Biophotonics approach for the study of leukocyte activation

Leukocytes are the main cells of immune system, but also contribute to other systems and participate in pathogenesis of different diseases. In particular, leukocytes are involved in the progression of diabetic retinopathy due to their hyperactivation in diabetes. However, a connection between diabetes and the dysfunction of leukocytes is poorly understood. For a more complete picture, studies of the leukocytes activation under the influence of various substances are necessary. Arachidonic acid (AA) and its metabolites are the strongest activating factors of leukocytes. However, the studies involving AA are complicated because it is water-insoluble. Here we describe the method to study activation using photolabile analogs of AA

Singlet oxygen luminescence detector based on low-cost InGaAs avalanche photodiode

Molecular oxygen excited to singlet state (Singlet oxygen, 1O2) becomes highly reactive and cytotoxic chemical. 1O2 is commonly generated by photoexcitation of dyes (photosensitizers), including the photodynamic therapy and diagnostics of cancer. However, the formation of singlet oxygen is often unwanted for various light-sensitive compounds, e.g. it causes the photobleaching of fluorescent probes. In either case, during a development of new photosensitive chemicals and drugs there is a need to evaluate the amount of 1O2 formed during photoexcitation. The direct approach in measuring the amount of singlet oxygen is based on the detection of its luminescence at 1270 nm. However, this luminescence is usually weak, which implies the use of highly sensitive single-photon detectors. Thus the existing instruments are commonly complicated and expensive. Here we suggest an approach and report a device to measure the 1O2 luminescence using low-cost InGaAs avalanche photodiode and simple electronics. The measurements can be performed in stationary (not time-resolved) mode in organic solvents such as tetrachloromethane (CCl4), ethanol and DMSO. In particular, we performed spectral-resolved measurements of the singlet oxygen luminescence in CCl4 with the device and demonstrated high complementarity to literature data. The simple setup allows to evaluate the efficiency (or speed) of singlet oxygen generation and hence facilitates the development and characterization of new photosensitizers and other photosensitive chemicals

Mathematical models for immunology:current state of the art and future research directions

The advances in genetics and biochemistry that have taken place over the last 10 years led to significant advances in experimental and clinical immunology. In turn, this has led to the development of new mathematical models to investigate qualitatively and quantitatively various open questions in immunology. In this study we present a review of some research areas in mathematical immunology that evolved over the last 10 years. To this end, we take a step-by-step approach in discussing a range of models derived to study the dynamics of both the innate and immune responses at the molecular, cellular and tissue scales. To emphasise the use of mathematics in modelling in this area, we also review some of the mathematical tools used to investigate these models. Finally, we discuss some future trends in both experimental immunology and mathematical immunology for the upcoming years

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

8-[4-(2-Hydroxypropane-2-yl)phenyl]-1,3,4,4,5,7-hexamethyl-4-boron-3a,4a-diaza-S-indacene

During recent years, the BODIPY core became a popular scaffold for designing photoremovable protecting groups (PPG). In this paper, we report the synthesis of a new molecule—8-[4-(2-hydroxypropane-2-yl)phenyl]-1,3,4,4,5,7-hexamethyl-4-boron-3a,4a-diaza-S-indacene—by the treatment of meso-(4-CO2Me-phenyl)-BODIPY with excess of MeMgI. The product was characterized by 1H, 13C NMR and HRMS. The combination of BODIPY core with tertiary benzilyc alcohol might be promising for utilizing this molecule as visible light removable PPG

8-[4-(2-Hydroxypropane-2-yl)phenyl]-1,3,4,4,5,7-hexamethyl-4-boron-3<i>a</i>,4<i>a</i>-diaza-<i>S</i>-indacene

During recent years, the BODIPY core became a popular scaffold for designing photoremovable protecting groups (PPG). In this paper, we report the synthesis of a new molecule—8-[4-(2-hydroxypropane-2-yl)phenyl]-1,3,4,4,5,7-hexamethyl-4-boron-3a,4a-diaza-S-indacene—by the treatment of meso-(4-CO2Me-phenyl)-BODIPY with excess of MeMgI. The product was characterized by 1H, 13C NMR and HRMS. The combination of BODIPY core with tertiary benzilyc alcohol might be promising for utilizing this molecule as visible light removable PPG

A point electric dipole: From basic optical properties to the fluctuation–dissipation theorem

We comprehensively review the deceptively simple concept of dipole scattering in order to uncover and resolve all ambiguities and controversies existing in the literature. First, we consider a point electric dipole in a non-magnetic environment as a singular point in space whose sole ability is to be polarized due to the external electric field. We show that the postulation of the Green’s dyadic of the specific form provides the unified description of the contribution of the dipole into the electromagnetic properties of the whole space. This is the most complete, concise, and unambiguous definition of a point dipole and its polarizability. All optical properties, including the fluctuation–dissipation theorem for a fluctuating dipole, are derived from this definition. Second, we obtain the same results for a small homogeneous sphere by taking a small-size limit of the Lorenz–Mie theory. Third, and most interestingly, we generalize this microscopic description to small particles of arbitrary shape. Both bare (static) and dressed (dynamic) polarizabilities are defined as the double integrals of the corresponding dyadic transition operator over the particle’s volume. While many derivations and some results are novel, all of them follow from or are connected with the existing literature, which we review throughout the paper