Local Heat Dissipation and Elasticity of Suspended Silicon Nanowires Revealed by Dual Scanning Electron and Thermal Microscopies.

A novel combined setup, with a scanning thermal microscope (SThM) embedded in a scanning electron microscope (SEM), is used to characterize a suspended silicon rough nanowire (NW), which is epitaxially clamped at both sides and therefore monolithically integrated in a microfabricated device. The rough nature of the NW surface, which prohibits vacuum-SThM due to loose contact for heat dissipation, is circumvented by decorating the NW with periodic platinum dots. Reproducible approaches over these dots, enabled by the live feedback image provided by the SEM, yield a strong improvement in thermal contact resistance and a higher accuracy in its estimation. The results-thermal resistance at the tip-sample contact of 188±3.7K µW-1 and thermal conductivity of the NW of 13.7±1.6W m-1 K-1-are obtained by performing a series of approach curves on the dots. Noteworthy, the technique allows measuring elastic properties at the same time-the moment of inertia of the NW is found to be (6.1±1.0) × 10-30m4-which permits to correlate the respective effects of the rough shell on heat dissipation and on the NW stiffness. The work highlights the capabilities of the dual SThM/SEM instrument, in particular the interest of systematic approach curves with well-positioned and monitored tip motion.

fastMRI: A Publicly Available Raw k-Space and DICOM Dataset of Knee Images for Accelerated MR Image Reconstruction Using Machine Learning.

A publicly available dataset containing k-space data as well as Digital Imaging and Communications in Medicine image data of knee images for accelerated MR image reconstruction using machine learning is presented.

A universal and ultrasensitive vectorial nanomechanical sensor for imaging 2D force fields.

The miniaturization of force probes into nanomechanical oscillators enables ultrasensitive investigations of forces on dimensions smaller than their characteristic length scales. It also unravels the vectorial character of the force field and how its topology impacts the measurement. Here we present an ultrasensitive method for imaging two-dimensional vectorial force fields by optomechanically following the bidimensional Brownian motion of a singly clamped nanowire. This approach relies on angular and spectral tomography of its quasi-frequency-degenerated transverse mechanical polarizations: immersing the nanoresonator in a vectorial force field not only shifts its eigenfrequencies but also rotates the orientation of the eigenmodes, as a nanocompass. This universal method is employed to map a tunable electrostatic force field whose spatial gradients can even dominate the intrinsic nanowire properties. Enabling vectorial force field imaging with demonstrated sensitivities of attonewton variations over the nanoprobe Brownian trajectory will have a strong impact on scientific exploration at the nanoscale.

Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021, Isolated from Clonal Clustered Cases in French Brittany.

Here, we announce the complete annotated genome sequence of the invasive Streptococcus pyogenes strain M/emm66, isolated in 2013 from a subcutaneous abscess in new clustered cases in French Brittany.

Complete Genome Sequence of Noninvasive Streptococcus pyogenes M/emm28 Strain STAB10015, Isolated from a Child with Perianal Dermatitis in French Brittany.

We report here the complete genome sequence of a noninvasive strain of Streptococcus pyogenes M/emm28, isolated from perianal dermatitis in a child. The genome is composed of 1,950,454 bp, with a G+C content of 38.2%, and it has 1,925 identified coding sequences and harbors two intact prophages and a new integrating conjugative element (ICE).

Full-Length Genome Sequence of Type M/emm83 Group A Streptococcus pyogenes Strain STAB1101, Isolated from Clustered Cases in Brittany.

Here, we announce the complete annotated genome sequence of a Streptococcus pyogenes M/emm83 strain, STAB1101, isolated from clustered cases in homeless persons in Brittany (France). The genome is composed of 1,709,790 bp, with a G+C content of 38.4% and 1,550 identified coding sequences (CDS), and it harbors a Tn916-like transposon.

First experience of a multicenter external quality assessment of molecular 16S rRNA gene detection in bone and joint infections.

