Publications

Scalable and high-throughput platforms to non-invasively record the Action Potentials (APs) of excitable cells are highly demanded to accelerate disease diagnosis and drug discovery. AP recordings are typically achieved with the invasive and low-throughput patch clamp technique. Non-invasive alternatives like planar multielectrode arrays cannot record APs without membrane poration, preventing accurate measurements of disease states and drug effects. Here, we disclose reliable and non-invasive recording of APs with patch clamp-like quality from human stem cell-derived cardiomyocytes using an inkjet-printed polymer semiconductor in an Electrolyte-Gated Field-Effect Transistor configuration. High sensitivity is proven by the detection of drug-induced pro-arrhythmic membrane potential oscillations as early/delayed afterdepolarizations. The higher throughput potential of this platform could significantly enhance disease modelling, drug screening, safety pharmacology and the study of abiotic/biotic interfaces.

JTD Keywords: Array, Cells, Neuron-silicon junction, Voltage

A multiplexed microarray chip (Immuno-mu SARS2) aiming at providing information on the prognosis of the COVID-19 has been developed. The diagnostic technology records information related to the profile of the immunological response of patients infected by the SARS-CoV-2 virus. The diagnostic technology delivers information on the avidity of the sera against 28 different peptide epitopes and 7 proteins printed on a 25 mm2 area of a glass slide. The peptide epitopes (12-15 mer) derived from structural proteins (Spike and Nucleocapsid) have been rationally designed, synthesized, and used to develop Immuno-mu SARS2 as a multiplexed and high-throughput fluorescent microarray platform. The analysis of 755 human serum samples (321 from PCR+ patients; 288 from PCR- patients; 115 from prepandemic individuals and classified as hospitalized, admitted to intensive-care unit (ICU), and exitus) from three independent cohorts has shown that the chips perform with a 98% specificity and 91% sensitivity identifying RT-PCR+ patients. Computational analysis utilized to correlate the immunological signatures of the samples analyzed indicate significant prediction rates against exitus conditions with 82% accuracy, ICU admissions with 80% accuracy, and 73% accuracy over hospitalization requirement compared to asymptomatic patients' fingerprints. The miniaturized microarray chip allows simultaneous determination of 96 samples (24 samples/slide) in 90 min and requires only 10 mu L of sera. The diagnostic approach presented for the first time here could have a great value in assisting clinicians in decision-making based on the information provided by the Immuno-mu SARS2 regarding progression of the disease and could be easily implemented in diagnostics of other infectious diseases.

JTD Keywords: Antibodies, Clinical diagnostic, Diagnosis, High-throughput, Machine learning, Microarray, Multiplexation, Nucleocapsid protein, Peptide epitopes, Sars-cov-, Sars-cov-2, Serological signature, Seroprevalence, Severity prediction, Spik

The accurate spatial segregation into distinct phases within cell membranes coordinates vital biochemical processes and functionalities in living organisms. One of nature's strategies to localize reactivity is the formation of dynamic raft domains. Most raft models rely on liquid-ordered L-0 phases in a liquid-disordered L-d phase lacking correlation and remaining static, often necessitating external agents for phase separation. Here, we introduce a synthetic system of bicomponent glycodendrimersomes coassembled from Janus dendrimers and Janus glycodendrimers (JGDs), where lactose-lactose interactions exclusively drive lateral organization. This mechanism results in modulated phases across two length scales, yielding raft-like microdomains featuring nanoarrays at the nanoscale. By varying the density of lactose and molecular architecture of JGDs, the nanoarray type and size, shape, and spacing of the domains were controlled. Our findings offer insight into the potential primordial origins of rudimentary raft domains and highlight the crucial role of glycans within the glycocalyx.

JTD Keywords: Article, Artificial cells, Atomic force microscopy, Bicomponents, Bilayer, Bilayer membrane, Biochemical functionality, Biochemical process, Biological-membranes, Cell component, Cell membrane, Cellular parameters, Chemical interaction, Chemical structure, Chemistry, Cytology, Defined janus glycodendrimers, Dehydration, Dendrimer, Dendrimers, Dilution, Dimer, External agents, Fourier transform, Giant vesicles, Glycan, Glycans, Glycocalyx, Glycodendrimers, Janus dendrimer, Janus glycodendrimer, Lactose, Lateral organization, Lectin, Lipid rafts, Living organisms, Membrane damage, Membrane microdomain, Membrane microdomains, Membrane structure, Metabolism, Modulated phases, Molecule, Monomer, Nanoarrays, Oligosaccharide, Organization, Periodicity, Phase separation, Phase-separation, Phospholipids, Polysaccharide, Polysaccharides, Raft like domain, Relative humidity, Spatial segregation, Structure analysis, Sugars, Synthetic systems, Tetramer, Unclassified drug, Unilamellar vesicles, Water

In Alzheimer's disease, fibrillar tau pathology accumulates and spreads through the brain and synapses are lost. Evidence from mouse models indicates that tau spreads trans-synaptically from pre- to postsynapses and that oligomeric tau is synaptotoxic, but data on synaptic tau in human brain are scarce. Here we used sub-diffraction-limit microscopy to study synaptic tau accumulation in postmortem temporal and occipital cortices of human Alzheimer's and control donors. Oligomeric tau is present in pre- and postsynaptic terminals, even in areas without abundant fibrillar tau deposition. Furthermore, there is a higher proportion of oligomeric tau compared with phosphorylated or misfolded tau found at synaptic terminals. These data suggest that accumulation of oligomeric tau in synapses is an early event in pathogenesis and that tau pathology may progress through the brain via trans-synaptic spread in human disease. Thus, specifically reducing oligomeric tau at synapses may be a promising therapeutic strategy for Alzheimer's disease.Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.

