COMPUTER BASED EYE TRACKER FOR DETECTION OF MANIFEST STRABISMUS.

Strabismus is a common disorder in which eyes are not aligned with their optical axis, resulting in an abnormal binocular interaction, thus leading to amblyopia. Accordingly, early detection and diagnosis are mandatory. Despite technology development and constant knowledge growth, the foundations of physiology and the diagnosis of strabismus were set back in the 19th or early 20th century and have not changed since. In this paper, a novel, properly tested and evaluated eye-tracking based method for manifest strabismus diagnosis is presented. The evaluation showed the aforementioned method to have both high sensitivity and specificity in detecting manifest strabismus without the need for a skilled examiner, thus being suitable for population screening and highlighting the need for future research regarding testing of latent strabismus.

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads.

MOTIVATION: Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how existing hybrid and non-hybrid de novo assembly methods perform on long and error prone nanopore reads. RESULTS: We benchmarked five non-hybrid (in terms of both error correction and scaffolding) assembly pipelines as well as two hybrid assemblers which use third generation sequencing data to scaffold Illumina assemblies. Tests were performed on several publicly available MinION and Illumina datasets of Escherichia coli K-12, using several sequencing coverages of nanopore data (20×, 30×, 40× and 50×). We attempted to assess the assembly quality at each of these coverages, in order to estimate the requirements for closed bacterial genome assembly. For the purpose of the benchmark, an extensible genome assembly benchmarking framework was developed. Results show that hybrid methods are highly dependent on the quality of NGS data, but much less on the quality and coverage of nanopore data and perform relatively well on lower nanopore coverages. All non-hybrid methods correctly assemble the E. coli genome when coverage is above 40×, even the non-hybrid method tailored for Pacific Biosciences reads. While it requires higher coverage compared to a method designed particularly for nanopore reads, its running time is significantly lower. AVAILABILITY AND IMPLEMENTATION: https://github.com/kkrizanovic/NanoMark CONTACT: mile.sikic@fer.hr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus.

Spike glycoprotein is essential for the reproduction of the SARS-CoV-2 virus, and its inhibition using already approved antiviral drugs may open new avenues for treatment of patients with the COVID-19 disease. Because of that we analyzed the inhibition of SARS-CoV-2 spike glycoprotein with FDA-approved antiviral drugs and their double and triple combinations. We used the VINI in silico model of cancer to perform this virtual drug screening, showing HIV drugs to be the most effective. Besides, the combination of cobicistat-abacavir-rilpivirine HIV drugs demonstrated the highest in silico efficacy of inhibiting SARS-CoV-2 spike glycoprotein. Therefore, a clinical trial of cobicistat-abacavir-rilpivirine on a limited number of COVID-19 patients in moderately severe and severe condition is warranted.

The sum-connectivity index--an additive variant of the Randic connectivity index.

This review discusses structure-property modeling applications of a novel variant of the Randic connectivity index that is called the sum-connectivity index. We compare published one-descriptor quantitative structure-property relationship (QSPR) models obtained with the new sum-connectivity index and with the Randic connectivity index, called here the product-connectivity index. Additionally, the efficiency of both variants of connectivity indices in QSPR modeling is tested on five datasets of alkanes and two datasets of polycyclic hydrocarbons. Several physicochemical properties of alkanes (i.e. boiling and melting points, retention index, molar volume, molar refraction, heat of vaporization, standard Gibbs energy of formation, critical temperature, critical pressure, surface tension, density) and π- electronic energies of two sets of polycyclic hydrocarbons were correlated with the product- and sum-connectivity indices. A comparison of these QSPR models shows that both variants of connectivity indices are equivalent, and only slightly (but not significantly) better results are obtained with the sum-connectivity index. Inter-correlations between the product- and sum-connectivity indices are mostly linear with a slope very close to 1.0 for alkanes, and with a slope more different from 1.0 (0.88) for polycyclic compounds. The comparative analysis presented here supports the use of the sumconnectivity index in QSPR/QSAR studies together with the product-connectivity index. Further studies on larger and more heterogeneous datasets should test the sum-connectivity index in QSPR/QSAR models.

Specific thermographic changes during Walker 256 carcinoma development: differential infrared imaging of tumour, inflammation and haematoma.

BACKGROUND: Infrared imaging measures spatial variations in the skin temperature aiming to determine pathological processes; hence possible use of this non-invasive analytical method in cancer detection is emerging. METHODS: Infrared thermal imaging was used to detect changes in rat skin surface temperature associated with experimental cancer development (Walker 256 carcinoma), inflammation (upon s.c. Sephadex injection) and haematoma (provoked by s.c. blood coagulate injection). Infrared camera with a geometric resolution of 76,800 pixels, spectral range of 8-14 microm and the minimal detectable temperature resolution of 0.07 degrees C with spatial resolution of 0.48 mm at measuring distance of 30 cm was used to obtain computerised thermal scans. Genuine ThermoWEB software developed for remote internet control as open source software was used. RESULTS: The raise of peripheral temperature was observed after induction of local inflammation or haematoma. Opposite to that, transient decrease of the skin surface temperature was observed after tumour transplantation. Progressive growth of tumour was associated with the raise of the skin surface temperature from the 10th day after tumour inoculation, when the tumours developed supportive neoangiogenic blood supply, as verified by histology. CONCLUSION: While the raise of peripheral temperature in advanced tumour was caused by neoangiogenesis, the reduction in skin surface temperature in an early period after tumour cell inoculation indicated a decay of transplanted tumour cells due to the immune response and the lack of blood supply. Thus, infrared thermal imaging may have considerable value in evaluation of the tumour development and discrimination of cancer from inflammation and haematoma.