The objective of this study was to assess the performance of seven French laboratories for 16S rRNA gene detection by real-time PCR in the diagnosis of bone and joint infection (BJI) to validate a large multicenter study. External quality control (QC) was required owing to the differences in extraction procedures and the molecular equipment used in the different laboratories. Three proficiency sets were organized, including four bacterial DNA extracts and four bead mill-pretreated osteoarticular specimens. Extraction volumes, 16S rRNA gene primers, and sequencing interpretation rules were standardized. In order to assess each laboratory's ability to achieve the best results, scores were assigned, and each QC series was classified as optimal, acceptable, or to be improved. A total of 168 QCs were sent, and 160 responses were analyzed. The expected results were obtained for 93.8%, with the same proportion for extracts (75/80) and clinical specimens (75/80). For the specimens, there was no significant difference between manual and automated extraction. This QC demonstrated the ability to achieve good and homogeneous results using the same 16S rRNA gene PCR with different equipment and validates the possibility of high-quality multicenter studies using molecular diagnosis for BJI.

Complete Genome Sequence of Streptococcus pyogenes M/emm44 Strain STAB901, Isolated in a Clonal Outbreak in French Brittany.

We report the complete genome sequence of an invasive isolate of Streptococcus pyogenes M/emm44, belonging to a clonal outbreak that occurred in French Brittany. The genome is composed of 1,795,608 bp, with a GC content of 38.5%, has 1,358 identified coding sequences (CDSs), and harbors a novel Tn916-like transposon (Tn6253).

Closed Genome Sequence of Noninvasive Streptococcus pyogenes M/emm3 Strain STAB902.

We report a closed genome sequence of group A Streptococcus genotype emm3 (GAS M/emm3) strain STAB902, isolated from a superficial pyodermatitis. The genome is composed of 1,892,124 bp, 6 integrated prophages, and has 1,858 identified coding sequences (CDSs). It has been fitted with the two available invasive GAS M/emm3 strains.

Evaluation of 16S rRNA gene PCR sensitivity and specificity for diagnosis of prosthetic joint infection: a prospective multicenter cross-sectional study.

There is no standard method for the diagnosis of prosthetic joint infection (PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis remains to be defined. We performed a prospective multicenter study to assess the contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all patients suspected to have PJIs and a few uninfected patients undergoing primary arthroplasty (control group) were included. Five perioperative samples per patient were collected for culture and 16S rRNA gene PCR sequencing and one for histological examination. Three multicenter quality control assays were performed with both DNA extracts and crushed samples. The diagnosis of PJI was based on clinical, bacteriological, and histological criteria, according to Infectious Diseases Society of America guidelines. A molecular diagnosis was modeled on the bacteriological criterion (≥ 1 positive sample for strict pathogens and ≥ 2 for commensal skin flora). Molecular data were analyzed according to the diagnosis of PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35 control cases were included. PJI was confirmed in 215/264 suspected cases, 192 (89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases [85%]; staphylococci, n = 108; streptococci, n = 22; Gram-negative bacilli, n = 16; anaerobes, n = 13; others, n = 4) or polymicrobial (29 cases [15%]). The molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases with bacteriological PJI documentation and 8 treated cases without bacteriological documentation) and in 2/49 cases without confirmed PJI (sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a lack of sensitivity in the diagnosis of PJI on a multicenter routine basis.

Helicobacter pylori urease and flagellin alter mucin gene expression in human gastric cancer cells.

BACKGROUND: Helicobacter pylori (Hp), which is one of the causative agents in human gastric adenocarcinoma, is known to interact with mucous gel and alter mucin gene expression. The aim of this work was to study, using an in vitro model of cell infection, the effects of urease, flagellin, and CagA virulence factors on the regulation of the four 11p15 mucin genes (MUC2, MUC5AC, MUC5B, and MUC6). METHODS: KATO-III and AGS gastric cancer cells were infected for 1, 3 or 6 h with Hp wild-type strains (ATCC 43504, N6, and SS1) or corresponding isogenic mutants deficient for urease subunit B, flagellin subunit A, and CagA. mRNA levels of MUC2, MUC5B, MUC5AC and MUC6 were assessed by RT-PCR, and functional activity of their promoters was measured by transient transfection assays. RESULTS: Infection of KATO-III cells with Hp wild-type strains resulted in an early (at 1 h) transient expression of MUC2, MUC5AC, and MUC6 mRNA concomitant with those of interleukin (IL)-1ß, IL-8, and TNF-α cytokines. In these cells, the UreB(-) isogenic mutant induced strong activation of MUC5AC expression, and UreB-responsive elements were located in the -486/-1 region of the promoter. FlaA(-) and CagA(-) mutants had no effect on mucin gene mRNA levels in KATO-III cells. In AGS cells, Hp-responsive elements were identified in all promoters, and overexpression of NF-κB induced upregulation of MUC5AC promoter activity when infected with the UreB(-) isogenic mutant. CONCLUSION: These results indicate that Hp infection of gastric cancer cells alters 11p15 mucin gene transcription and that MUC5AC downregulation is mediated by urease virulence factor.