JTD Keywords: accumulation, alpha-synuclein, array tomography, cognitive impairment, dendritic spines, mouse model, neurodegeneration, neurons, synapses, Alzheimer, Amyloid-beta, Synapse, Tau

Smoldering fires are characterized by the production of early gas emissions that can include high levels of CO and Volatile Organic Compounds (VOCs) due to pyrolysis or thermal degradation. Nowadays, standalone CO sensors, smoke detectors, or a combination of these, are standard components for fire alarm systems. While gas sensor arrays together with pattern recognition techniques are a valuable alternative for early fire detection, in practice they have certain drawbacks-they can detect early gas emissions, but can show low immunity to nuisances, and sensor time drift can render calibration models obsolete. In this work, we explore the performance of a gas sensor array for detecting smoldering and plastic fires while ensuring the rejection of a set of nuisances. We conducted variety of fire and nuisance experiments in a validated standard fire room (240 m(3)). Using PLS-DA and SVM, we evaluate the performance of different multivariate calibration models for this dataset. We show that calibration models remain predictive after several months, but perfect performance is not achieved. For example, 4 months after calibration, a PLS-DA model provides 100% specificity and 85% sensitivity since the system has difficulties in detecting plastic fires, whose signatures are close to nuisance scenarios. Nevertheless, our results show that systems based on gas sensor arrays are able to provide faster fire alarm response than conventional smoke-based fire alarms. We also propose the use of small-scale fire experiments to increase the number of calibration conditions at a reduced cost. Our results show that this is an effective way to increase the performance of the model, even when evaluated on a standard fire room. Finally, the acquired datasets are made publicly available to the community (doi: 10.5281/zenodo.5643074).

JTD Keywords: Calibration, Chemical sensors, Co2, Early fire, Early fire detection, En-54, Fire alarm, Fire detection, Fire room, Fires, Gas detectors, Gas emissions, Gas sensors, Pattern recognition, Public dataset, Sensor arrays, Sensors array, Signatures, Smoke, Smoke detector, Smoke detectors, Standard fire, Standard fire room, Support vector machines, Temperature, Toxicity, Volatile organic compounds

Tolerances in the fabrication of metal oxide (MOX) gas sensors lead to inter-device variability in baseline and sensitivity, even for sensors of the same fabrication batch. This has traditionally forced the use of individual calibration models (ICMs) built specifically for each sensor unit, which requires an expensive and time-consuming calibration process and hinders sensor replacement. We propose Global calibration models (GCMs) built using the responses of multiple sensor units, and then applied to a new sensor unit that is not part of the calibration set. GCM have been already successfully applied to transfer calibration models between sensor arrays (electronic noses) for classification tasks. In this work, we investigate the use of such models for regression purposes in temperature-modulated sensors, aiming at the quantification of low concentrations of carbon monoxide (CO) in the presence of variable humidity levels (20–80% r.h. at 26 ± 1 °C). Using a laboratory dataset containing data from 6 replicas of the FIS SB-500–12 model, we evaluate the performance of global models built with data from 1 to 4 sensors when applied to unseen sensor units. Results show that the performance of global models improves with an increasing number of sensors in the calibration set, approaching the performance of individual calibration models (1.38 ± 0.15 ppm for GCM; 1.05 ± 0.24 ppm for ICM), and surpassing their performance only if few calibration conditions per sensor are available (2.09 ± 0.10 ppm for GCM;; 2.76 ± 0.22 ppm for ICM, if only 5 samples per sensor are used).

JTD Keywords: design, recognition, Arrays

Quantification of odor emissions in wastewater treatment plants (WWTPs) is key to minimize odor impact to surrounding communities. Odor measurements in WWTPs are usually performed via either expensive and discontinuous olfactometry hydrogen sulfide detectors or via fixed electronic noses. We propose a portable lightweight electronic nose specially designed for real-time odor monitoring in WWTPs using small drones. The so-called RHINOS e-nose allows odor measurements with high spatial resolution, and its accuracy is only slightly worse than that of dynamic olfactometry. The device has been calibrated using odor samples collected in a WWTP in Spain over a period of six months and validated in the same WWTP three weeks after calibration. The promising results obtained support the suitability of the proposed instrument to identify the odor sources having the highest emissions, which may give a useful indication to the plant managers as regards odor control and abatement.© 2021 The Author(s).

JTD Keywords: biofiltration, calibration transfer, chemical sensor arrays, chemistry, drift compensation, engineering, environmental chemical engineering, h2s, model, oxide gas sensors, removal, sensor, system, Chemistry, Engineering, Environmental chemical engineering, Sensor, Sensor system, Variable selection methods

This paper describes the fabrication of microfluidic devices with a focus on controlling the orientation of photosystem I (PSI) complexes, which directly affects the performance of biophotovoltaic devices by maximizing the efficiency of the extraction of electron/hole pairs from the complexes. The surface chemistry of the electrode on which the complexes assemble plays a critical role in their orientation. We compared the degree of orientation on self-assembled monolayers of phenyl-C61-butyric acid and a custom peptide on nanostructured gold electrodes. Biophotovoltaic devices fabricated with the C61 fulleroid exhibit significantly improved performance and reproducibility compared to those utilizing the peptide, yielding a 1.6-fold increase in efficiency. In addition, the C61-based devices were more stable under continuous illumination. Our findings show that fulleroids, which are well-known acceptor materials in organic photovoltaic devices, facilitate the extraction of electrons from PSI complexes without sacrificing control over the orientation of the complexes, highlighting this combination of traditional organic semiconductors with biomolecules as a viable approach to coopting natural photosynthetic systems for use in solar cells.

