Discrimination of constructed air samples using multivariate analysis of full scan membrane introduction mass spectrometry (MIMS) data.

RATIONALE: Volatile and semi-volatile organic compounds (S/VOCs) are important atmospheric pollutants affecting both human and environmental health. They are directly measured as an unresolved mixture using membrane introduction mass spectrometry (MIMS). We apply chemometric techniques to discriminate, classify, and apportion air samples from a variety of sources. METHODS: Full scan mass spectra of lab-constructed air samples were obtained using a polydimethylsiloxane membrane interface and an electron ionization ion trap mass spectrometer. Normalized full scan spectra were analyzed using principal component analysis (PCA), cluster analysis, and k-nearest neighbours (kNN) for sample discrimination and classification. Multivariate curve resolution (MCR) was used to extract pure component contributions. Similar techniques were applied to VOC mixtures sampled from different woodsmoke emissions and from the headspace above aqueous hydrocarbon solutions. RESULTS: PCA successfully discriminated 32 constructed VOC mixtures from nearly 300 air samples, with cluster analysis showing similar results. Further, kNN classification (k = 1) correctly classified all but one test set sample, and MCR successfully identified the pure compounds used to construct the VOC mixtures. Real-world samples resulting from the combustion of different wood species and those associated with water contaminated with different commercial hydrocarbon products were similarly discriminated by PCA. CONCLUSIONS: Chemometric techniques have been evaluated using full scan MIMS spectra with a series of VOC mixtures of known composition containing known compounds, and successfully applied to samples with known sources, but unknown molecular composition. These techniques have application to source identification and apportionment in real-world environmental samples impacted by atmospheric pollutants.

The identification of short linear motif-mediated interfaces within the human interactome.

MOTIVATION: Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances. RESULTS: In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM-domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs. AVAILABILITY: iELM is freely available at http://elmint.embl.de CONTACT: toby.gibson@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Discrimination and geo-spatial mapping of atmospheric VOC sources using full scan direct mass spectral data collected from a moving vehicle.

Volatile and semi-volatile organic compounds (S/VOCs) are ubiquitous in the environment, come from a wide variety of anthropogenic and biogenic sources, and are important determinants of environmental and human health due to their impacts on air quality. They can be continuously measured by direct mass spectrometry techniques without chromatographic separation by membrane introduction mass spectrometry (MIMS) and proton-transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS). We report the operation of these instruments in a moving vehicle, producing full scan mass spectral data to fingerprint ambient S/VOC mixtures with high temporal and spatial resolution. We describe two field campaigns in which chemometric techniques are applied to the full scan MIMS and PTR-ToF-MS data collected with a mobile mass spectrometry lab. Principal Component Analysis (PCA) has been successfully employed in a supervised analysis to discriminate VOC samples collected near known VOC sources including internal combustion engines, sawmill operations, composting facilities, and pulp mills. A Gaussian mixture model and a density-based spatial clustering of application with noise (DBSCAN) algorithm have been used to identify sample clusters within the full time series dataset collected and we present geospatial maps to visualize the distribution of VOC sources measured by PTR-ToF-MS.

The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.

Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised. The protein motif biology field does not have sufficient resources to curate the corpus of motif-related literature and, to date, only a fraction of the available articles have been curated. In this study, we develop a set of tools and a web resource, 'articles.ELM', to rapidly identify the motif literature articles pertinent to a researcher's interest. At the core of the resource is a manually curated set of about 8000 motif-related articles. These articles are automatically annotated with a range of relevant biological data allowing in-depth search functionality. Machine-learning article classification is used to group articles based on their similarity to manually curated motif classes in the Eukaryotic Linear Motif resource. Articles can also be manually classified within the resource. The 'articles.ELM' resource permits the rapid and accurate discovery of relevant motif articles thereby improving the visibility of motif literature and simplifying the recovery of valuable biological insights sequestered within scientific articles. Consequently, this web resource removes a critical bottleneck in scientific productivity for the motif biology field. Database URL: http://slim.icr.ac.uk/articles/.

