Combined cold-water immersion and breathwork may be associated with improved mental health and reduction in the duration of upper respiratory tract infection - a case-control study.

A polar plunge is a term referring to an ice-cold water immersion (CWI), usually in the winter period. It is also a part of a specific training program (STP) which currently gains popularity worldwide and was proven to display paradigm-shifting characteristics. The aim of this study was to compare the indices of mental functioning (including depression, anxiety, mindfulness) and duration of upper respiratory tract infection (URTI) measured among the study participants. A set of questionnaires was distributed via the Internet. Participants declaring regular STP practice were selected (N = 77). Two groups were matched based on a case-control principle: the first one (the control group) comprised participants who did not declare nor CWI practice, nor STP practice. The second one comprised participants declaring regular CWI practice only. The CWI only group displayed better mental health indices and shorter URTIs compared to the control group. Moreover, the STP group also displayed better general mental health, less somatic complaints, and shorter URTIs compared to the CWI only group. This study suggests the existence of CWI's potential in boosting mental health and immune system functioning, however when complemented by a specific breathwork, this potential can be increased. However, further research is required.

Substitution mutational signatures in whole-genome-sequenced cancers in the UK population.

Whole-genome sequencing (WGS) permits comprehensive cancer genome analyses, revealing mutational signatures, imprints of DNA damage and repair processes that have arisen in each patient's cancer. We performed mutational signature analyses on 12,222 WGS tumor-normal matched pairs, from patients recruited via the UK National Health Service. We contrasted our results to two independent cancer WGS datasets, the International Cancer Genome Consortium (ICGC) and Hartwig Foundation, involving 18,640 WGS cancers in total. Our analyses add 40 single and 18 double substitution signatures to the current mutational signature tally. Critically, we show for each organ, that cancers have a limited number of 'common' signatures and a long tail of 'rare' signatures. We provide a practical solution for utilizing this concept of common versus rare signatures in future analyses.

A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.

Mutational signatures are patterns of mutations that arise during tumorigenesis. We present an enhanced, practical framework for mutational signature analyses. Applying these methods on 3,107 whole genome sequenced (WGS) primary cancers of 21 organs reveals known signatures and nine previously undescribed rearrangement signatures. We highlight inter-organ variability of signatures and present a way of visualizing that diversity, reinforcing our findings in an independent analysis of 3,096 WGS metastatic cancers. Signatures with a high level of genomic instability are dependent on TP53 dysregulation. We illustrate how uncertainty in mutational signature identification and assignment to samples affects tumor classification, reinforcing that using multiple orthogonal mutational signature data is not only beneficial, it is essential for accurate tumor stratification. Finally, we present a reference web-based tool for cancer and experimentally-generated mutational signatures, called Signal (https://signal.mutationalsignatures.com), that also supports performing mutational signature analyses.

Metabolic Pathway Mining.

Understanding metabolic pathways is one of the most important fields in bioscience in the post-genomic era, but curating metabolic pathways requires considerable man-power. As such there is a lack of reliable, experimentally verified metabolic pathways in databases and databases are forced to predict all but the most immediately useful pathways.Text-mining has the potential to solve this problem, but while sophisticated text-mining methods have been developed to assist the curation of many types of biomedical networks, such as protein-protein interaction networks, the mining of metabolic pathways from the literature has been largely neglected by the text-mining community. In this chapter we describe a pipeline for the extraction of metabolic pathways built on freely available open-source components and a heuristic metabolic reaction extraction algorithm.

Interfacial Layer Properties of a Polyaromatic Compound and its Role in Stabilizing Water-in-Oil Emulsions.

Physical properties of interfacial layers formed at the xylene-water interface by the adsorption of a polyaromatic organic compound, N-(1-hexylheptyl)-N'-(5-carbonylicpentyl) perylene-3,4,9,10-tetracarboxylic bisimide (in brief, C5Pe), were studied systematically. The deprotonation of the carboxylic group of C5Pe at alkaline pH made it highly interfacially active, significantly reducing the xylene-water interfacial tension. Thin liquid film experiments showed a continuous buildup of heterogeneous C5Pe interfacial layers at the xylene-water interfaces, which contributed to the formation of stable W/O emulsions. Continual accumulation and rearrangement of C5Pe aggregates at the xylene-water interface to form a thick layer was confirmed by in situ Brewster angle microscopy (BAM) and atomic force microscopy (AFM). The rheology measurement of the interfacial layer by double-wall ring interfacial rheometry under oscillatory shear showed that the interfacial layers formed from C5Pe solutions of high concentrations were substantially more elastic and rigid. The presence of elastically dominant interfacial layers of C5Pe led to the formation of stable water-in-xylene emulsions.

