bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Control Method of Surface Morphology and Etch Rates for Silicon Etch Process With Extremely Deep and High Aspect Ratio
Authors: Xu Tiantong , Tao Zhi , Tan Xiao , Li Haiwang 
Published: March 2016

The manufacture method based on the silicon etching process is one of the most important methods to fabricate micro mechanical structure, e.g. micro-engine. In the processing, the high aspect ratio silicon etch process (HARSE process) is very important to improve the efficiency of structure. At the same time, the surface morphology should be controlled exactly to keep the performance of structure.
In this paper, the feasibilities of controlling the surface morphology and Si etch rates were experimentally investigated. In the experiments, the width of structure changes from 15um to 1500um and the depth changes from 50um to 500um. The parameters of surface morphology including sidewall angle, surface roughness, and so on were measured and compared. The influence mechanisms of etching parameters were analyzed.
The etching process were completed in a surface technology system (STS) multiplex advanced silicon etcher inductively coupled plasma (ICP) system with SF6/O2 plasma as etching plasma and C4F8 as passivation plasma. In the experiments, the etching experiments were conducted in a low pressure (5–50mTorr), high density, inductively coupled plasma etching reactor (ICP) with a planar coil. The Si etches rates and sidewall angle were investigated as a function of chamber pressure, cathode RF-power, and gas flow.
The results indicated that the increasing of total etching time results in an acceleration in etch rate as well as the decrease in sidewall angle (the top width of trench is narrow than the bottom width). Meanwhile, the total passivation time has an opposite effect in the influence of etch rate and sidewall angle. All the experiments indicate that the quick shift between etch and passivation period leads to a smoother surface. An interesting phenomenon were discovered that the etch rate will not change with the changing of width parameter in most of the high aspect ratio silicon etch recipes when the width-depth ratio is upper than 0.34. An experiential function formula were fitted based on four parameters, including width and depth of the structure, and total etching and passivation time.
Acquisition of Extended-Spectrum β-Lactamases by Escherichia coli and Klebsiella pneumoniae in Gut Microbiota of Pilgrims during the Hajj Pilgrimage of 2013
Authors: Leangapichart Thongpan , Dia Ndèye Méry , Olaitan Abiola Olumuyiwa , Gautret Philippe , Brouqui Philippe , Rolain Jean-Marc 
Published: March 2016

ABSTRACT

We reported the acquisition of extended-spectrum-β-lactamase (ESBL)-producing bacteria in rectal samples of 129 pilgrims during the 2013 Hajj (pilgrimage to Makkah). When returning from the Hajj, there was a significant increase in the number of pilgrims carrying
E. coli
resistant to ceftriaxone (
P
= 0.008). The CTX-M gene was detected in rectal samples, with the detection rate increasing from 10.08% to 32.56% of samples after the Hajj (
P
< 0.001).
Evaluation of the
In Vitro
Activity of Ceftazidime-Avibactam and Ceftolozane-Tazobactam against Meropenem-Resistant Pseudomonas aeruginosa Isolates
Authors: Buehrle Deanna J. , Shields Ryan K. , Chen Liang , Hao Binghua , Press Ellen G. , Alkrouk Ammar , Potoski Brian A. , Kreiswirth Barry N. , Clancy Cornelius J. , Nguyen M. Hong 
Published: March 2016

ABSTRACT

We compared ceftazidime-avibactam, ceftolozane-tazobactam, ceftazidime, cefepime, and piperacillin-tazobactam MICs for 38 meropenem-resistant
Pseudomonas aeruginosa
isolates. No isolates harbored carbapenemases; 74% were
oprD
mutants. Ceftazidime-avibactam and ceftolozane-tazobactam were active against 92% of the isolates, including 80% that were resistant to all three β-lactams. Forty-three percent of ceftazidime-avibactam-susceptible isolates and 6% of ceftolozane-tazobactam-susceptible isolates exhibited MICs at the respective breakpoints. Ceftolozane-tazobactam and ceftazidime-avibactam are therapeutic options for meropenem-resistant
P. aeruginosa
infections that should be used judiciously to preserve activity.
Inactivation of Lytic Transglycosylases Increases Susceptibility to Aminoglycosides and Macrolides by Altering the Outer Membrane Permeability of Stenotrophomonas maltophilia
Authors: Wu Chao-Jung , Huang Yi-Wei , Lin Yi-Tsung , Yang Tsuey-Ching 
Published: March 2016

