Ben de Lacy Costello

An investigation of fecal volatile organic metabolites in irritable bowel syndrome.

Diagnosing irritable bowel syndrome (IBS) can be a challenge; many clinicians resort to invasive investigations in order to rule out other diseases and reassure their patients. Volatile organic metabolites (VOMs) are emitted from feces; understanding changes in the patterns of these VOMs could aid our understanding of the etiology of the disease and the development of biomarkers, which can assist in the diagnosis of IBS. We report the first comprehensive study of the fecal VOMs patterns in patients with diarrhea-predominant IBS (IBS-D), active Crohns disease (CD), ulcerative colitis (UC) and healthy controls. 30 patients with IBS-D, 62 with CD, 48 with UC and 109 healthy controls were studied. Diagnosis of IBS-D was made using the Manning criteria and all patients with CD and UC met endoscopic, histologic and/or radiologic criteria. Fecal VOMs were extracted by solid phase microextraction (SPME) and analyzed by gas chromatography-mass spectrometry (GC-MS). 240 VOMs were identified. Univariate analysis showed that esters of short chain fatty acids, cyclohexanecarboxylic acid and its ester derivatives were associated with IBS-D (p<0.05), while aldehydes were more abundant in IBD (p<0.05). A predictive model, developed by multivariate analysis, separated IBS-D from active CD, UC and healthy controls with a sensitivity of 94%, 96% and 90%; and a specificity of 82%, 80% and 80% respectively (p<0.05). The understanding of the derivation of these VOMs may cast light on the etiology of IBS-D and IBD. These data show that fecal VOMs analyses could contribute to the diagnosis of IBS-D, for which there is no laboratory test, as well as IBD.

UNIVERSAL COMPUTATION WITH LIMITED RESOURCES: BELOUSOV–ZHABOTINSKY AND PHYSARUM COMPUTERS

Using the examples of an excitable chemical system (the Belousov–Zhabotinsky medium) and plasmodium of Physarum polycephalum we show that universal computation in a geometrically unconstrained medium is only possible when resources (excitability or concentration of nutrients) are limited. In situations of limited resources the systems studied develop traveling localizations. These localizations are the elementary units of dynamical logical circuits in collision-based computing architectures.

Analysis of faecal volatile organic compounds in preterm infants who develop necrotising enterocolitis: a pilot study.

Objective: To determine differences in the profiles of volatile organic compounds (VOCs) in faecal samples from preterm infants who develop necrotising enterocolitis (NEC) compared with non-NEC controls. Materials and Methods: Daily faecal samples from preterm infants were collected prospectively during an 8-month period from a level 3 regional neonatal intensive care unit. Six infants subsequently developed NEC and were matched with 7 non-NEC infants. Solid-phase microextraction and gas chromatography and mass spectrometry were used to extract and identify the VOCs from the headspace above the faecal samples taken before the onset of NEC and after the disease was diagnosed. Faecal samples at similar ages were also studied from the control infants. Results: Two hundred twenty-four different VOCs were extracted from 65 samples. Volatile organic compounds increased in number with age for non-NEC infants. In the days before and after the diagnosis of NEC a reduction in the number of VOCs extracted was observed. In addition, 4 specific esters present in controls—2-ethylhexyl acetic ester, decanoic acid ethyl ester, dodecanoic acid ethyl ester, and hexadecanoic acid ethyl ester—were consistently absent from all faecal samples in those infants who developed NEC in the 4 days before the onset of the disease. Conclusion: This pilot study shows that VOC extraction from faeces may be used to identify infants that are at risk of developing NEC.

THE FORMATION OF VORONOI DIAGRAMS IN CHEMICAL AND PHYSICAL SYSTEMS: EXPERIMENTAL FINDINGS AND THEORETICAL MODELS

The work discusses the formation of Voronoi diagrams in spatially extended nonlinear systems taking experimental and theoretical results into account. Concerning experimental systems a number of chemical systems used previously as prototype chemical processors and a barrier gas-discharge system are investigated. Although the underlying microscopic processes are very different, both types of systems show self-organized Voronoi diagrams for suitable parameters. Indeed certain chemical systems exhibit Voronoi diagrams as an output state for two distinct sets of parameters one that corresponds to the interaction of stable forced trigger waves and the other that corresponds to the spontaneous initiation and interaction of waves due to point instabilities in the system. In the case of the chemical systems front initiation, propagation and interaction (annihilation) are the primary mechanisms for Voronoi diagram formation, in the case of the barrier gas-discharge system regions of vanishing electric field define the medial axes of the Voronoi diagram. On the basis of cellular automata models the general concept of the formation of Voronoi diagrams has been explained, and related mechanisms have been simulated. Another intuitive approach towards the understanding of self-organized Voronoi diagrams has been given on the basis of reaction–diffusion models explaining the formation of Voronoi diagrams as a result of the mutual interactions of trigger fronts. The variety of systems exhibiting Voronoi diagrams as stationary states indicates that Voronoi diagrams are a generic and natural pattern formation phenomenon.