JTD Keywords: architecture, arrays, construction, metal, nanotubes, performance, photosynthetic proteins, polymer-fullerene, solar-cells, Photocurrent generation

Membrane fission triggered by the endosomal sorting complex required for transport (ESCRT) is an important process observed in several pathogenic and non-pathogenic cellular events. From a synthetic-biology viewpoint, ESCRT proteins represent an interesting machinery for the construction of cell mimetic sub-compartments produced by fission. Since their discovery, the studies on ESCRT-III-mediated action, have mainly focused on protein dynamics, ignoring the role of lipid organization and membrane phase state. Recently, it has been suggested that membrane buds formed by the action of ESCRT-III are generated from transient microdomains in endosomal membranes. However, the interplay between membrane domain formation and ESCRT remodeling pathways has not been investigated. Here, giant unilamellar vesicles made of ternary lipid mixtures, either homogeneous in phase or exhibiting liquid-ordered/liquid-disordered phase coexistence, were employed as a model membrane system. These vesicles were incubated with purified recombinant ESCRT-III proteins from the parasite Entamoeba histolytica. In homogeneous membranes, we observe that EhVps32 can trigger domain formation while EhVps20 preferentially co-localizes in the liquid disordered phase. The addition of EhVps24 appears to induce the formation of intraluminal vesicles produced from the liquid-ordered phase. In phase separated membranes, the intraluminal vesicles are also generated from the liquid-ordered phase and presumably emerge from the phase boundary region. Our findings reinforce the hypothesis that ESCRT-mediated remodeling depends on the membrane phase state. Furthermore, the obtained results point to a potential synthetic biology approach for establishing eukaryotic mimics of artificial cells with microcompartments of specific membrane composition, which can also differ from that of the mother vesicle.

JTD Keywords: cell-membranes, coexistence, complex, escrt-iii, fission, guvs, lipid domains, lipid rafts, membrane fission, microcompartments, microscopy, phase separation, plasma-membrane, protein microarrays, structural basis, ternary mixtures, Escrt-iii, Giant unilamellar vesicles, Guvs, Lipid domains, Membrane fission, Microcompartments, Phase separation, Ternary mixtures

The human olfactory system remains one of the most challenging biological systems to replicate. Humans use it without thinking, where it can equally offer protection from harm and bring enjoyment in equal measure. It is the system’s ability to detect and analyze complex odors, without the need for specialized infra-structure, that is the envy of many scientists. The field of artificial olfaction has recruited and stimulated interdisciplinary research and commercial development for several applications that include malodor measurement, medical diagnostics, food and beverage quality, environment and security. Over the last century, innovative engineers and scientists have been focused on solving a range of problems associated with measurement and control of odor. The IEEE Sensors Journal has published Special Issues on olfaction in 2002 and 2012. Here we continue that coverage. In this article, we summarize early work in the 20th Century that served as the foundation upon which we have been building our odor-monitoring instrumental and measurement systems. We then examine the current state of the art that has been achieved over the last two decades as we have transitioned into the 21st Century. Much has been accomplished, but great progress is needed in sensor technology, system design, product manufacture and performance standards. In the final section, we predict levels of performance and ubiquitous applications that will be realized during in the mid to late 21st Century.

JTD Keywords: air-quality, breath analysis, calibration transfer, chemical sensor arrays, chemosensor arrays, drift compensation, electronic nose, gas sensors, headspace sampling, machine learning, machine olfaction, odor detection, plume structure, voc analysis, Artificial olfaction, Electrodes, Electronic nose, Electronic nose technology, Headspace sampling, Instruments, Machine learning, Machine olfaction, Monitoring, Odor detection, Olfactory, Sensor phenomena and characterization, Sensors, Temperature sensors, Voc analysis

Organ-on-a-chip (OOC) devices offer new approaches for metabolic disease modeling and drug discovery by providing biologically relevant models of tissues and organs in vitro with a high degree of control over experimental variables for high-content screening applications. Yet, to fully exploit the potential of these platforms, there is a need to interface them with integrated non-labeled sensing modules, capable of monitoring, in situ, their biochemical response to external stimuli, such as stress or drugs. In order to meet this need, we aim here to develop an integrated technology based on coupling a localized surface plasmon resonance (LSPR) sensing module to an OOC device to monitor the insulin in situ secretion in pancreatic islets, a key physiological event that is usually perturbed in metabolic diseases such as type 2 diabetes (T2D). As a proof of concept, we developed a biomimetic islet-on-a-chip (IOC) device composed of mouse pancreatic islets hosted in a cellulose-based scaffold as a novel approach. The IOC was interfaced with a state-of-the-art on-chip LSPR sensing platform to monitor the in situ insulin secretion. The developed platform offers a powerful tool to enable the in situ response study of microtissues to external stimuli for applications such as a drug-screening platform for human models, bypassing animal testing.