Mining biological networks from full-text articles.

The study of biological networks is playing an increasingly important role in the life sciences. Many different kinds of biological system can be modelled as networks; perhaps the most important examples are protein-protein interaction (PPI) networks, metabolic pathways, gene regulatory networks, and signalling networks. Although much useful information is easily accessible in publicly databases, a lot of extra relevant data lies scattered in numerous published papers. Hence there is a pressing need for automated text-mining methods capable of extracting such information from full-text articles. Here we present practical guidelines for constructing a text-mining pipeline from existing code and software components capable of extracting PPI networks from full-text articles. This approach can be adapted to tackle other types of biological network.

Role of asphaltenes in stabilizing thin liquid emulsion films.

Drainage kinetics, thickness, and stability of water-in-oil thin liquid emulsion films obtained from asphaltenes, heavy oil (bitumen), and deasphalted heavy oil (maltenes) diluted in toluene are studied. The results show that asphaltenes stabilize thin organic liquid films at much lower concentrations than maltenes and bitumen. The drainage of thin organic liquid films containing asphaltenes is significantly slower than the drainage of the films containing maltenes and bitumen. The films stabilized by asphaltenes are much thicker (40-90 nm) than those stabilized by maltenes (∼10 nm). Such significant variation in the film properties points to different stabilization mechanisms of thin organic liquid films. Apparent aging effects, including gradual increase of film thickness, rigidity of oil/water interface, and formation of submicrometer size aggregates, were observed for thin organic liquid films containing asphaltenes. No aging effects were observed for films containing maltenes and bitumen in toluene. The increasing stability and lower drainage dynamics of asphaltene-containing thin liquid films are attributed to specific ability of asphaltenes to self-assemble and form 3D network in the film. The characteristic length of stable films is well beyond the size of single asphaltene molecules, nanoaggregates, or even clusters of nanoaggregates reported in the literature. Buildup of such 3D structure modifies the rheological properties of the liquid film to be non-Newtonian with yield stress (gel like). Formation of such network structure appears to be responsible for the slower drainage of thin asphaltenes in toluene liquid films. The yield stress of liquid film as small as ∼10(-2) Pa is sufficient to stop the drainage before the film reaches the critical thickness at which film rupture occurs.

A text-mining system for extracting metabolic reactions from full-text articles.

BACKGROUND: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway - metabolic pathways - has been largely neglected.Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein-protein interactions. RESULTS: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. CONCLUSIONS: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein-protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed.

A microfluidic electrochemical detection technique for assessing stability of thin films and emulsions.

An experimental technique is developed for assessing stability of thin liquid films by application of electric potential to compress the liquid film and to simultaneously measure the electrical properties of the system. The concept involves creating a thin film at the intersection of two microchannels etched onto a glass substrate. A ramped DC potential difference is applied across the film, which develops an electrical stress across the film. Increasing the potential to a critical value leads to the rupture of the film. The critical potential is used to assess the stability of the liquid film. Small channel dimensions in this microfluidic platform allow characterization of thin films formed between micron-sized droplets representing systems with high capillary pressures, analysis of which are typically beyond the scope of conventional thin film characterization techniques. The results of DC potential breakdown of films show that critical potential can be considered as a measure of thin film stability.

Aqueous foam films stabilized by sodium naphthenates.

Stratification of a foam liquid film drawn from aqueous solutions of sodium naphthenate at relatively high concentration is likely due to a lamellar liquid crystal-like structure within the film. Film stratification, resulting in stepwise thinning, has been observed in foam films formed from systems containing either moderate to high concentrations of surfactant or in films formed from solutions containing solid particles. At moderate surfactant concentrations, film stratification is likely due to layers of ordered spherical micelles as postulated in Wasan and Nikolov's model of film stratification. At high surfactant concentrations, stepwise thinning of the films and occurrence of domains of uniform color within the film suggest a lamellar liquid crystal-like structure within the film, potentially up to hundred or more oriented layers. The LLC-like structure inside the film can occur at concentrations below the lower limit of the LLC existence as a bulk phase.