Is biofilm formation related to the hypermutator phenotype in clinical Enterobacteriaceae isolates?

In bacteria, complex adaptive processes are involved during transition from the planktonic to the biofilm mode of growth, and mutator strains are more prone to producing biofilms. Enterobacteriaceae species were isolated from urinary tract infections (UTIs; 222 strains) and from bloodstream infections (BSIs; 213 strains). Relationship between the hypermutable phenotype and biofilm forming capacity was investigated in these clinical strains. Mutation frequencies were estimated by monitoring the capacity of each strain to generate mutations that conferred rifampicin resistance on supplemented medium. Initiation of biofilm formation was assayed by determining the ability of the cells to adhere to a 96-well polystyrene microtitre plate. UTI Enterobacteriaceae strains showed significantly higher biofilm-forming capacity: 63.1% (54.0% for E. coli strains) vs. 42.3% for BSI strains (47.7% for E. coli). Strains isolated from UTIs did not present higher mutation frequencies than those from BSIs: contrary to what has been widely described for P. aeruginosa strains, isolated from pulmonary samples in patients suffering from cystic fibrosis, no relationship was found between the hypermutator phenotype in Enterobacteriaceae and the ability to initiate a biofilm.

Representation learning: a review and new perspectives.

The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different explanatory factors of variation behind the data. Although specific domain knowledge can be used to help design representations, learning with generic priors can also be used, and the quest for AI is motivating the design of more powerful representation-learning algorithms implementing such priors. This paper reviews recent work in the area of unsupervised feature learning and deep learning, covering advances in probabilistic models, autoencoders, manifold learning, and deep networks. This motivates longer term unanswered questions about the appropriate objectives for learning good representations, for computing representations (i.e., inference), and the geometrical connections between representation learning, density estimation, and manifold learning.

Current saturation in field emission from H-passivated Si nanowires.

This paper explores the field emission (FE) properties of highly crystalline Si nanowires (NWs) with controlled surface passivation. The NWs were batch-grown by the vapor-liquid-solid process using Au catalysts with no intentional doping. The FE current-voltage characteristics showed quasi-ideal current saturation that resembles those predicted by the basic theory for emission from semiconductors, even at room temperature. In the saturation region, the currents were extremely sensitive to temperature and also increased linearly with voltage drop along the nanowire. The latter permits the estimation of the doping concentration and the carrier lifetime, which is limited by surface recombination. The conductivity could be tuned over 2 orders of magnitude by in situ hydrogen passivation/desorption cycles. This work highlights the role of dangling bonds in surface leakage currents and demonstrates the use of hydrogen passivation for optimizing the FE characteristics of Si NWs.

A connection between score matching and denoising autoencoders.

Denoising autoencoders have been previously shown to be competitive alternatives to restricted Boltzmann machines for unsupervised pretraining of each layer of a deep architecture. We show that a simple denoising autoencoder training criterion is equivalent to matching the score (with respect to the data) of a specific energy-based model to that of a nonparametric Parzen density estimator of the data. This yields several useful insights. It defines a proper probabilistic model for the denoising autoencoder technique, which makes it in principle possible to sample from them or rank examples by their energy. It suggests a different way to apply score matching that is related to learning to denoise and does not require computing second derivatives. It justifies the use of tied weights between the encoder and decoder and suggests ways to extend the success of denoising autoencoders to a larger family of energy-based models.

Effect of non-ideal clamping shape on the resonance frequencies of silicon nanocantilevers.

In this paper, we investigate the effects of non-ideal clamping shapes on the dynamic behavior of silicon nanocantilevers. We fabricated silicon nanocantilevers using silicon on insulator (SOI) wafers by employing stepper ultraviolet (UV) lithography, which permits a resolution of under 100 nm. The nanocantilevers were driven by electrostatic force inside a scanning electron microscope (SEM). Both lateral and out-of-plane resonance frequencies were visually detected with the SEM. Next, we discuss overhanging of the cantilever support and curvature at the clamping point in the silicon nanocantilevers, which generally arises in the fabrication process. We found that the fundamental out-of-plane frequency of a realistically clamped cantilever is always lower than that for a perfectly clamped cantilever, and depends on the cantilever width and the geometry of the clamping point structure. Using simulation with the finite-elements method, we demonstrate that this discrepancy is attributed to the particular geometry of the clamping point (non-zero joining curvatures and a flexible overhanging) that is obtained in the fabrication process. The influence of the material orthotropy is also investigated and is shown to be negligible.