ABSTRACT

Stenotrophomonas maltophilia
harbors six lytic transglycosylases (LTs):
mltA
,
mltB1
,
mltB2
,
mltD1
,
mltD2
, and
slt
. LT deletion increased susceptibility of
S. maltophilia
to aminoglycosides (AGs) and macrolides, and the underlying mechanisms were investigated. The expression of AG-modifying enzymes and efflux pumps was evaluated by quantitative reverse transcription-PCR (qRT-PCR). Susceptibility to 1-
N
-phenylnaphthylamine, vancomycin, SDS, and bile salts was measured to assess outer membrane permeability. In conclusion, increased outer membrane permeability contributes to LT deletion-mediated increase in aminoglycoside and macrolide susceptibility.
Bacterial Dose-Dependent Role of G Protein-Coupled Receptor Kinase 5 in Escherichia coli-Induced Pneumonia
Authors: Packiriswamy Nandakumar , Steury Michael , McCabe Ian C. , Fitzgerald Scott D. , Parameswaran Narayanan 
Published: March 2016

ABSTRACTG protein-coupled receptor kinase 5 (GRK5) is a serine/threonine kinase previously shown to mediate polymicrobial sepsis-induced inflammation. The goal of the present study was to examine the role of GRK5 in monomicrobial pulmonary infection by using an intratrachealEscherichia coliinfection model of pneumonia. We used sublethal and lethal doses ofE. colito examine the mechanistic differences between low-grade and high-grade inflammation induced byE. coliinfection. With a sublethal dose ofE. coli, GRK5 knockout (KO) mice exhibited higher plasma CXCL1/KC levels and enhanced lung neutrophil recruitment early after infection, and lower bacterial loads, than wild-type (WT) mice. The inflammatory response was also diminished, and resolution of inflammation advanced, in the lungs of GRK5 KO mice. In contrast to the reduced bacterial loads in GRK5 KO mice following a sublethal dose, at a lethal dose ofE. coli, the bacterial burdens remained high in GRK5 KO mice relative to those in WT mice. This occurred in spite of enhanced plasma CXCL1 levels as well as neutrophil recruitment in the KO mice. But the recruited neutrophils (following high-dose infection) exhibited decreased CD11b expression and reduced reactive oxygen species production, suggesting decreased neutrophil activation or increased neutrophil exhaustion in the GRK5 KO mice. In agreement with the increased bacterial burden, KO mice showed poorer survival than WT mice followingE. coliinfection at a lethal dose. Overall, our data suggest that GRK5 negatively regulates CXCL1/KC levels during bacterial pneumonia but that the role of GRK5 in the clinical outcome in this model is dependent on the bacterial dose.
Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions
Authors: Pienaar Elsje , Matern William M. , Linderman Jennifer J. , Bader Joel S. , Kirschner Denise E. 
Published: March 2016

ABSTRACTGranulomas are a hallmark of tuberculosis. Inside granulomas, the pathogenMycobacterium tuberculosismay enter a metabolically inactive state that is less susceptible to antibiotics. UnderstandingM. tuberculosismetabolism within granulomas could contribute to reducing the lengthy treatment required for tuberculosis and provide additional targets for new drugs. Two key adaptations ofM. tuberculosisare a nonreplicating phenotype and accumulation of lipid inclusions in response to hypoxic conditions. To explore how these adaptations influence granuloma-scale outcomesin vivo, we present a multiscalein silicomodel of granuloma formation in tuberculosis. The model comprises host immunity,M. tuberculosismetabolism,M. tuberculosisgrowth adaptation to hypoxia, and nutrient diffusion. We calibrated our model toin vivodata from nonhuman primates and rabbits and apply the model to predictM. tuberculosispopulation dynamics and heterogeneity within granulomas. We found that bacterial populations are highly dynamic throughout infection in response to changing oxygen levels and host immunity pressures. Our results indicate that a nonreplicating phenotype, but not lipid inclusion formation, is important for long-termM. tuberculosissurvival in granulomas. We used virtualM. tuberculosisknockouts to predict the impact of both metabolic enzyme inhibitors and metabolic pathways exploited to overcome inhibition. Results indicate that knockouts whose growth rates are below ∼66% of the wild-type growth rate in a culture medium featuring lipid as the only carbon source are unable to sustain infections in granulomas. By mapping metabolite- and gene-scale perturbations to granuloma-scale outcomes and predicting mechanisms of sterilization, our method provides a powerful tool for hypothesis testing and guiding experimental searches for novel antituberculosis interventions.
Trypanosoma cruzi Differentiates and Multiplies within Chimeric Parasitophorous Vacuoles in Macrophages Coinfected with Leishmania amazonensis
Authors: Pessoa Carina Carraro , Ferreira Éden Ramalho , Bayer-Santos Ethel , Rabinovitch Michel , Mortara Renato Arruda , Real Fernando 
Published: March 2016