Development and immunochemical evaluation of antibodies Y for the poorly immunogenic polypeptide prothymosin alpha.

Since conserved mammalian polypeptides are believed to exhibit enhanced immunogenicity in avian species, hens were immunized against the poorly immunogenic, highly conserved mammalian polypeptide prothymosin alpha (ProTalpha), i.e. against either non-conjugated ProTalpha (isolated from bovine thymus) or ProTalpha conjugated to keyhole limpet hemocyanin (ProTalpha/KLH). The antibodies Y were isolated from the egg yolk and evaluated through suitable dot-blot and ELISA systems in parallel with antibodies G isolated from the antiserum of rabbits immunized against the same immunogens. As revealed, antibodies Y and G of low titer and/or affinity were obtained against non-conjugated ProTalpha, while antibodies Y against ProTalpha/KLH had a better apparent titer, could better discriminate between ProTalpha and the closely related bioactive peptide thymosin alpha 1, and were obtained at much larger quantities than the corresponding antibodies G.

On the nature of Athabasca Oil Sands.

The existence of a thin aqueous film, separating bitumen (a form of heavy oil) from inorganic solids in Athabasca Oil Sands, is analysed based on "first principles". There is a general consensus in the literature on the hydrophilic character of the solids in oil sands. However, a review of the references cited in support of the solids being encapsulated in thin water envelopes produced a surprising lack of evidence. A theoretical analysis indicates that a water film separating clean, hydrophilic quartz and bitumen is stable under most conditions, and unstable for acidic oil sand ores. The existence of water-wet solids in the Athabasca Oil Sands remains a reasonable yet unproven postulate. It could therefore be dangerous to accept the water-wet solids postulate and then use it to interpret other phenomena.

Adsorption isotherms of associating asphaltenes at oil/water interfaces based on the dependence of interfacial tension on solvent activity.

In the Gibbs adsorption equation, the application of solvent activity for the calculation of the surface/interfacial excess is proposed for nonideal or associating or pseudocomponents such as asphaltenes. For the aforementioned systems, only the mass-based phenomenological interfacial excess can be determined based on interfacial tension versus activity data. The use of the mole fraction is compared to the use of the activity when the adsorbed amount of associating asphaltenes is calculated at a water/toluene interface. Langmuir-type isotherms describe the adsorption of asphaltenes at toluene/water interfaces. Asphaltenes were treated to remove the resins and natural surfactants using cyclic precipitation and dissolution of asphaltenes at a fixed aliphatic/aromatic ratio. Different fractions of asphaltenes were obtained by changing the aliphatic/aromatic ratio of the precipitating solvent. The limiting molar masses of asphaltenes measured by vapor pressure osmometry are different for fractions precipitated at different heptane to toluene ratios. The mass-based adsorbed amounts at the water/toluene interface, at a 0.1 asphaltene-to-toluene mass-ratio, varied in the range of 0.8-2.8 mg/m(2), depending on the molar mass of asphaltenes.

Stepwise thickening in aqueous foam films stabilized by sodium naphthenates.

During drainage of a foam film formed from an aqueous sodium naphthenate solution, a transient, local, stepwise thickening process was observed. Film stratification is related to the stepwise thinning drainage process where individual layers of material are drained from a film. The process typically involves the appearance of a sequence of small, uniformly thick spots that eventually expand to the size of the film. The appearance and growth of each spot represents a discrete decrease in the thickness of the film. The size of each decrease or step typically corresponds to the size of one or more lamella layers of the stratified film. Stepwise thinning was observed in a foam film formed from an aqueous sodium naphthenate solution, as frequently reported for a variety of systems. However, during the drainage process, a transient stepwise thickening process was also observed. Bright spots began to appear and grow, indicate a discrete increase in the thickness of a portion of the film. This local, stepwise thickening process appeared to be an alternate and temporary drainage process directly related to the expansion of the stepwise thinning spots.

Electroosmotic dispersion in microchannels with a thin double layer.