The Use of MIMS-MS-MS in field locations as an on-line quantitative environmental monitoring technique for trace contaminants in air and water.

Membrane introduction mass spectrometry (MIMS) is emerging as an important technique for on-line, real-time environmental monitoring. Because MIMS interfaces are simple and robust, they are ideally suited for operation in MS instrumentation used for in-field applications. We report the use of an on-line permeation tube to continuously infuse an isotopically labeled internal standard for continuous quantitative determinations in atmospheric and aqueous samples without the need for off-line calibration. This approach also provides important information on the operational performance of the analytical system during multi-day deployments. We report measured signal stability during on-line deployments in air and water of 7% based on variation of the internal standard response and have used this technique to quantify BTEX (benzene, toluene, ethylbenzenes, and xylenes), pinenes, naphthalene and 2-methoxyphenol (guaiacol) in urban air plumes at parts-per-billion by volume levels. Presented are several recent applications of MIMS-MS-MS for on-line environmental monitoring in atmospheric and aqueous environmental samples demonstrating laboratory, remote and mobile deployments. We also present the use of a thermally assisted MIMS interface for the direct measurement of polyaromatic hydrocarbons, alkylphenols, and other SVOCs in the low ppb range in aqueous environmental samples and discuss improvements in both the sensitivity and response times for selected SVOCs. The work presented in this paper represents significant improvements in field deployable mass spectrometric techniques, which can be applied to direct on-site analytical measurements of VOC and SVOCs in environmental samples.

The effect of an energy drink containing glucose and caffeine on human corticospinal excitability.

Glucose- and caffeine-containing energy drinks are said to influence the cognitive and cellular function within the brain. In this study, we have used the size of motor-evoked potentials (MEPs) produced in response to transcranial magnetic stimulation (TMS) of the motor cortex as an index of corticospinal excitability after ingestion of Lucozade and control drinks of glucose-containing or caffeine-containing carbonated water or carbonated water alone. With local ethical approval and informed consent, 10 healthy volunteers took part; surface electromyographic (EMG) recordings were taken from the thenar muscles of the dominant hand. In each assessment, 15 TMS stimuli were delivered over the motor cortex at an intensity of 1.1 T. Six subjects ingested a 380-ml bottle of carbonated Lucozade drink containing 68 g of glucose and 46 mg caffeine. Four subjects took part in three control trials drinking: (A) carbonated water with caffeine, (B) carbonated water with glucose and (C) carbonated water alone. Assessments were made before and at 30-min intervals after each drink. Mean fasting blood glucose concentrations and mean areas of MEPs rose after the Lucozade, remaining elevated for 90 min. Similar rises in MEP areas were seen in trials after drinking carbonated water with caffeine or with glucose, but not after drinking carbonated water alone. No change was seen in the M-wave evoked by electrical stimulation of the ulnar nerve. We conclude that Lucozade can affect the size of MEPs to activation of the motor cortex with fixed-intensity TMS. The underlying mechanism is likely to relate to the combined effects of caffeine and glucose on the brain.

The application of machine learning to the modelling of percutaneous absorption: an overview and guide.

Machine learning (ML) methods have been applied to the analysis of a range of biological systems. This paper reviews the application of these methods to the problem domain of skin permeability and addresses critically some of the key issues. Specifically, ML methods offer great potential in both predictive ability and their ability to provide mechanistic insight to, in this case, the phenomena of skin permeation. However, they are beset by perceptions of a lack of transparency and, often, once a ML or related method has been published there is little impetus from other researchers to adopt such methods. This is usually due to the lack of transparency in some methods and the lack of availability of specific coding for running advanced ML methods. This paper reviews critically the application of ML methods to percutaneous absorption and addresses the key issue of transparency by describing in detail - and providing the detailed coding for - the process of running a ML method (in this case, a Gaussian process regression method). Although this method is applied here to the field of percutaneous absorption, it may be applied more broadly to any biological system.