JTD Keywords: biosensor, cytoarchitecture, dna hybridization, gelatin, in situ insulin monitoring, langerhans, lspr sensors, microfluidic device, organ-on-a-chip, parallel, platform, scaffold, Animals, Biosensing techniques, Diabetes mellitus, type 2, Drug discovery, Drug evaluation, preclinical, Human pancreatic-islets, Humans, In situ insulin monitoring, Insulin secretion, Insulins, Lab-on-a-chip devices, Lspr sensors, Oligonucleotide array sequence analysis, Organ-on-a-chip, Surface plasmon resonance

Commercial printers based on fused deposition modeling (FDM) are widely adopted for 3D printing applications. This method consists of the heating of polymeric filaments over the melting point followed by their deposition onto a solid base to create the desirable 3D structure. Prior investigation using chromatographic techniques has shown that chemical compounds (e.g. VOCs), which can be harmful to users, are emitted during the printing process, producing adverse effects to human health and contributing to indoor air pollution. In this study, we present a simple, inexpensive and disposable paperbased optoelectronic nose (i.e. colorimetric sensor array) to identify the gaseous emission fingerprint of five different types of thermoplastic filaments (ABS, TPU, PETG, TRITAN and PLA) in the indoor environment. The optoelectronic nose is comprised of selected 15 dyes with different chemical properties deposited onto a microfluidic paper-based device with spots of 5 mm in diameter each. Digital images were obtained from an ordinary flatbed scanner, and the RGB information collected before and after air exposure was extracted by using an automated routine designed in MATLAB, in which the color changes provide a unique fingerprint for each filament in 5 min of printing. Reproducibility was obtained in the range of 2.5-10% (RSD). Hierarchical clustering analysis (HCA) and principal component analysis (PCA) were successfully employed, showing suitable discrimination of all studied filaments and the non-polluted air. Besides, air spiked with vapors of the most representative VOCs were analyzed by the optoelectronic nose and visually compared to each filament. The described study shows the potential of the paper-based optoelectronic nose to monitor possible hazard emissions from 3D printers. (C) 2020 Elsevier B.V. All rights reserved.

JTD Keywords: 3d printing, colorimetric sensor array, indoor air pollution, optoelectronic nose, paper-based, 3d printing, Colorimetric sensor array, Emissions, Indoor air pollution, Optoelectronic nose, Paper-based, Thermoplastic filaments

Goel and colleagues show that CDK4/6 inhibition induces global chromatin changes mediated by AP-1 factors, which mediate key biological and clinical effects in breast cancer. Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing cancer cell immunogenicity, apoptotic responses and differentiation. Using cell-based and mouse models of breast cancer together with clinical specimens, we show that CDK4/6 inhibitors induce remodeling of cancer cell chromatin characterized by widespread enhancer activation, and that this explains many of these effects. The newly activated enhancers include classical super-enhancers that drive luminal differentiation and apoptotic evasion, as well as a set of enhancers overlying endogenous retroviral elements that are enriched for proximity to interferon-driven genes. Mechanistically, CDK4/6 inhibition increases the level of several activator protein-1 transcription factor proteins, which are in turn implicated in the activity of many of the new enhancers. Our findings offer insights into CDK4/6 pathway biology and should inform the future development of CDK4/6 inhibitors.

JTD Keywords: Abemaciclib, Androgen receptor, Animal experiment, Animal model, Animal tissue, Apoptosis, Article, Breast cancer, C-jun, Cancer cell, Carcinoembryonic antigen related cell adhesion molecule 1, Caspase 3, Cell cycle arrest, Cells, Chromatin, Chromatin immunoprecipitation, Controlled study, Cyclin dependent kinase 4, Cyclin dependent kinase 6, Dna damage, Epidermal growth factor receptor 2, Estrogen receptor, Female, Flow cytometry, Fulvestrant, Hla drb1 antigen, Human, Human cell, Immunoblotting, Immunogenicity, Immunoprecipitation, Interferon, Luciferase assay, Mcf-7 cell line, Mda-mb-231 cell line, Microarray analysis, Morphogenesis, Mouse, Nonhuman, Palbociclib, Protein, Protein expression, Rb, Resistance, Rna polymerase ii, Rna sequence, Selective-inhibition, Senescence, Short tandem repeat, Signal transduction, Tamoxifen, Transcription elongation, Transcription factor, Transcription factor ap 1, Transcriptome, Tumor biopsy, Tumor differentiation, Tumor spheroid, Tumor xenograft, Vinculin, Whole exome sequencing

Inherent sensor variability limits mass-production applications for metal oxide (MOX) gas sensor arrays because calibration for replicas of a sensor array needs to be performed individually. Recently, calibration transfer strategies have been proposed to alleviate calibration costs of new replicas, but they still require the acquisition of transfer samples. In this work, we present calibration models that can be extended to uncalibrated replicas of sensor arrays without acquiring new samples, i.e., general or global calibration models. The developed methodology consists in including multiple replicas of a sensor array in the calibration process such that sensor variability is rejected by the general model. Our approach was tested using replicas of a MOX sensor array in the classification task of six gases and synthetic air, presented at different background humidity and concentration levels. Results showed that direct transfer of individual calibration models provides poor classification accuracy. However, we also found that general calibration models kept predictive performance when were applied directly to new copies of the sensor array. Moreover, we explored, through feature selection, whether particular combinations of sensors and operating temperatures can provide predictive performances equivalent to the calibration model with the complete array, favoring thereby the existence of more robust calibration models.

JTD Keywords: Gas sensor array, MOX sensor, Robust calibration, Calibration transfer, Machine olfaction

A methodology to calculate analytical figures of merit is not well established for detection systems that are based on sensor arrays with low sensor selectivity. In this work, we present a practical approach to estimate the Resolving Power of a sensory system, considering non-linear sensors and heteroscedastic sensor noise. We use the definition introduced by Shannon in the field of communication theory to quantify the number of symbols in a noisy environment, and its version adapted by Gardner and Barlett for chemical sensor systems. Our method combines dimensionality reduction and the use of algorithms to compute the convex hull of the empirical data to estimate the data volume in the sensor response space. We validate our methodology with synthetic data and with actual data captured with temperature-modulated MOX gas sensors. Unlike other methodologies, our method does not require the intrinsic dimensionality of the sensor response to be smaller than the dimensionality of the input space. Moreover, our method circumvents the problem to obtain the sensitivity matrix, which usually is not known. Hence, our method is able to successfully compute the Resolving Power of actual chemical sensor arrays. We provide a relevant figure of merit, and a methodology to calculate it, that was missing in the literature to benchmark broad-response gas sensor arrays.