ABSTRACT

The trypanosomatids
Leishmania amazonensis
and
Trypanosoma cruzi
are excellent models for the study of the cell biology of intracellular protozoan infections. After their uptake by mammalian cells, the parasitic protozoan flagellates
L. amazonensis
and
T. cruzi
lodge within acidified parasitophorous vacuoles (PVs). However, whereas
L. amazonensis
develops in spacious, phagolysosome-like PVs that may enclose numerous parasites,
T. cruzi
is transiently hosted within smaller vacuoles from which it soon escapes to the host cell cytosol. To investigate if parasite-specific vacuoles are required for the survival and differentiation of
T. cruzi
, we constructed chimeric vacuoles by infection of
L. amazonensis
amastigote-infected macrophages with
T. cruzi
epimastigotes (EPIs) or metacyclic trypomastigotes (MTs). These chimeric vacuoles, easily observed by microscopy, allowed the entry and fate of
T. cruzi
in
L. amazonensis
PVs to be dynamically recorded by multidimensional imaging of coinfected cells. We found that although
T. cruzi
EPIs remained motile and conserved their morphology in chimeric vacuoles,
T. cruzi
MTs differentiated into amastigote-like forms capable of multiplying. These results demonstrate that the large adaptive vacuoles of
L. amazonensis
are permissive to
T. cruzi
survival and differentiation and that noninfective EPIs are spared from destruction within the chimeric PVs. We conclude that
T. cruzi
differentiation can take place in
Leishmania
-containing vacuoles, suggesting this occurs prior to their escape into the host cell cytosol.
The RipA and RipB Peptidoglycan Endopeptidases Are Individually Nonessential to Mycobacterium smegmatis
Authors: Martinelli Daniel J. , Pavelka Martin S. 
Published: March 2016

ABSTRACT

Mycobacteria possess a series of Rip peptidoglycan endopeptidases that have been characterized in various levels of detail. The RipA and RipB proteins have been extensively studied and are
dl
-endopeptidases, and RipA has been considered essential to
Mycobacterium smegmatis
and
Mycobacterium tuberculosis
. We show here that the
ripA
and
ripB
genes are individually dispensable in
M. smegmatis
and that at least one of the genes must be expressed for viability. We characterized strains carrying in-frame deletion mutations of
ripA
and
ripB
and found that both mutant strains exhibited increased susceptibility to a limited number of antibiotics and to detergent but that only the Δ
ripA
mutant displayed hypersusceptibility to lysozyme. We also constructed and characterized Δ
ripD
and Δ
ripA
Δ
ripD
mutants and found that the single mutant had only an intermediate lysozyme hypersusceptibility phenotype compared to that of wild-type cells while loss of
ripD
in the Δ
ripA
background partially rescued the antibiotic and lysozyme phenotypes of the Δ
ripA
mutant.

IMPORTANCE
We show that the RipA endopeptidase, which has been considered essential for cell division in certain mycobacteria, is not essential but that at least it or a similar protein, RipB, must be expressed by the bacteria for viability. This work is the first description of strains carrying single deletion mutations of RipA, RipB, and a novel endopeptidase-like protein, RipD.
Effects of different metabolic states and surgical models on glucose metabolism and secretion of ileal L-cell peptides: protocol for a cross-sectional study
Authors: Celik Alper , Dixon John B , Pouwels Sjaak , Celik Bahri Onur , Karaca Fatih Can , Gupta Adarsh , Santoro Sergio , Ugale Surendra 
Published: March 2016

