Grating coupler integrated photodiodes for plasmon resonance based sensing

Cataloged from PDF version of article.In this work, we demonstrate an integrated sensor combining a grating-coupled plasmon resonance surface with a planar photodiode. Plasmon enhanced transmission is employed as a sensitive refractive index (RI) sensing mechanism. Enhanced transmission of light is monitored via the integrated photodiode by tuning the angle of incidence of a collimated beam near the sharp plasmon resonance condition. Slight changes of the effective refractive index (RI) shift the resonance angle, resulting in a change in the photocurrent. Owing to the planar sensing mechanism, the design permits a high areal density of sensing spots. In the design, absence of holes that facilitate resonant transmission of light, allows an easy-to-implement fabrication procedure and relative insensitivity to fabrication errors. Theoretical and experimental results agree well. An equivalent long-term RI noise of 6.3 x 10(-6) RIU/root Hz is obtained by using an 8 mW He-Ne laser, compared to a shot-noise limited theoretical sensitivity of 5.61 x 10(-9) RIU/root Hz. The device features full benefits of grating-coupled plasmon resonance, such as enhancement of sensitivity for non-zero azimuthal angle of incidence. Further sensitivity enhancement using balanced detection and optimal plasmon coupling conditions are discussed

Short-term plasticity of neuro-auditory processing induced by musical active listening training

Although there is strong evidence for the positive effects of musical training on auditory perception, processing, and training-induced neuroplasticity, there is still little knowledge on the auditory and neurophysiological short-term plasticity through listening training. In a sample of 37 adolescents (20 musicians and 17 nonmusicians) that was compared to a control group matched for age, gender, and musical experience, we conducted a 2-week active listening training (AULOS: Active IndividUalized Listening OptimizationS). Using magnetoencephalography and psychoacoustic tests, the short-term plasticity of auditory evoked fields and auditory skills were examined in a pre-post design, adapted to the individual neuro-auditory profiles. We found bilateral, but more pronounced plastic changes in the right auditory cortex. Moreover, we observed synchronization of the auditory evoked P1, N1, and P2 responses and threefold larger amplitudes of the late P2 response, similar to the reported effects of musical long-term training. Auditory skills and thresholds benefited largely from the AULOS training. Remarkably, after training, the mean thresholds improved by 12 dB for bone conduction and by 3–4 dB for air conduction. Thus, our findings indicate a strong positive influence of active listening training on neural auditory processing and perception in adolescence, when the auditory system is still developing

Measuring vertebrate telomeres: applications and limitations

Telomeres are short tandem repeated sequences of DNA found at the ends of eukaryotic chromosomes that function in stabilizing chromosomal end integrity. In vivo studies of somatic tissue of mammals and birds have shown a correlation between telomere length and organismal age within species, and correlations between telomere shortening rate and lifespan among species. This result presents the tantalizing possibility that telomere length could be used to provide much needed information on age, ageing and survival in natural populations where longitudinal studies are lacking. Here we review methods available for measuring telomere length and discuss the potential uses and limitations of telomeres as age and ageing estimators in the fields of vertebrate ecology, evolution and conservation

The relation of the pleural thickening in tuberculosis pleurisy with the activity of adenosine deaminase

Selvi, A. Kant, S. Arslan, M. Ozgel. Background: Residual pleural thickening (RPT) still occurs in most patients with tuberculosis pleurisy despite advances in the treatment of tuberculosis. The aim of this study was to evaluate the significance of RPT in tuberculosis pleurisy with the patients clinical findings, biochemical and microbiological properties of pleural effusion and with the total adenosine deaminase (ADA) and isoenzymes levels. Methods: 121 tuberculosis pleurisy patients were evaluated retrospectively. According to posteroanterior chest x-rays, the 63 (52%) cases with the thickness 2 mm or more in lower lateral hemithorax were grouped as I and the 58 (48%) cases without pleural thickness were grouped as II. The amount of pleural effusion was classified into small, medium or massive according to their chest x-rays. In both groups; sex, age, symptoms score, bacteriological and biochemical tests and ADA levels were recorded. Results: 81 (67%) male and 40 (33%) female, overall 121 patients were enrolled into the study. RPT was found higher in males (p=0.014) and the increase ran parallel with the amount of cigarette smoking (p=0.014). RPT was found to be lower in small effusions (p=0.001). The group with RPT, the serum albumin was found lower (p=0.002), pleural fluid total protein (p=0.047) and the ratio of pleural fluid protein to serum protein (p=0.002) were found higher. In group I, total ADA: 69.5±38.9 IU/L and ADA2: 41.3±31.6 IU/L were higher than the cases without RPT (p=0.032, p=0.017, respectively). Conclusions: We suggest that the immunological mechanisms are effective in the development of pleural thickening