Digital and FM demodulation of a doubly clamped single-walled carbon-nanotube oscillator: towards a nanotube cell phone.

Electromechanical resonators are a key element in radio-frequency telecommunication devices and thus new resonator concepts from nanotechnology can readily find important industrial opportunities. Here, the successful experimental realization of AM, FM, and digital demodulation with suspended single-walled carbon-nanotube resonators in a field-effect transistor configuration is reported. The crucial role played by the electromechanical resonance in demodulation is clearly demonstrated. The FM technique is shown to lead to the suppression of unwanted background signals and the reduction of noise for a better detection of the mechanical motion of nanotubes. The digital data-transfer rate of standard cell-phone technology is within the reach of these devices.

Peptide Extracts from Cultures of Certain Lactobacilli Inhibit Helicobacter pylori.

Helicobacter pylori inhibition by probiotic lactobacilli has been observed in vitro and in vivo. Carefully selected probiotic Lactobacillus strains could therefore play an important role in the treatment of H. pylori infection and eradication. However, the underlying mechanism for this inhibition is not clear. The aim of this study was to examine if peptide extracts, containing bacteriocins or other antibacterial peptides, from six Lactobacillus cultures (Lactobacillus acidophilus La1, Lactobacillus amylovorus DCE 471, Lactobacillus casei YIT 9029, Lactobacillus gasseri K7, Lactobacillus johnsonii La1, and Lactobacillus rhamnosus GG) contribute to the inhibition of H. pylori. Peptide extracts from cultures of Lact. amylovorus DCE 471 and Lact. johnsonii La1 were most active, reducing the viability of H. pylori ATCC 43504 with more than 2 log units within 4 h of incubation (P < 0.001). The four other extracts were less or not active. When six clinical isolates of H. pylori were tested for their susceptibility towards five inhibitory peptide extracts, similar observations were made. Again, the peptide extracts from Lact. amylovorus DCE 471 and Lact. johnsonii La1 were the most inhibitory, while the three other extracts resulted in a much lower inhibition of H. pylori. Protease-treated extracts were inactive towards H. pylori, confirming the proteinaceous nature of the inhibitory substance.

Increased detection rate of Kawasaki disease using new diagnostic algorithm, including early use of echocardiography.

OBJECTIVE: To determine the incidence of Kawasaki disease (KD) in Northern France by using new American Heart Association (AHA) criteria. STUDY DESIGN: A 1-year prospective multicenter cohort study was performed in all pediatric departments. Patients <18 years old, who were admitted for prolonged but initially unexplained fever or suspected KD were included. All patients received the standard treatment considered appropriate by their physicians. A descriptive analysis and comparison of patients with complete and incomplete forms of KD were performed. The incidence of confirmed cases of KD (complete and incomplete forms) was calculated. RESULTS: Seventy-seven children were included (39 in whom KD was diagnosed). Of the patients with KD, 26 (67%) met the classic AHA case definition, and 7 (18%) had incomplete KD. Cardiac ultrasound scanning was helpful in the diagnosis of 6 of 7 patients with incomplete KD (86%). The final incidence of confirmed KD was 9 of 100,000 children <5 years of age. In 6 children (15%) the diagnosis of KD was uncertain, but they were successfully treated for it. Coronary disease was identified in 48% of patients with confirmed KD. CONCLUSION: The incidence of KD is higher than previously reported, in part because earlier reports did not include incomplete forms. New AHA criteria (laboratory tests and early echocardiography) were helpful for the diagnosis of incomplete forms of KD.

Sudden onset of pseudotuberculosis in humans, France, 2004-05.

Cases of Yersinia pseudotuberculosis infection increased in France during the winter of 2004-05 in the absence of epidemiologic links between patients or strains. This increase represents transient amplification of a pathogen endemic to the area and may be related to increased prevalence of the pathogen in rodent reservoirs.