IntroductionObesity and type 2 diabetes mellitus are increasing worldwide, reaching pandemic proportions. The understanding of the role of functional restriction and gut hormones can be a beneficial tool in treating obesity and diabetes. However, the exact hormonal profiles in different metabolic states and surgical models are not known.Methods and analysisThe HIPER-1 Study is a single-centre cross-sectional study in which 240 patients (in different metabolic states and surgical models) will receive an oral mixed-meal tolerance test (OMTT). At baseline and after 30, 60 and 120 min, peptide YY and glucagon-like peptide 1 levels and glucose and insulin sensitivity will be measured. The primary end point of the study will be the area under the glucagon-like peptide 1 and peptide YY curves after the OMTT. Secondary study end points will include examination of the difference in plasma levels of the distal ileal hormones in subjects with various health statuses and in patients who have been treated with different surgical techniques.Ethics and disseminationAn independent ethics committee, the Institutional Review Board of Istanbul Sisli Kolan International Hospital, Turkey, has approved the study protocol. Dissemination will occur via publication, national and international conference presentations, and exchanges with regional, provincial and national stakeholders.Trial registration numberNCT02532829; Pre-results.
Active push deployment technique improves stent/vessel-wall interaction in endovascular treatment of acute stroke with stent retrievers
Authors: Wiesmann Martin , Brockmann Marc-Alexander , Heringer Sarah , Müller Marguerite , Reich Arno , Nikoubashman Omid 
Published: March 2016

BackgroundThe optimal interaction between stent struts and thrombus is crucial for successful revascularization in endovascular stroke therapy with stent retrievers. Deploying the stent retriever by actively pushing it into the thrombus increases the radial force with which the stent struts expand into the thrombus.ObjectiveTo examine theactive push deployment(APD) technique in an in vitro model and present our clinical experience with this technique.MethodsIn an in vitro experiment we investigated the configuration of a Solitaire and a Trevo ProVue device (both 4×20 mm), depending on whether the devices were deployed using the APD technique or simple unsheathing. We retrospectively assessed the effectiveness and safety of this technique by analyzing 130 patients with large vessel occlusions (carotid T or M1 segment of the middle cerebral artery), who received endovascular treatment with a Trevo device (4×20 mm) that was deployed using the APD technique.ResultsIn vitro experiment:the APD technique improved apposition of the devices to the vessel wall. There was widening of 30% (Trevo) and 19% (Solitaire) at the cost of a shortening of 5% and 4%, respectively, when the devices were deployed in a carotid T model.Clinical study: the revascularization rate (Thrombolysis in Cerebral Infarction ≥2b) with the Trevo device was 90%. There were no retriever-associated dissections or perforations in 278 retrieval maneuvers.ConclusionsThe APD technique improves apposition of the tested devices to the vessel wall. The widening effect comes at the cost of minimal shortening of the devices. Our clinical experience shows that using the APD technique to deploy the Trevo device is effective and safe.
Pharmacokinetic Properties of Clarithromycin: A Comparison with Erythromycin and Azithromycin
Authors: LeBel Marc 
Published: March 2016

Objective: To compare the pharmacokinetic properties of two new macrolide antibiotics, clarithromycin and azithromycin, with those of the prototype macrolide, erythromycin.Data Sources: Primarily peer review journals were searched for papers describing the pharmacokinetics of these new macrolides.Study Selection: Fifteen in vitro and clinical studies of clarithromycin and azithromycin and one clinical abstract on clarithromycin from the past four years were selected for review.Data Extraction: Data relevant to the pharmacokinetic characteristics of clarithromycin, azithromycin and, to a lesser extent, erythromycin were selected for presentation in this comparison.Data Synthesis: By reviewing the available studies, it was possible to construct pharmacokinetic profiles of the new compounds, and to compare them with each other and with erythromycin.Conclusions: Both clarithromycin and azithromycin have been shown to have an antibacterial spectrum and pharmacokinetic profile superior to that of erythromycin. The differences between the new compounds, however, may not be that significant. Each is likely to become a first‐line therapeutic option in specific instances, which will become better delineated as clinical research on these new macrolides continues.
Prevalence of Antibody to Current Influenza Virus Strains in a 1992 Canadian Serosurvey and Crude Estimates of 1991–92 Season A/Beijing/353/89 Infections
Authors: Weber John M 
Published: March 2016