Measurement of cytotoxic T lymphocyte precursor frequencies reveals cryptic HLA class I mismatches in the context of unrelated donor bone marrow transplantation.

BACKGROUND: In this large, two-center study, 260 cytotoxic T lymphocyte precursor (CTLp) frequency assays, performed to assess patient-donor compatibility, were analyzed in relation to the degree of HLA matching. METHODS: While the tissue-typing techniques used at the Royal Postgraduate Medical School (RPMS) and Anthony Nolan Bone Marrow Trust (ANBMT) differ, the results of the analyses on the two sites are analogous, with high CTLp frequencies (>1:100,000) in 42% and 41% of recipient-donor pairs, respectively. RESULTS: Recipient-donor combinations with class I mismatches and class II identity were associated with high CTLp frequencies (collectively 83% vs. 17% low CTLp). This correlation was not as strong in pairs where class II mismatches were demonstrated (61% high vs. 39% low). Despite using different matching procedures, the RPMS and ANBMT both show that 32% of the "perfectly" matched pairs (i.e., where no mismatch was detected by any of the techniques used here) had high frequencies of recipient-specific CTLp. CONCLUSIONS: The failure of conventional methods to identify such a level of histoincompatibilities indicates that the CTLp assay has an important role in the selection of unrelated donors for bone marrow transplantation.

A correlation between HLA-C matching and donor antirecipient CTL precursor frequency in bone marrow transplantation.

A newly developed, reliable, DNA-based method for typing for alleles of the HLA-C locus has been applied in the context of unrelated, volunteer donors for bone marrow transplantation. Some donors matched for HLA-A, -B, -DR, and -DQ have been found to generate in vitro high frequencies of CTL reactive with the recipient's cells. Here we demonstrate that there is a highly significant correlation of the frequencies of CTL precursors and incompatibility at the HLA-C locus. These data indicate that HLA-C locus incompatibility should be avoided in unrelated donor bone marrow transplantation.

Renal transplantation following immunoadsorption in highly sensitized recipients.

Five highly sensitized patients, with panel reactivity greater than 80% for 1.75-5 years, were treated by extracorporeal staphylococcal protein-A immunoadsorption, prednisolone, and cyclophosphamide. The five patients underwent treatment of 18-40 (mean 31) liters of plasma, respectively in 4-7 (mean 5.6) sessions. This reduced the titer of cytotoxic antibodies to sensitizing antigens to < 1/8 in all cases and abolished reactivity to crossreacting antigens. Two patients required retreatment following resynthesis of cytotoxic antibodies. All five patients have been transplanted, and four of these now have stable serum creatinines of 168 mumol/L at 34 months, 208 mumol/L at 29 months, 96 mumol/L at 5 months, and 125 mumol/L at 3 months posttransplantation. One patient had primary graft dysfunction due to acute tubular necrosis; the kidney was removed after eight weeks and showed cortical necrosis without evidence of acute rejection.

C4 complement allotypes in juvenile dermatomyositis.

Twenty probands with juvenile dermatomyositis and their relatives were studied to determine the inherited segregation patterns of class I, II, and III HLA region markers including C4A, C4B, Bf, and C2 complement polymorphisms. The extended haplotype B8, DR3, C4A*Q0, C4B*1, C2*C, and Bf*S was present in 13 of the 20 probands. Three other probands also carried a haplotype with a null allele for C4A and two further probands carried a null allele for C4B; only two probands had no detectable C4 null allele. These data confirm previous studies showing high frequencies of B8 and DR3 in patients with juvenile dermatomyositis, but show that there is a higher association with null alleles of C4. This suggests that the C4 genes are either themselves the disease-susceptibility genes or are in very strong linkage disequilibrium with such genes.