Slime Mould Memristors

In laboratory experiments, we demonstrate that protoplasmic tubes of the acellular slime mould Physarum polycephalum show current versus voltage profiles consistent with memristive systems, and that this effect is due to the living protoplasm of the mould. This complements previous findings on memristive properties of other living systems (human skin and blood) and contributes to the development of self-growing bio-electronic circuits. Distinctive asymmetric V–I curves which were occasionally observed when the internal current is on the same order as the driven current, are well-modelled by the concept of active memristors.

Computational modalities of Belousov–Zhabotinsky encapsulated vesicles

Abstract We present both simulated and partial empirical evidences for the computational utility of many connected vesicle analogues of an encapsulated nonlinear chemical processing medium. By connecting small vesicles containing a solution of sub-excitable Belousov–Zhabotinsky (BZ) reaction, sustained and propagating wave fragments are modulated by both spatial geometry, network connectivity and their interaction with other waves. The processing ability is demonstrated through the creation of simple Boolean logic gates and then by the combination of those gates to create more complex circuits.

Slime mould logic gates based on frequency changes of electrical potential oscillation

Physarum polycephalum is a large single amoeba cell, which in its plasmodial phase, forages and connects nearby food sources with protoplasmic tubes. The organism forages for food by growing these tubes towards detected foodstuff, this foraging behaviour is governed by simple rules of photoavoidance and chemotaxis. The electrical activity of the tubes oscillates, creating a peristaltic like action within the tubes, forcing cytoplasm along the lumen; the frequency of this oscillation controls the speed and direction of growth. External stimuli such as light and food cause changes in the oscillation frequency. We demonstrate that using these stimuli as logical inputs we can approximate logic gates using these tubes and derive combinational logic circuits by cascading the gates, with software analysis providing the output of each gate and determining the input of the following gate. Basic gates OR, AND and NOT were correct 90%, 77.8% and 91.7% of the time respectively. Derived logic circuits XOR, half adder and full adder were 70.8%, 65% and 58.8% accurate respectively. Accuracy of the combinational logic decreases as the number of gates is increased, however they are at least as accurate as previous logic approximations using spatial growth of P. polycephalum and up to 30 times as fast at computing the logical output. The results shown here demonstrate a significant advancement in organism-based computing, providing a solid basis for hybrid computers of the future.

Boolean Logic Gates from a Single Memristor via Low-Level Sequential Logic

By using the memristor’s memory to both store a bit and perform an operation with a second input bit, simple Boolean logic gates have been built with a single memristor. The operation makes use of the interaction of current spikes (occasionally called current transients) found in both memristors and other devices. The sequential time-based logic methodology allows two logical input bits to be used on a one-port by sending the bits separated in time. The resulting logic gate is faster than one relying on memristor’s state switching, low power and requires only one memristor. We experimentally demonstrate working OR and XOR gates made with a single flexible Titanium dioxide sol-gel memristor.

Drop-coated titanium dioxide memristors

The fabrication of memristors by drop-coating sol–gel Ti(OH)4 solution onto either aluminium foil or sputter-coated aluminium on plastic is presented. The gel layer is thick, 37 μm, but both devices exhibit good memristance I–V profiles. The drop coated aluminium foil memristors compare favourably with the sputter-coated ones, demonstrating an expansion in the accessibility of memristor fabrication. A comparison between aluminium and gold for use as the sputter-coated electrodes shows that aluminium is the better choice as using gold leads to device failure. The devices do not require a forming step.

Urinary Volatile Organic Compounds for the Detection of Prostate Cancer.

The aim of this work was to investigate volatile organic compounds (VOCs) emanating from urine samples to determine whether they can be used to classify samples into those from prostate cancer and non-cancer groups. Participants were men referred for a trans-rectal ultrasound-guided prostate biopsy because of an elevated prostate specific antigen (PSA) level or abnormal findings on digital rectal examination. Urine samples were collected from patients with prostate cancer (n = 59) and cancer-free controls (n = 43), on the day of their biopsy, prior to their procedure. VOCs from the headspace of basified urine samples were extracted using solid-phase micro-extraction and analysed by gas chromatography/mass spectrometry. Classifiers were developed using Random Forest (RF) and Linear Discriminant Analysis (LDA) classification techniques. PSA alone had an accuracy of 62–64% in these samples. A model based on 4 VOCs, 2,6-dimethyl-7-octen-2-ol, pentanal, 3-octanone, and 2-octanone, was marginally more accurate 63–65%. When combined, PSA level and these four VOCs had mean accuracies of 74% and 65%, using RF and LDA, respectively. With repeated double cross-validation, the mean accuracies fell to 71% and 65%, using RF and LDA, respectively. Results from VOC profiling of urine headspace are encouraging and suggest that there are other metabolomic avenues worth exploring which could help improve the stratification of men at risk of prostate cancer. This study also adds to our knowledge on the profile of compounds found in basified urine, from controls and cancer patients, which is useful information for future studies comparing the urine from patients with other disease states.