Objectives: The annual influenza serosurvey was conducted to monitor influenza activity and gauge susceptibility to currently circulating and emerging influenza viruses.Design: Six hundred and thirty sera from among specimens received for various tests were selected from all age groups and sent with age and geographic identifiers to the Laboratory Centre for Disease Control. Forty sera per province were selected during a one‐week period beginning May 31, 1992 except for the province of Alberta which submitted 80 specimens, and Ontario and Quebec which each submitted 160 sera during a four‐week period. Sera were tested for hemagglutination inhibiting (HI) antibodies against the 1992–93 vaccine strains and A/Taiwan/1/86 (H1N1).Main Results: The percentage of sera from all ages having HI antibody to A/Beijing/353/89 (H3N2) at a titre of 1:40 or greater more than doubled from 22% in the 1991 sample to 53% in 1992. The percentage of sera in all ages having antibody titre at 1:40 or greater to H1N1 strains A/Texas/36/91 and A/Taiwan/1/86 was 55% and 57%, respectively, in 1992, up from 45% with antibody titre 1:40 or greater to A/Taiwan/1/86 in 1991. Twenty‐seven per cent of sera had antibody titre 1:40 or greater to B/Panama/45/90 compared with 19% in 1991.Conclusion: The relative increase in the percentage of sera with antibody with a titre of 1:40 or greater likely reflected vaccination efforts and the relative level of activity of the various influenza types and subtypes during the 1991–92 influenza season. The data also suggested that influenza B had the greatest potential for significant activity during the 1992–93 influenza season.
Etiology of Cervicitis and Treatment with Minocycline
Authors: Bowie William R , Willetts Val , Binns Bernard A , Brunham Robert C 
Published: March 2016

Objective: To evaluate the etiology of cervicitis using the recommended Canadian definition, and to evaluate the efficacy and tolerability of seven days of minocycline treatment, 100 versus 200 mg at bedtime.Design: Randomized double‐blind study with initial microbiological evaluation, and intended follow‐up through 12 weeks.Setting: Women attending the major sexually transmitted disease clinic in Vancouver and the major teaching hospital in Winnipeg.Population Studied: Women with cervicitis (inclusion criteria were an off‐white or yellow colour of cervical mucus when viewed on a white‐tipped swab, and a mean of 10 or more polymorphonuclear leukocytes per oil immersion [× 1000] field on Gram stain of cervical mucus). Fourty‐four women were enrolled but two were excluded because of contaminated cultures.Interventions: Treatment with two identical appearing capsules of 50 mg (100 mg dose) or 100 mg (200 mg dose) of minocycline taken at bedtime with water for seven days.Main Results: Of the 42 evaluable women, Chlamydia trachomatis was initially isolated from 19 (45%) and Neisseria gonorrhoeae from four (10%). The study was prematurely terminated because of an unacceptable and significantly higher frequency of adverse reactions on the higher dose regimen of minocycline – severe reactions in one (4%) on 100 mg compared with six (30%) on 200 mg (P=0.05). Major reactions were dizziness, mood alterations and nausea. Clinical parameters, but not numbers of polymorphonuclear leukocytes, improved significantly irrespective of initial microbiology or the regimen received. Cultures became and stayed negative for C trachomatis in seven of eight on minocycline 100 mg and five of six on minocycline 200 mg. Both ‘failures’ had an intervening negative culture and were re‐exposed to untreated sexual partners.Conclusions: Although not a definitive study in terms of proving efficacy of lower dose regimens, the results are consistent with efficacy and demonstrate the significant advantage of the lower dose regimen in terms of adverse reactions.
Salmonella thomson Outbreak in a Canadian Newborn Nursery
Authors: Lalonde Richard G 
Published: March 2016

Objective: To determine the mode of salmonella transmission during an outbreak in a newborn nursery.Design: Outbreak investigation with retrospective review of medical, microbiological and work records, active case‐finding, and active surveillance. A case was defined as a newborn with salmonella isolated from any site.Setting: University affiliated community hospital near Montreal with 125 active care beds and 3000 deliveries annually.Patients: Cases were identified from the microbiology reports and public health notifications for one month before to six months after detection of the outbreak. All neonates with diarrhea had stool cultures during the period of observation.Results: Four cases of neonatal salmonella infection were detected. The index infection was acquired at birth from a mother with severe gastroenteritis from contaminated chicken. The first of five secondary cases – three other neonates and two mothers – was only detected 11 days after departure of the index case. Three of the four infants required intensive treatment and one remained a chronic carrier and was rejected for daycare services. No food or health care worker was associated with infection of neonates. The diapering technique had been changed one month earlier because the hospital had stopped purchasing disposable washcloths.Conclusions: Three of the four neonatal salmonella infections caused severe morbidity. The organism was easily transmitted when breaks in technique probably allowed contamination of fomites, survival in the inanimate environment, and subsequent cross‐infection to other neonates. Simple unexpected changes in the availability of material resources such as washcloths may have adversely influenced clinical practises with a resultant breakdown in infection control procedures.