Drug2ways: Reasoning over causal paths in biological networks for drug discovery

Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and, accordingly, guide drug repositioning and discovery. In essence, the topology of a network can reveal the impact a drug candidate may have on a given biological state, leading the way for enhanced disease characterization and the design of advanced therapies. Network-based approaches, in particular, are highly suited for these purposes as they hold the capacity to identify the molecular mechanisms underlying disease. Here, we present drug2ways, a novel methodology that leverages multimodal causal networks for predicting drug candidates. Drug2ways implements an efficient algorithm which reasons over causal paths in large-scale biological networks to propose drug candidates for a given disease. We validate our approach using clinical trial information and demonstrate how drug2ways can be used for multiple applications to identify: i) single-target drug candidates, ii) candidates with polypharmacological properties that can optimize multiple targets, and iii) candidates for combination therapy. Finally, we make drug2ways available to the scientific community as a Python package that enables conducting these applications on multiple standard network formats.     

Statistical Analysis of Sleep Spindle Occurrences

Spindles - a hallmark of stage II sleep - are a transient oscillatory phenomenon in the EEG believed to reflect thalamocortical activity contributing to unresponsiveness during sleep. Currently spindles are often classified into two classes: fast spindles, with a frequency of around 14 Hz, occurring in the centro-parietal region; and slow spindles, with a frequency of around 12 Hz, prevalent in the frontal region. Here we aim to establish whether the spindle generation process also exhibits spatial heterogeneity. Electroencephalographic recordings from 20 subjects were automatically scanned to detect spindles and the time occurrences of spindles were used for statistical analysis. Gamma distribution parameters were fit to each inter-spindle interval distribution, and a modified Wald-Wolfowitz lag-1 correlation test was applied. Results indicate that not all spindles are generated by the same statistical process, but this dissociation is not spindle-type specific. Although this dissociation is not topographically specific, a single generator for all spindle types appears unlikely.     

Reversible DIDS binding to Band 3 protein in human erythrocyte membranes

Reversible binding of DIDS [4,4'-diisothiocyanato-2,2'-stilbenedisulphonate] to Band 3 protein, the anion exchanger located in erythrocyte plasma membrane, was studied in human erythrocytes. For this purpose, the tritiated form of DIDS ([³H]DIDS) has been synthesized and the filtering technique has been used to follow the kinetics of DIDS binding to the sites on Band 3 protein. The obtained results showed monophasic kinetics both for dissociation and association of the 'DIDS-Band 3' complex at 0° C in the presence of 165 mM KCl outside the cell (pH 7.3). A pseudo-first order association rate constant k₊₁     

The altered expression of MHC-class II determinants on monocytes of cancer patients

Summary The expression of MHC class II determinants Ia.7 (detected by cross reactive mouse anti-Ia^k antibody) and HLA-DR on monocytes (MO) of gastric and colorectal cancer patients was examined. An increased proportion of MO bearing the Ia.7 determinant was found, while the number of MO expressing DR was not elevated. In gastric cancer patients the increased expression of the Ia.7 determinant was most pronounced in advanced cancer (stage IVA and IVB). The increased expression of this determinant was related to the presence of the tumour as the number of MO expressing Ia.7 decreased 6 months following surgical resection of the tumour. Further, the increased expression of Ia.7 on MO correlated with the tumour infiltration of the serosa. The Ia.7 determinants were mainly expressed on MO which also expressed the receptor for the Fc part of immunoglobulin. Immunostaining in cellular infiltrates surrounding the tumour revealed that Ia.7⁺ macrophages (MØ) were more numerous than in normal gastric mucosa and severe chronic gastritis and were mostly present in close proximity to tumour cells, while DR⁺ MØ were mainly localized within the stromal tissue of the tumour and their number was not increased in cancer infiltrates. These observations indicate that the Ia.7⁺ subpopulation of MØ may be involved in the anti-tumour response of the host.     

Characteristics of action potentials in Helianthus annuus

The action potentials induced by nondamaging electrical stimuli in 16- to 22-day-old plants of Helianthus annuus were examined. Typical recordings are presented. Mean values of their amplitudes and conduction velocities in the stem, the strength-duration relation, the 'all-or-none' law and the refractory periods have been determined. The amplitude and velocity of propagation were essentially identical in the upward and downward direction, but greater in the upper than in the lower half. In 'electrically active' plants, the rheobase value is 2 V, the minimum period for stimulation is 1.8 s. and the chronaxie 2.3 s. It is noted that the excitability level between similar plants on the same day and in the same plant on different days is highly variable and undergoes periodic changes.     

A burst of CO2 from photosynthesizing leaves after a temperature decrease under constant light conditions

A transient CO₂ burst from seedlings of some plant species was observed after a rapid temperature decrease. The magnitude of the CO₂ release depended on initial temperature, oxygen concentration and light intensity. To obtain a maximal value of CO₂ release, the temperature had to decrease by more than 8°C. The phenomenon was detected only in the light, and was confined to C₃ species. It was inhibited by low oxygen concentration, indicating its possible connection with photorespiration.