccharides (EPS), Kdo-rich capsular polysaccharides, lipopolysaccharides, and cyclic β-(1,2)-glucans. These polymers are actors of a successful symbiosis with legumes. We focus here on studying the EPS produced by
Rhizobium sullae
bacteria that nodulate
Hedysarum coronarium
L., largely distributed in Algeria. We describe the influence of the carbon source on the production and on the composition of EPS produced by
R. sullae
A6 and RHF strains. High-molecular-weight EPS preserve the bacteria from desiccation. The structural characterization of the EPS produced by
R. sullae
strains has been performed through sugar analysis by gas chromatography-mass spectrometry. The low-molecular-weight EPS of one strain (RHF) has been totally elucidated using nuclear magnetic resonance and quantitative time-of-flight tandem mass spectrometry analyses. An unusual fucose-rich EPS has been characterized. The presence of this deoxy sugar seems to be related to nodulation capacity.
Outer Cell Surface Components Essential for Fe(III) Oxide Reduction by Geobacter metallireducens
Authors: Smith Jessica A. , Lovley Derek R. , Tremblay Pier-Luc
Published: November 2012

Geobacter
species are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail in
Geobacter sulfurreducens
, but a number of the most thoroughly studied outer surface components of
G. sulfurreducens
, particularly
c
-type cytochromes, are not well conserved among
Geobacter
species. In order to identify cellular components potentially important for Fe(III) oxide reduction in
Geobacter metallireducens
, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes for
c
-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified six
c
-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of the
c
-type cytochromes which were essential for Fe(III) oxide reduction in
G. metallireducens
have homologs in
G. sulfurreducens
that are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1–HT2A–Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer between
G. metallireducens
and
G. sulfurreducens
but the outer-surface
c
-type cytochromes involved in Fe(III) oxide reduction are different.
Interplay between Manganese and Iron in Pneumococcal Pathogenesis: Role of the Orphan Response Regulator RitR
Authors: Ong Cheryl-Lynn Y. , Potter Adam J. , Trappetti Claudia , Walker Mark J. , Jennings Michael P. , Paton James C. , McEwan Alastair G.
Published: November 2012

Streptococcus pneumoniae
(the pneumococcus) is a major human pathogen that is carried asymptomatically in the nasopharynx by up to 70% of the human population. Translocation of the bacteria into internal sites can cause a range of diseases, such as pneumonia, otitis media, meningitis, and bacteremia. This transition from nasopharynx to growth at systemic sites means that the pneumococcus needs to adjust to a variety of environmental conditions, including transition metal ion availability. Although it is an important nutrient, iron potentiates oxidative stress, and it is established that in
S. pneumoniae
, expression of iron transport systems and proteins that protect against oxidative stress are regulated by an orphan response regulator, RitR. In this study, we investigated the effect of iron and manganese ion availability on the growth of a
ritR
mutant. Deletion of
ritR
led to impaired growth of bacteria in high-iron medium, but this phenotype could be suppressed with the addition of manganese. Measurement of metal ion accumulation indicated that manganese prevents iron accumulation. Furthermore, the addition of manganese also led to a reduction in the amount of hydrogen peroxide produced by bacterial cells. Studies of virulence in a murine model of infection indicated that RitR was not essential for pneumococcal survival and suggested that derepression of iron uptake systems may enhance the survival of pneumococci in some niches.
Identification of a Potent Combination of Key Plasmodium falciparum Merozoite Antigens That Elicit Strain-Transcending Parasite-Neutralizing Antibodies
Authors: Pandey Alok K. , Reddy K. Sony , Sahar Tajali , Gupta Sonal , Singh Hina , Reddy E. Jyotheeswara , Asad Mohd , Siddiqui Faiza A. , Gupta Pankaj , Singh Bijender , More Kunal R. , Mohmmed Asif , Chitnis Chetan E. , Chauhan Virander S. , Gaur Deepak
Published: November 2012

Blood-stage malaria vaccines that target single
Plasmodium falciparum
antigens involved in erythrocyte invasion have not induced optimal protection in field trials. Blood-stage malaria vaccine development has faced two major hurdles, antigenic polymorphisms and molecular redundancy, which have led to an inability to demonstrate potent, strain-transcending, invasion-inhibitory antibodies. Vaccines that target multiple invasion-related parasite proteins may inhibit erythrocyte invasion more efficiently. Our approach is to develop a receptor-blocking blood-stage vaccine against
P. falciparum
that targets the erythrocyte binding domains of multiple parasite adhesins, blocking their interaction with their receptors and thus inhibiting erythrocyte invasion. However, with numerous invasion ligands, the challenge is to identify combinations that elicit potent strain-transcending invasion inhibition. We evaluated the invasion-inhibitory activities of 20 different triple combinations of antibodies mixed
in vitro
against a diverse set of six key merozoite ligands, including the novel ligands
P. falciparum
apical asparagine-rich protein (PfAARP), EBA-175 (PfF2),
P. falciparum
reticulocyte binding-like homologous protein 1 (PfRH1), PfRH2, PfRH4, and
Plasmodium
thrombospondin apical merozoite protein (PTRAMP), which are localized in different apical organelles and are translocated to the merozoite surface at different time points during invasion. They bind erythrocytes with different specificities and are thus involved in distinct invasion pathways. The antibody combination of EBA-175 (PfF2), PfRH2, and PfAARP produced the most efficacious strain-transcending inhibition of erythrocyte invasion against diverse
P. falciparum
clones. This potent antigen combination was selected for coimmunization as a mixture that induced balanced antibody responses against each antigen and inhibited erythrocyte invasion efficiently. We have thus demonstrated a novel two-step screening approach to identify a potent antigen combination that elicits strong strain-transcending invasion inhibition, supporting its development as a receptor-blocking malaria vaccine.
Closed trauma,Mycoplasma hominisosteomyelitis, and the elusive diagnosis of Good's syndrome
Authors: Noska Amanda , Nasr Rawad , Williams David Neville
Published: November 2012

Mycoplasma hominisseptic arthritis has a well-established association with hypogammaglobulinaemia, but is rarely seen in immunocompetent hosts. An association also exists with a closed trauma and a predisposition toM hominisbone infections. In this clinical case report, a patient withM hominisosteomyelitis following a closed trauma was diagnosed using 16S ribosomal studies, and led to the diagnosis of a severe underlying immunodeficiency syndrome known as Good's syndrome.