Dispersion of a nonelectrolyte solute due to the electroosmotic flow in long straight microchannels was analyzed theoretically. A version of the Aris-Taylor procedure was employed to predict the dispersion coefficient for arbitrary geometry of the microchannel cross section. The analysis was conducted using a thin double-layer approximation, which is valid when the Debye length is much smaller than the characteristic dimensions of the cross section. For thin double layers, the obtained results describe the electroosmotic dispersion for arbitrary surface potential, electrolyte type, and cross-section geometry. Dispersion for several cases of the cross-section geometries was discussed. It was shown that, for given values of the surface potential and the Debye length, both the cross-section geometry and the electrolyte content of the driven solution substantially affect the dispersion of a nonelectrolyte solute. In the relevant particular cases, the obtained results agree with predictions of the previous theories.

Emulsion stability based on phase behavior in sodium naphthenates containing systems: gels with a high organic solvent content.

Addition of heptane to a sodium naphthenates/toluene/water system at 25 degrees C reduces the lamellar liquid-crystal phase range and increases the microemulsion phase range. Both of these effects result in the extension of the composition range where emulsions have low stability. This effect is even stronger at 40 degrees C. Heptane addition also results in the formation of very stable emulsions within the overlapping phase-existence ranges of aqueous (L1) and organic (L2) phases. Stable non-birefringent gel observed in equilibrium with L1 and L2 phases contains only a small percentage of water and sodium naphthenates. The swelling behavior of an unstable gel, an emulsion previously compressed by centrifugation, appears to be due to a stepwise thickening of the thin liquid films between the droplets.

Disjoining pressure isotherms of water-in-bitumen emulsion films.

In the oil sands industry, undesirable water-in-oil emulsions are often formed during the bitumen recovery process where water is used to liberate bitumen from sand grains. Nearly all of the water is removed except for a small percentage (approximately 1 to 2%), which remains in the solvent-diluted bitumen as micrometer-sized droplets. Knowledge of the colloidal forces that stabilized these water droplets would help to increase our understanding of how these emulsions are stabilized. In this study, the thin liquid film-pressure balance technique has been used to measure isotherms of disjoining pressure in water/toluene-diluted bitumen/water films at five different toluene-bitumen mass ratios. Even though a broad range of mass ratios was studied, only two isotherms are obtained, indicating a possible change in the molecular orientation of surfactant molecules at the bitumen/water interfaces. At low toluene-bitumen mass ratios, the film stability appears to be due to a strong, short-range steric repulsion created by a surfactant bilayer. Similar isotherms were obtained for water/toluene-diluted asphaltene/water films, indicating that the surface active material at the interface probably originated from the asphaltene fraction of the bitumen. However, unlike the bitumen films, films of toluene-diluted asphaltenes often formed very rigid interfaces similar to the "protective skin" described by other researcher.

Sandwich structures at oil-water interfaces under alkaline conditions.

Equilibrium liquid crystal (LC) layer on an interface between crude oils and water was observed at high pH. This layer is composed mainly of sodium naphthenates produced in situ at the water/oil interface. Transient LC layer was also evolved at the interface of aqueous phase of sodium hydroxide solutions and oleic phase of naphthenic acid (NA) solutions as result of a chemical reaction between NaOH and NA. This chemical reaction causes transport process resulting in a disturbance of the interface. Optical observation of this interface disturbance reviled that the interface covered with LC shows considerably lower flexibility as compared to LC free interface. The LC layer eventually dissolves in the water phase at low oil-to-water ratio, while at high oil-to-water ratio it can form an equilibrium phase, which spreads spontaneously at the oil-water interface.

Liquid Crystals in Aqueous Solutions of Sodium Naphthenates.

The phase diagram of the sodium naphthenates (SN)/water system was determined between -5 and 95 degrees C. Oil, isotropic water solution, and birefringent gel phases were observed. The appearance of the oil phase was caused by the hydrolysis of SN. After the system was allowed to stand for 3 weeks, a lamellar liquid crystal (LLC) phase separated from the rest of the system at 25 degrees C. This phase was always observed together with other phases. This phase behavior is attributed to different partition coefficient values of the individual constituents of sodium naphthenates between the phases. The partition coefficient difference also caused the appearance of a clear LLC and a turbid gel phase. Under the influence of agitation, the LLC phase with isotropic water solution transformed to giant vesicles; however the equilibrium state of the LLC is of parallel stacked layer structure. Macroscopic dislocations of the liquid crystal were observed, and they were anchored to the interface of the isotropic solution and the liquid crystal phases. These dislocations are similar to screw-type dislocations. The solubilization curve of toluene by SN is analogous to that of hydrophobic materials by a hydrotrope. Copyright 2001 Academic Press.