JTD Keywords: Gas sensor array, MOX sensors, Resolving Power, Sensor resolution, Dimensionality reduction, Machine olfaction

Advances in analytical instrumentation have provided the possibility of examining thousands of genes, peptides, or metabolites in parallel. However, the cost and time-consuming data acquisition process causes a generalized lack of samples. From a data analysis perspective, omics data are characterized by high dimensionality and small sample counts. In many scenarios, the analytical aim is to differentiate between two different conditions or classes combining an analytical method plus a tailored qualitative predictive model using available examples collected in a dataset. For this purpose, partial least squares-discriminant analysis (PLS-DA) is frequently employed in omics research. Recently, there has been growing concern about the uncritical use of this method, since it is prone to overfitting and may aggravate problems of false discoveries. In many applications involving a small number of subjects or samples, predictive model performance estimation is only based on cross-validation (CV) results with a strong preference for reporting results using leave one out (LOO). The combination of PLS-DA for high dimensionality data and small sample conditions, together with a weak validation methodology is a recipe for unreliable estimations of model performance. In this work, we present a systematic study about the impact of the dataset size, the dimensionality, and the CV technique used on PLS-DA overoptimism when performance estimation is done in cross-validation. Firstly, by using synthetic data generated from a same probability distribution and with assigned random binary labels, we have obtained a dataset where the true classification rate (CR) is 50%. As expected, our results confirm that internal validation provides overoptimistic estimations of the classification accuracy (i.e., overfitting). We have characterized the CR estimator in terms of bias and variance depending on the internal CV technique used and sample to dimensionality ratio. In small sample conditions, due to the large bias and variance of the estimator, the occurrence of extremely good CRs is common. We have found that overfitting peaks when the sample size in the training subset approaches the feature vector dimensionality minus one. In these conditions, the models are neither under- or overdetermined with a unique solution. This effect is particularly intense for LOO and peaks higher in small sample conditions. Overoptimism is decreased beyond this point where the abundance of noisy produces a regularization effect leading to less complex models. In terms of overfitting, our study ranks CV methods as follows: Bootstrap produces the most accurate estimator of the CR, followed by bootstrapped Latin partitions, random subsampling, K-Fold, and finally, the very popular LOO provides the worst results. Simulation results are further confirmed in real datasets from mass spectrometry and microarrays.

JTD Keywords: Metabolomics, Mass spectrometry, Microarrays, Chemometrics, Data analysis, Classification, Method validation

Conventional fire alarms are based on smoke detection. Nevertheless, in some fire scenarios volatiles are released before smoke. Fire detectors based only on chemical sensors have already been proposed as they may provide faster response, but they are still prone to false alarms in the presence of nuisances. These systems rely heavily on pattern recognition techniques to discriminate fires from nuisances. In this context, it is important to test the systems according to international standards for fires and testing the system against a diversity of nuisances. In this work, we investigate the behavior of a gas sensor array coupled to sensor fusion algorithms for fire detection when exposed to standardized fires and several nuisances. Results confirmed the ability to detect fires (97% Sensitivity), although the system still produces a significant rate of false alarms (35%) for nuisances not presented in the training set.

JTD Keywords: Fire alarm, Gas sensor array, Machine Olfaction, Multisensor system, Sensor fusion

A novel suspended planar-array chips technology is described, which effectively allows molecular multiplexing using a single suspended chip to analyze extraordinarily small volumes. The suspended chips are fabricated by combining silicon-based technology and polymer-pen lithography, obtaining increased molecular pattern flexibility, and improving miniaturization and parallel production. The chip miniaturization is so dramatic that it permits the intracellular analysis of living cells.

JTD Keywords: Chip-in-a-cell, Suspended-arrays, Planar-arrays, Silicon chips, Single-cell analysis

Abstract Shifts in working temperature are an important issue that prevents the successful transfer of calibration models from one chemical instrument to another. This effect is of special relevance when working with gas sensor arrays modulated in temperature. In this paper, we study the use of multivariate techniques to transfer the calibration model from a temperature modulated gas sensor array to another when a global change of temperature occurs. To do so, we built 12 identical master sensor arrays composed of three different types of commercial Figaro sensors and acquired a dataset of sensor responses to three pure substances (ethanol, acetone and butanone) dosed at 7 concentrations. The master arrays are then shifted in temperature (from −50 to 50 °C, ΔT = 10 °C) and considered as slave arrays. Data correction is performed for an increasing number of transfer samples with 4 different calibration transfer techniques: Direct Standardization, Piece-wise Direct Standardization, Orthogonal Signal Correction and Generalized Least Squares Weighting. In order to evaluate the performance of the calibration transfer, we compare the Root Mean Square Error of Prediction (RMSEP) of master and slave arrays, for each instrument correction. Best results are obtained from Piece-wise Direct standardization, which exhibits the lower RMSEP values after correction for the smaller number of transfer samples.