Multiple sclerosis and HLA: is the susceptibility gene really HLA-DR or -DQ?

Seventy-one patients with multiple sclerosis (MS) were classified into four subgroups according to the clinical pattern of their disease; their HLA-DR and DQ polymorphisms were defined by serological methods and analysis of Taq1 digestion fragments hybridizing with DRB, DQA, and DQB cDNA probes. The frequencies of the polymorphisms in the patients were compared with those of 100 control subjects. The frequencies of a 3.25-kb fragment from Mspl digests of genomic DNA which hybridized to DQA were also defined in the same groups of patients and control subjects. HLA-DR2 (DRw 15 subtype) and the associated HLA-DQw6 were observed in significant excess in the patients compared with the normal subjects (63% vs. 32% for DRw15; 65% vs. 42% for DQw6). There were no significant differences in the distribution of the DR or DQ alleles between the groups of patients showing different clinical patterns of disease, nor was there an excess in the patients of DQw8 and DQw9 which share hypervariable region sequences of the DQB chain in common with DQw6. The results argue against two recently proposed hypotheses of MS. First, they are not consistent with the proposal that susceptibility to MS is associated with expression of a hypervariable region of DQB shared by DQw6, 8, and 9. Second, they do not support the concept that primarily chronic progressive and relapsing/remitting MS are two immunogenetically distinct disease entities. Our evidence is consistent with the hypothesis that one of the true disease susceptibility genes for MS lies elsewhere within the HLA region and in Northern European populations is found in significant association with DRw15 and DQw6.

Segmental influence of slowly-adapting cutaneous mechanoreceptors on gamma motoneurones revealed by cross-correlation of unit discharges in the cat.

Cross-correlations between the discharges of individual cutaneous afferents and gamma motoneurones have been constructed in the spinal, decerebrated cat. The discharges of single receptors in the sural nerve field from the heel were recorded in dorsal root ganglia. Background discharges of gamma motoneurones and the responses to heel stimulation were recorded from cut filaments of the muscle nerve to gastrocnemius medialis of the same leg. Slowly-adapting afferents were stimulated by steady application of a probe to the receptive field whereas rapidly-adapting afferents required continuous movement to sustain discharge of a receptor. Cross-correlation between the discharges of 17 out of 39 slowly-adapting, type-1 (SA1) mechanoreceptors and gamma motoneurones revealed sharp increases in probability of gamma motoneurone discharge that were delayed with respect to the afferent discharge. The peaks were of short duration with widths at half maximum in the range 2-7 ms and rise times of 1 to 4 ms. Deducting peripheral conduction times gave central delays of 3-6.5 ms for gamma motoneurone facilitation. These delays were comparable to those of gamma motoneurone excitation seen in response to electrical stimulation of the sural nerve at 1.5 to 4 times threshold. No short duration peaks were seen in correlograms between hair follicle (n = 29) or slowly-adapting type-2 (SA2) (n = 11) afferents and gamma motoneurones. It is concluded that a single impulse from a SA1 afferent from the hairy skin of the heel is able to facilitate the discharge of gamma motoneurones to the ipsilateral gastrocnemius muscle.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytotoxic T lymphocyte precursor (CTL-p) frequency analysis in unrelated donor bone marrow transplantation: two case studies.