VEZF1 elements mediate protection from DNA methylation

There is growing consensus that genome organization and long-range gene regulation involves partitioning of the genome into domains of distinct epigenetic chromatin states. Chromatin insulator or barrier elements are key components of these processes as they can establish boundaries between chromatin states. The ability of elements such as the paradigm β-globin HS4 insulator to block the range of enhancers or the spread of repressive histone modifications is well established. Here we have addressed the hypothesis that a barrier element in vertebrates should be capable of defending a gene from silencing by DNA methylation. Using an established stable reporter gene system, we find that HS4 acts specifically to protect a gene promoter from de novo DNA methylation. Notably, protection from methylation can occur in the absence of histone acetylation or transcription. There is a division of labor at HS4; the sequences that mediate protection from methylation are separable from those that mediate CTCF-dependent enhancer blocking and USF-dependent histone modification recruitment. The zinc finger protein VEZF1 was purified as the factor that specifically interacts with the methylation protection elements. VEZF1 is a candidate CpG island protection factor as the G-rich sequences bound by VEZF1 are frequently found at CpG island promoters. Indeed, we show that VEZF1 elements are sufficient to mediate demethylation and protection of the APRT CpG island promoter from DNA methylation. We propose that many barrier elements in vertebrates will prevent DNA methylation in addition to blocking the propagation of repressive histone modifications, as either process is sufficient to direct the establishment of an epigenetically stable silent chromatin stat

Aberrant Epigenetic Silencing Is Triggered by a Transient Reduction in Gene Expression

Aberrant epigenetic silencing plays a major role in cancer formation by inactivating tumor suppressor genes. While the endpoints of aberrant silencing are known, i.e., promoter region DNA methylation and altered histone modifications, the triggers of silencing are not known. We used the tet-off system to test the hypothesis that a transient reduction in gene expression will sensitize a promoter to undergo epigenetic silencing.The tet responsive promoter (P(TRE)) was used to drive expression of the selectable human HPRT cDNA in independent transfectants of an Hprt deficient mouse cell line. In this system, high basal HPRT expression is greatly reduced when doxycycline (Dox) is added to the culture medium. Exposure of the P(TRE)-HPRT transfectants to Dox induced HPRT deficient clones in a time dependent manner. A molecular analysis demonstrated promoter region DNA methylation, loss of histone modifications associated with expression (i.e., H3 lysine 9 and 14 acetylation and lysine 4 methylation), and acquisition of the repressive histone modification H3 lysine 9 methylation. These changes, which are consistent with aberrant epigenetic silencing, were not present in the Dox-treated cultures, with the exception of reduced H3 lysine 14 acetylation. Silenced alleles readily reactivated spontaneously or after treatment of cells with inhibitors of histone deacetylation and/or DNA methylation, but re-silencing of reactivated alleles did not require a new round of Dox exposure. Inhibition of histone deacetylation inhibited both the induction of silencing and re-silencing, whereas inhibition of DNA methylation had no such effect.This study demonstrates that a transient reduction in gene expression triggers a pathway for aberrant silencing in mammalian cells and identifies histone deacetylation as a critical early step in this process. DNA methylation, in contrast, is a secondary step in the silencing pathway under study. A model to explain these observations is offered

Thiolated chitosan nanoparticles enhance anti-inflammatory effects of intranasally delivered theophylline