JTD Keywords: Calibration transfer, Gas sensor array, MOX, Temperature modulation

A simple method for constructing versatile ordered biotin/avidin arrays on UV-curable perfluoropolyethers (PFPEs) is presented. The goal is the realization of a versatile platform where any biotinylated biological ligands can be further linked to the underlying biotin/avidin array. To this end, microcontact arrayer and microcontact printing technologies were developed for photobiotin direct printing on PFPEs. As attested by fluorescence images, we demonstrate that this photoactive form of biotin is capable of grafting onto PFPEs surfaces during irradiation. Bioaffinity conjugation of the biotin/avidin system was subsequently exploited for further self-assembly avidin family proteins onto photobiotin arrays. The excellent fouling release PFPEs surface properties enable performing avidin assembly step simply by arrays incubation without PFPEs surface passivation or chemical modification to avoid unspecific biomolecule adsorption. Finally, as a proof of principle biotinylated heparin was successfully grafted onto photobiotin/avidin arrays.

JTD Keywords: Antifouling, Heparin, Malaria, Microcontact arrayer, Microcontact printing, Micropatterning, Perfluoropolyether, Photobiotin, Polymers, Soft lithography

Here we describe the design and evaluation of a fluidic device for the automatic processing of microarrays, called microarray processing station or MPS. The microarray processing station once installed on a commercial microarrayer allows automating the washing, and drying steps, which are often performed manually. The substrate where the assay occurs remains on place during the microarray printing, incubation and processing steps, therefore the addressing of nL volumes of the distinct immunoassay reagents such as capture and detection antibodies and samples can be performed on the same coordinate of the substrate with a perfect alignment without requiring any additional mechanical or optical re-alignment methods. This allows the performance of independent immunoassays in a single microarray spot.

JTD Keywords: Automation, Customization, High-throughput screening, Immunoassays, Microarrays

Abstract Recent studies in neuroscience suggest that sniffing, namely sampling odors actively, plays an important role in olfactory system, especially in certain scenarios such as novel odorant detection. While the computational advantages of high frequency sampling have not been yet elucidated, here, in order to motivate further investigation in active sampling strategies, we share the data from an artificial olfactory system made of 16 MOX gas sensors under gas flow modulation. The data were acquired on a custom set up featured by an external mechanical ventilator that emulates the biological respiration cycle. 58 samples were recorded in response to a relatively broad set of 12 gas classes, defined from different binary mixtures of acetone and ethanol in air. The acquired time series show two dominant frequency bands: the low-frequency signal corresponds to a conventional response curve of a sensor in response to a gas pulse, and the high-frequency signal has a clear principal harmonic at the respiration frequency. The data are related to the study in [1], and the data analysis results reported there should be considered as a reference point.

JTD Keywords: Gas sensor array, MOX sensor, Flow modulation, Early detection, Biomimetics, Respiration, Sniffing

Abstract The design of bioinspired systems for chemical sensing is an engaging line of research in machine olfaction. Developments in this line could increase the lifetime and sensitivity of artificial chemo-sensory systems. Such approach is based on the sensory systems known in live organisms, and the resulting developed artificial systems are targeted to reproduce the biological mechanisms to some extent. Sniffing behaviour, sampling odours actively, has been studied recently in neuroscience, and it has been suggested that the respiration frequency is an important parameter of the olfactory system, since the odour perception, especially in complex scenarios such as novel odourants exploration, depends on both the stimulus identity and the sampling method. In this work we propose a chemical sensing system based on an array of 16 metal-oxide gas sensors that we combined with an external mechanical ventilator to simulate the biological respiration cycle. The tested gas classes formed a relatively broad combination of two analytes, acetone and ethanol, in binary mixtures. Two sets of low-frequency and high-frequency features were extracted from the acquired signals to show that the high-frequency features contain information related to the gas class. In addition, such information is available at early stages of the measurement, which could make the technique suitable in early detection scenarios. The full data set is made publicly available to the community.11 http://archive.ics.uci.edu/ml/datasets/Gas+sensor+array+under+flow+modulation.

JTD Keywords: Gas sensor array, MOX sensor, Flow modulation, Early detection, Biomimetics, Sniffing

Abstract In this paper we study the role of redundant sensory information to prevent the performance degradation of a chemical sensor array for different distributions of sensor failures across sensor types. The large amount of sensing conditions with two different types of redundancy provided by our sensor array makes possible a comprehensive experimental study. Particularly, our sensor array is composed of 8 different types of commercial MOX sensors modulated in temperature with two redundancy levels: (1) 12 replicates of each sensor type for a total of 96 sensors and (2) measurements using 16 load resistors per sensors for a total of 1536 redundant measures per second. We perform two experiments to determine the performance degradation of the array with increasing number of damaged sensors in two different scenarios of sensor faults distributions across sensor types. In the first experiment, we characterize the diversity and redundancy of the array for increasing number of damaged sensors. To measure diversity and redundancy, we proposed a functional definition based on clustering of sensor features. The second experiment is devoted to determine the performance degradation of the array for the effect of faulty sensors. To this end, the system is trained to separate ethanol, acetone and butanone at different concentrations using a PCA–LDA model. Test set samples are corrupted by means of three different simulated types of faults. To evaluate the performance of the array we used the Fisher score as a measure of odour separability. Our results show that to exploit to the utmost the redundancy of the sensor array faulty sensory units have to be distributed uniformly across the different sensor types.

JTD Keywords: Gas sensor arrays, Sensor redundancy, Sensor diversity, Sensor faults aging, Sensor damage, MOX sensors, Large sensor arrays

Over the last two decades, electronic nose research has produced thousands of research works. Many of them were describing the ability of the e-nose technology to solve diverse applications in domains ranging from food technology to safety, security, or health. It is, in fact, in the biomedical field where e-nose technology is finding a research niche in the last years. Although few success stories exist, most described applications never found the road to industrial or clinical exploitation. Most described methodologies were not reliable and were plagued by numerous problems that prevented practical application beyond the lab. This work emphasizes the need of external validation in machine olfaction. I describe some statistical and methodological pitfalls of the e-nose practice and I give some best practice recommendations for researchers in the field.

