High-fidelity nano-FTIR spectroscopy by on-pixel normalization of signal harmonics

Scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared nanospectroscopy (nano-FTIR) are emerging tools for physical and chemical nanocharacterization of organic and inorganic composite materials. Being based on (i) diffraction-limited illumination of a scanning probe tip for nanofocusing of light and (ii) recording of the tip-scattered radiation, the efficient suppression of background scattering has been critical for their success. Here, we show that indirect tip illumination via far-field reflection and scattering at the sample can produce s-SNOM and nano-FTIR signals of materials that are not present at the tip position – despite full background suppression. Although these artefacts occur primarily on or near large sample structures, their understanding and recognition are of utmost importance to ensure correct interpretation of images and spectra. Detailed experimental and theoretical results show how such artefacts can be identified and eliminated by a simple signal normalization step, thus critically strengthening the analytical capabilities of s-SNOM and nano-FTIR spectroscopy.

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes

Background Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure. However, most methods commonly used for the normalization of ChIP-seq binding intensity signals across conditions, e.g., the normalization to the same number of reads, either assume a constant signal-to-noise ratio across conditions or base the estimates of correction factors on genomic regions with intrinsically different signals between conditions. Inaccurate normalization of ChIP-seq signal may, in turn, lead to erroneous biological conclusions. Results We developed a new R package, CHIPIN, that allows normalizing ChIP-seq signals across different conditions/samples when spike-in information is not available, but gene expression data are at hand. Our normalization technique is based on the assumption that, on average, no differences in ChIP-seq signals should be observed in the regulatory regions of genes whose expression levels are constant across samples/conditions. In addition to normalizing ChIP-seq signals, CHIPIN provides as output a number of graphs and calculates statistics allowing the user to assess the efficiency of the normalization and qualify the specificity of the antibody used. In addition to ChIP-seq, CHIPIN can be used without restriction on open chromatin ATAC-seq or DNase hypersensitivity data. We validated the CHIPIN method on several ChIP-seq data sets and documented its superior performance in comparison to several commonly used normalization techniques. Conclusions The CHIPIN method provides a new way for ChIP-seq signal normalization across conditions when spike-in experiments are not available. The method is implemented in a user-friendly R package available on GitHub: https://github.com/BoevaLab/CHIPIN

Gas Monitoring in Human Frontal Sinuses–Stability Considerations and Gas Exchange Studies

Acute rhinosinusitis is a common infectious disease, which, in more than 90% of cases, is caused by viruses rather than by bacteria. Even so, antibiotics are often unnecessarily prescribed, and in the long run this contributes to the alarming level of antibiotics resistance. The reason is that there are no good guiding tools for defining the background reason of the infection. One main factor for the clearance of the infection is if there is non-obstructed ventilation from the sinus to the nasal cavity. Gas in Scattering Media Absorption Spectroscopy (GASMAS) has potential for diagnosing this. We have performed a study of frontal sinuses of volunteers with a focus on signal stability and reproducibility over time, accurate oxygen concentration determination, and assessment of gas transport through passages, naturally and after decongestant spray administration. Different from earlier studies on frontal sinuses, water vapor, serving the purpose of oxygen signal normalization, was measured at 818 nm rather than earlier at 937 nm, now closer to the 760 nm oxygen absorption band and thus resulting in more reliable results. In addition, the action of decongestants was objectively demonstrated for the first time. Evaluated oxygen concentration values for left- and right-hand side sinus cavities were found to agree within 0.3%, and a left-right geometrical asymmetry parameter related to anatomical differences was stable within 10%.

Second generation of the diagnostic tool for the In vivo measurement of strontium levels in human bone

Strontium (Sr) is an element collected naturally in the human body through diet. It has a paradoxical effect on bone health, where at low doses Sr enhances bone health. The beneficial effects of Sr warranted its use as a complimentary treatment for osteoporosis. The current source-bases Sr in vivo x-ray fluorescence (IVXRF) system is in clinical use to study the incorporation and retention of Sr in bone after administration of Sr supplements. This system however can only monitor relative changes in bone with a limited level of accuracy. Therefore a second generation of the diagnostic tool has been developed and optimized aiming to improve the accuracy and precision of an IVXRF measurement. The system comprises of an optically focused x-ray tube producing monochromatic x-rays and a silicon drift detector. Furthermore, optimal parameters to run the system are investigated, along with three different means of signal normalization.

Second generation of the diagnostic tool for the In vivo measurement of strontium levels in human bone

Strontium (Sr) is an element collected naturally in the human body through diet. It has a paradoxical effect on bone health, where at low doses Sr enhances bone health. The beneficial effects of Sr warranted its use as a complimentary treatment for osteoporosis. The current source-bases Sr in vivo x-ray fluorescence (IVXRF) system is in clinical use to study the incorporation and retention of Sr in bone after administration of Sr supplements. This system however can only monitor relative changes in bone with a limited level of accuracy. Therefore a second generation of the diagnostic tool has been developed and optimized aiming to improve the accuracy and precision of an IVXRF measurement. The system comprises of an optically focused x-ray tube producing monochromatic x-rays and a silicon drift detector. Furthermore, optimal parameters to run the system are investigated, along with three different means of signal normalization.

Improving Air Pollutant Metal Oxide Sensor Quantification Practices through: An Exploration of Sensor Signal Normalization, Multi-Sensor and Universal Calibration Model Generation, and Physical Factors Such as Co-Location Duration and Sensor Age

As low-cost sensors have become ubiquitous in air quality measurements, there is a need for more efficient calibration and quantification practices. Here, we deploy stationary low-cost monitors in Colorado and Southern California near oil and gas facilities, focusing our analysis on methane and ozone concentration measurement using metal oxide sensors. In comparing different sensor signal normalization techniques, we propose a z-scoring standardization approach to normalize all sensor signals, making our calibration results more easily transferable among sensor packages. We also attempt several different physical co-location schemes, and explore several calibration models in which only one sensor system needs to be co-located with a reference instrument, and can be used to calibrate the rest of the fleet of sensor systems. This approach greatly reduces the time and effort involved in field normalization without compromising goodness of fit of the calibration model to a significant extent. We also explore other factors affecting the performance of the sensor system quantification method, including the use of different reference instruments, duration of co-location, time averaging, transferability between different physical environments, and the age of metal oxide sensors. Our focus on methane and stationary monitors, in addition to the z-scoring standardization approach, has broad applications in low-cost sensor calibration and utility.