BACKGROUND: Chitosan, a polymer derived from chitin, has been used for nasal drug delivery because of its biocompatibility, biodegradability and bioadhesiveness. Theophylline is a drug that reduces the inflammatory effects of allergic asthma but is difficult to administer at an appropriate dosage without causing adverse side effects. It was hypothesized that adsorption of theophylline to chitosan nanoparticles modified by the addition of thiol groups would improve theophylline absorption by the bronchial epithelium and enhance its anti-inflammatory effects. OBJECTIVES: We sought to develop an improved drug-delivery matrix for theophylline based on thiolated chitosan, and to investigate whether thiolated chitosan nanoparticles (TCNs) can enhance theophylline's capacity to alleviate allergic asthma. METHODS: A mouse model of allergic asthma was used to test the effects of theophylline in vivo. BALB/c mice were sensitized to ovalbumin (OVA) and OVA-challenged to produce an inflammatory allergic condition. They were then treated intranasally with theophylline alone, chitosan nanoparticles alone or theophylline adsorbed to TCNs. The effects of theophylline on cellular infiltration in bronchoalveolar lavage (BAL) fluid, histopathology of lung sections, and apoptosis of lung cells were investigated to determine the effectiveness of TCNs as a drug-delivery vehicle for theophylline. RESULTS: Theophylline alone exerts a moderate anti-inflammatory effect, as evidenced by the decrease in eosinophils in BAL fluid, the reduction of bronchial damage, inhibition of mucus hypersecretion and increased apoptosis of lung cells. The effects of theophylline were significantly enhanced when the drug was delivered by TCNs. CONCLUSION: Intranasal delivery of theophylline complexed with TCNs augmented the anti-inflammatory effects of the drug compared to theophylline administered alone in a mouse model of allergic asthma. The beneficial effects of theophylline in treating asthma may be enhanced through the use of this novel drug delivery system

Detecting natural disasters, damage, and incidents in the wild

Responding to natural disasters, such as earthquakes, floods, and wildfires, is a laborious task performed by on-the-ground emergency responders and analysts. Social media has emerged as a low-latency data source to quickly understand disaster situations. While most studies on social media are limited to text, images offer more information for understanding disaster and incident scenes. However, no large-scale image datasets for incident detection exists. In this work, we present the Incidents Dataset, which contains 446,684 images annotated by humans that cover 43 incidents across a variety of scenes. We employ a baseline classification model that mitigates false-positive errors and we perform image filtering experiments on millions of social media images from Flickr and Twitter. Through these experiments, we show how the Incidents Dataset can be used to detect images with incidents in the wild. Code, data, and models are available online at http://incidentsdataset.csail.mit.edu.Comment: ECCV 202

An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection

Hundreds of genes show aberrant DNA hypermethylation in cancer, yet little is known about the causes of this hypermethylation. We identified RIL as a frequent methylation target in cancer. In search for factors that influence RIL hypermethylation, we found a 12-bp polymorphic sequence around its transcription start site that creates a long allele. Pyrosequencing of homozygous tumors revealed a 2.1-fold higher methylation for the short alleles (P<0.001). Bisulfite sequencing of cancers heterozygous for RIL showed that the short alleles are 3.1-fold more methylated than the long (P<0.001). The comparison of expression levels between unmethylated long and short EBV-transformed cell lines showed no difference in expression in vivo. Electrophorectic mobility shift assay showed that the inserted region of the long allele binds Sp1 and Sp3 transcription factors, a binding that is absent in the short allele. Transient transfection of RIL allele-specific transgenes showed no effects of the additional Sp1 site on transcription early on. However, stable transfection of methylation-seeded constructs showed gradually decreasing transcription levels from the short allele with eventual spreading of de novo methylation. In contrast, the long allele showed stable levels of expression over time as measured by luciferase and ∼2–3-fold lower levels of methylation by bisulfite sequencing (P<0.001), suggesting that the polymorphic Sp1 site protects against time-dependent silencing. Our finding demonstrates that, in some genes, hypermethylation in cancer is dictated by protein-DNA interactions at the promoters and provides a novel mechanism by which genetic polymorphisms can influence an epigenetic state

Salicylic acid functionalized silica-coated magnetite nanoparticles for solid phase extraction and preconcentration of some heavy metal ions from various real samples

A method for the preconcentration of trace heavy metal ions in environmental samples has been reported. The presented method is based on the sorption of Cu(II), Cd(II), Ni(II) and Cr(III) ions with salicylic acid as respective chelate on silica-coated magnetite nanoparticles. Prepared adsorbent was characterized by XRD, SEM, BET and FT-IR measurements. The metals content of the sorbed complexes are eluted using 4.0 mL of 1.0 mol L-1 nitric acid. The influences of the analytical parameters including pH, amount of solid phase and condition of eluting solution, the effects of matrix ions on the retention of the analytes were examined. The accuracy and precision of suggested method were tested by analyzing of certified reference materials. The detection limits (3Sb/m, N = 8) for Cu(II), Cd(II), Ni(II) and Cr(III) ions are 0.22, 0.11, 0.27 and 0.15 μg L-1, respectively, and the maximum preconcentration factor is 200. The method was successfully applied to the evaluation of these trace and toxic metals in various waters, foods and other samples