JTD Keywords: Chemical sensor arrays, Pattern recognition, Chemometrics, Electronic noses, Robustness, Signal and data processing

Abstract In this paper we study the role of redundant sensory information to prevent the performance degradation of a chemical sensor array as the number of faulty sensors increases. The large amount of sensing conditions with two different types of redundancy provided by our sensor array makes possible a comprehensive experimental study. Particularly, our sensor array is composed of 8 different types of commercial MOX sensors modulated in temperature with two redundancy levels: 1) 12 replicates of each sensor type for a total of 96 sensors, and 2) measurements using 16 load resistors per sensors for a total of 1536 redundant measures per second. The system is trained to identify ethanol, acetone and butanone using a PCA-LDA model. Test set samples are corrupted by means of three different simulated types of faults. To evaluate the tolerance of the array against sensor failure, the Fisher Score is used as a figure of merit for the corrupted test set samples projected on the PCA-LDA model.

JTD Keywords: Gas ensor arrays, sensor redundancy, MOX sensors, large sensor arrays.

The prion protein (PrP) plays a key role in prion disease pathogenesis. Although the misfolded and pathologic variant of this protein (PrPSC) has been studied in depth, the physiological role of PrPC remains elusive and controversial. PrPC is a cell-surface glycoprotein involved in multiple cellular functions at the plasma membrane, where it interacts with a myriad of partners and regulates several intracellular signal transduction cascades. However, little is known about the gene expression changes modulated by PrPC in animals and in cellular models. In this article, we present PrPC-dependent gene expression signature in N2a cells and its implication in the most overrepresented functions: cell cycle, cell growth and proliferation, and maintenance of cell shape. PrPC over-expression enhances cell proliferation and cell cycle re-entrance after serum stimulation, while PrPC silencing slows down cell cycle progression. In addition, MAP kinase and protein kinase B (AKT) pathway activation are under the regulation of PrPC in asynchronous cells and following mitogenic stimulation. These effects are due in part to the modulation of epidermal growth factor receptor (EGFR) by PrPC in the plasma membrane, where the two proteins interact in a multimeric complex. We also describe how PrPC over-expression modulates filopodia formation by Rho GTPase regulation mainly in an AKT-Cdc42-N-WASP-dependent pathway.

JTD Keywords: Cell signaling, Cellular prion protein, Filopodia, Gene expression, Microarray, Proliferation

This manuscript introduces a software tool that allows for the design of synthetic experiments in machine olfaction. The proposed software package includes both, a virtual sensor array that reproduces the diversity and response of a polymer array and tools for data generation. The synthetic array of sensors allows for the generation of chemosensor data with a variety of characteristics: unlimited number of sensors, support of multicomponent gas mixtures and full parametric control of the noise in the system. The artificial sensor array is inspired from a reference database of seventeen polymeric sensors with concentration profiles for three analytes. The main features in the sensor data, like sensitivity, diversity, drift and sensor noise, are captured by a set of models under simplified assumptions. The generator of sensor signals can be used in applications related to test and benchmarking of signal processing methods, neuromorphic simulations in machine olfaction and educational tools. The software is implemented in R language and can be freely accessed.

JTD Keywords: Gas Sensor Array, Conducting Polymers, Electronic Nose, Sensor Simulation, Synthetic Dataset, Benchmark, Educational Tool

The sensitivity and selectivity of metal oxide (MOX) gas sensors change significantly when the sensors operate at different temperatures. While previous investigations have presented systematic approaches to optimize the operating temperature of a single MOX sensor, in this paper we present a methodology to select the optimal operating temperature of all the MOX sensors constituent of a gas sensor array based on the multivariate response of all the sensing elements. Our approach estimates a widely used Information Theory measure, the so-called Mutual Information (MI), which quantifies the amount of information that the state of one random variable (response of the gas sensor array) can provide from the state of another random variable representing the gas quality. More specifically, our methodology builds sensor models from experimental data to solve the technical problem of populating the joint probability distribution for the MI estimation. We demonstrate the relevance of our approach by maximizing the MI and selecting the best operating temperatures of a four-sensor array sampled at 94 different temperatures to optimize the discrimination task of ethanol, acetic acid, 2-butanone, and acetone. In addition to being applicable in principle to sensor arrays of any size, our approach gives precise information on the ability of the system to discriminate odors according to the temperature of the MOX sensors, for either the optimal set of temperatures or the temperatures that may render inefficient operation of the system itself.

JTD Keywords: MOX gas sensor, Temperature optimization, Limit of detection, Mutual Information, E-nose, Sensor array, Information Theory, Chemical sensing

We propose the use of multi-way methods to analyze the contribution of diversity and redundancy to odor identification and concentration estimation in a large chemical sensor array. We use a chemical sensing system based on a large array of metal oxide sensors (MOX) and inspired on the diversity and redundancy of the olfactory epithelium. In order to analyze the role of diversity (different sensor type and temperature modulation) and redundancy (replicates of sensors and different load resistors) in odor quantification and discrimination tasks, we have acquired two datasets and modeled the data using multi-way techniques.

JTD Keywords: Artificial Olfaction, Large array, MOX gas sensor, Multi-way methods

Signal and data processing are essential elements in electronic noses as well as in most chemical sensing instruments. The multivariate responses obtained by chemical sensor arrays require signal and data processing to carry out the fundamental tasks of odor identification (classification), concentration estimation (regression), and grouping of similar odors (clustering). In the last decade, important advances have shown that proper processing can improve the robustness of the instruments against diverse perturbations, namely, environmental variables, background changes, drift, etc. This article reviews the advances made in recent years in signal and data processing for machine olfaction and chemical sensing.