HLA 'matched' unrelated donor bone marrow transplantation (BMT) is associated with an increased incidence and severity of acute graft-versus-host disease (GVHD) in comparison with HLA-identical sibling transplants. Using a limiting dilution analysis system for quantitating frequencies of alloreactive cytotoxic T lymphocyte precursors (CTL-p), we previously demonstrated a correlation between CTL-p frequency and HLA disparity between responder and stimulator, and between CTL-p frequency and the incidence of acute GVHD following HLA A, B, DR matched unrelated donor BMT. In this study we assayed CTL-p frequencies in two HLA 'matched' unrelated donor/patient pairs, with single HLA antigenic mismatches detected by allogenotyping or isoelectric focusing but not by HLA serology, and demonstrated that the CTL-ps were specifically directed at the mismatched antigen. Both class I and class II antigens were detected. These data, and our previous work, suggest that high CTL-p frequencies in HLA 'matched' unrelated pairs are indicative of HLA antigenic variants undetected by serology but recognized by molecular typing, and that these are responsible for the value of the assay in predicting acute GVHD after BMT. We propose that this assay system be used in aiding final donor selection before unrelated or mismatched related donor BMT.

Current orientation induced by magnetic stimulation influences a cognitive task.

The direction of the current induced by transcranial magnetic stimulation (TMS) over the motor cortex has been observed to influence the threshold and latency of evoked muscle responses. This study investigates the effect of TMS-induced current orientation (ICO) over the prefrontal cortex, on a specific cognitive task (memory-guided saccade). TMS was applied with a figure-of-eight coil, placed at one of eight different orientations over the prefrontal cortex. The most effective ICO was antero-lateral, which is a different optimal ICO from that seen over the hand area of the motor cortex. This demonstrates that ICO can alter the effect of TMS on cognitive functions and that ICO is an independent variable that should not be ignored when designing TMS studies.

Statistical limits for detecting change in the cumulative sum derivative of the peristimulus time histogram.

The peristimulus time histogram (psth) provides a means of correlating the discharges of neurones with other events. The cumulative sum (cusum) derived from the psth facilitates the detection of small changes in the psth that may be obscured by random fluctuations in counts. The cusum integrates differences from the mean control level of counts in the psth. Any signal in the data that is related to the stimulus appears as a slope in the cusum. Psth's constructed from the rhythmic discharges of single neurones are shown to contain periodical fluctuations in counts that arise from refractoriness. This periodicity results in a cusum which deviates less from the horizontal line than predicted from a Poisson distribution of points. The more regular the spike train, i.e., the lower the coefficient of variation of the distribution of interspike intervals, the flatter is the cusum. The theory of stochastic point processes is used to derive an algorithm for calculating the best approximation of variance of the cusum. Significance limits set at 3 standard deviations of the cusum are shown to provide a good fit to cusums for unit discharges over a wide range of coefficients of variation (0.09-0.60).

Controlled trial of a back support ('Lumbotrain') in patients with non-specific low back pain.

A randomized, controlled, parallel-group clinical trial was carried out in general practice to assess the clinical efficacy of a new back support ('Lumbotrain') compared with 'standard therapy' of advice on rest and lifestyle in the treatment of patients with non-specific low back pain. A total of 216 patients entered this study (111 'Lumbotrain' group, 105 control group). All patients were allowed to take 1 g paracetamol up to 4-times daily if necessary for control of pain. Self-assessments were made daily by patients, over a period of 21 days, of pain levels at rest, on activity, at night, and limitation of activity using visual analogue scales. Details were also recorded of their ability to work or not, and the number of doses of paracetamol taken. At the end of the study period, patients assessed their overall response to treatment and those in the 'Lumbotrain' group were questioned on the comfort and ease of use of the back support. A clinical examination was carried out by the doctor at the start and end of the study period and an assessment made of the total range of active and passive back movement. Analysis of the daily diary records showed there were progressive, significant reductions in mean scores for all the pain and activity criteria in both groups and these were significantly greater in the 'Lumbotrain' group from Day 7 onwards. The times taken for reduction of symptom scores to 10% of initial values were significantly less in the 'Lumbotrain' group, such a degree of recovery occurring 2 to 4 days more rapidly than in the control group. A significantly higher proportion of patients in the 'Lumbotrain' group became able to work normally. After 3 weeks, 85% of patients in the 'Lumbotrain' group could work normally, as compared with 67% in the control group (p less than 0.02). Total analgesic consumption during the trial was significantly lower (p less than 0.0001) in the 'Lumbotrain' group (median 24.5 doses) than in the control group (median 51 doses). Overall clinical assessment scores were significantly superior in the 'Lumbotrain' group (p less than 0.002). Improvement was seen in 106 (95%) of 111 patients in the 'Lumbotrain' group, as compared with 79 (77%) of 103 of those in the control group (p less than 0.0002).(ABSTRACT TRUNCATED AT 400 WORDS)

Voluntary motor function in patients with chronic fatigue syndrome.

INTRODUCTION: The pathogenesis of chronic fatigue syndrome (CFS) remains unknown. In particular, little is known of the involvement of the motor cortex and corticospinal system. METHODS: Transcranial magnetic stimulation (TMS) was used to assess corticospinal function in terms of latency and threshold of motor-evoked potentials (MEPs) in thenar muscles. Reaction times and speed of movement were assessed using button presses in response to auditory tones. RESULTS: Patients had higher (P<.05) self-assessed indices of fatigue (7/10) than for pain (5/10), anxiety (4/10) or depression (3/10). Mean (+/-S.E.M.) simple reaction times (SRTs) were longer (P<.05) in the patients (275+/-19 ms) than in the controls (219+/-9 ms); choice reaction times (CRTs) were not significantly longer in the patients. Movement times, once a reaction task had been initiated, were longer (P<.05) in the patients in both SRTs (patients, 248+/-13 ms; controls, 174+/-9 ms) and CRTs (patients, 269+/-13 ms; controls, 206+/-12 ms). There was no difference (P>.05) in threshold or latency of MEPs in hand muscles between the patients (threshold, 54.5+/-2.2% maximum stimulator output [% MSO]; latency 22+/-0.3 ms) and controls (threshold 54.6+/-3.6% MSO; latency 22.9+/-0.5 ms). Regression analysis showed no correlation (P>.05) of SRTs with either threshold for MEPs or fatigue index. CONCLUSION: Corticospinal conduction times and excitability were within the normal range despite a slower performance time for motor tasks and an increased feeling of fatigue. This suggests that the feeling of fatigue and the slowness of movement seen in CFS are manifest outside the corticospinal system.

The application of discriminant analysis and Machine Learning methods as tools to identify and classify compounds with potential as transdermal enhancers.

Discriminant analysis (DA) has previously been shown to allow the proposal of simple guidelines for the classification of 73 chemical enhancers of percutaneous absorption. Pugh et al. employed DA to classify such enhancers into simple categories, based on the physicochemical properties of the enhancer molecules (Pugh et al., 2005). While this approach provided a reasonable accuracy of classification it was unable to provide a consistently reliable estimate of enhancement ratio (ER, defined as the amount of hydrocortisone transferred after 24h, relative to control). Machine Learning methods, including Gaussian process (GP) regression, have recently been employed in the prediction of percutaneous absorption of exogenous chemicals (Moss et al., 2009; Lam et al., 2010; Sun et al., 2011). They have shown that they provide more accurate predictions of these phenomena. In this study several Machine Learning methods, including the K-nearest-neighbour (KNN) regression, single layer networks, radial basis function networks and the SVM classifier were applied to an enhancer dataset reported previously. The SMOTE sampling method was used to oversample chemical compounds with ER>10 in each training set in order to improve estimation of GP and KNN. Results show that models using five physicochemical descriptors exhibit better performance than those with three features. The best classification result was obtained by using the SVM method without dealing with imbalanced data. Following over-sampling, GP gives the best result. It correctly assigned 8 of the 12 "good" (ER>10) enhancers and 56 of the 59 "poor" enhancers (ER<10). Overall success rates were similar. However, the pharmaceutical advantages of the Machine Learning methods are that they can provide more accurate classification of enhancer type with fewer false-positive results and that, unlike discriminant analysis, they are able to make predictions of enhancer ability.