JTD Keywords: Chemical sensors, Electronic nose, Intelligent sensors, Measurement techniques, Sensor arrays, Sensor systems

Background: Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer. Results: By applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions. Conclusions: We propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing) can be used to generate more reliable datasets. This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.

JTD Keywords: Gene-expression measurements, Quality-control maqc, Cancer-cell-lines, Real-time pcr, Oligonucleotide microarrays, Phosphorylation dynamics, In-vivo, Networks, Signal, Technologies

Cellular microarray developments and its applications are the next step after DNA and protein microarrays. The choice of the surface chemistry of the substrates used for the implementation of this technique, that must favor proper protein immobilization while avoiding cell adhesion on the nonspotted areas, presents a complex challenge. This is a key issue since usually the best nonfouling surfaces are also the ones that retain immobilized the smallest amounts of printed protein. To quantitatively assess the amount of protein immobilization, in this study several combinations of fluorescently labeled fibronectin (Fn*) and streptavidin (SA*) were microspotted, with and without glycerol addition in the printing buffer, on several substrates suitable for cellular microarrays. The substrates assayed included chemically activated surfaces as well as Poly ethylene oxide (PEO) films that are nonfouling in solution but accept adhesion of proteins in dry conditions. The results showed that the spotted Fn* was retained by all the surfaces, although the PEO surface did show smaller amounts of immobilization. The SA*, on the other hand, was only retained by the chemically activated surfaces. The inclusion of glycerol in the printing buffer significantly reduced the immobilization of both proteins. The results presented in this article provide quantitative evidence of the convenience of using a chemically activated surface to immobilize proteins relevant for cellular microarray applications, particularly when ECM proteins are cospotted with smaller factors which are more difficult to be retained by the surfaces.

JTD Keywords: Protein immobilization, Quantification, Microarray, Substrate, Surface chemistry

A new drift compensation method based on Common Principal Component Analysis (CPCA) is proposed. The drift variance in data is found as the principal components computed by CPCA. This method finds components that are common for all gasses in feature space. The method is compared in classification task with respect to the other approaches published where the drift direction is estimated through a Principal Component Analysis (PCA) of a reference gas. The proposed new method - employing no specific reference gas, but information from all gases -has shown the same performance as the traditional approach with the best-fitted reference gas. Results are shown with data lasting 7-months including three gases at different concentrations for an array of 17 polymeric sensors.

JTD Keywords: Gas sensor array, Drift, Common principal component, Analysis, Component correction, Electronic nose

Drift is an important issue that impairs the reliability of gas sensing systems. Sensor aging, memory effects and environmental disturbances produce shifts in sensor responses that make initial statistical models for gas or odor recognition useless after a relatively short period (typically few weeks). Frequent recalibrations are needed to preserve system accuracy. However, when recalibrations involve numerous samples they become expensive and laborious. An interesting and lower cost alternative is drift counteraction by signal processing techniques. Orthogonal Signal Correction (OSC) is proposed for drift compensation in chemical sensor arrays. The performance of OSC is also compared with Component Correction (CC). A simple classification algorithm has been employed for assessing the performance of the algorithms on a dataset composed by measurements of three analytes using an array of seventeen conductive polymer gas sensors over a ten month period.

JTD Keywords: Gas sensor array, Drift, Orthogonal signal correction, Component correction, Cross-validation, Electronic nose, Data shift

This paper presents a chemical sensing system that takes inspiration from the combination of sensory diversity and redundancy at the olfactory epithelium to enhance the chemical information obtained from the odorants. The system is based on commercial MOS sensors and achieves, first, diversity trough different types of MOS along with modulation of their temperatures, and second redundancy including 12 MOS sensors for each type (12×8) combined with a high-speed multiplexing system that allows connecting 16 load resistors with each and every one of the 96 sensors in about two seconds. Exposition of the system to ethanol, ammonia, and acetone at different concentrations shows how the system is able to capture a large amount of information of the identity and the concentration of the odorant.

JTD Keywords: Gas sensor array, Biologically inspired system, Redundancy, Diversity, MOX sensors, Temperature modulation

In this work, we report the detection of proteins by means of simultaneous fluorescence and impedance measurements in a cyclo olefin polymer (COP) chip containing an ordered pillar array column, used for reversed-phase liquid chromatography, with integrated microband gold electrodes at the end of the channel.

JTD Keywords: Cyclo olefin polymer, Gold microelectrodes, Impedance, Pillar array, Protein detection

We report a new strategy for immunochemical screening of small organic molecules based on the use of a hapten microarray. Using DNA-directed immobilization strategies, we have been able to convert a DNA chip into a hapten microarray by taking advantage of all the benefits of the structural and electrostatic homogeneous properties of DNA. The hapten microarray uses hapten-oligonucleotide probes instead of proteins, avoiding the limitations of preparing stochiometrically-defined protein-oligonucleotide bioconjugates. As proof of concept, we show here the development of a microarray for analysis of anabolic androgenic steroids. The microchip is able to detect several illegal substances with sufficient detectability to be used as a screening method, according to the regulations of the World Anti-Doping Agency for sport and the European Commision for food safety. The results that we show corroborate the universal possibilities of the DNA chip, and, in this case, they open the way to develop hapten microarrays for the immunochemical analysis of small organic molecules.

JTD Keywords: Anti-doping, DNA chip, DNA-directed immobilization (DDI), Fluorescence, Food safety, Hapten microarray, Immunochemical screening, Proof of concept, Small organic molecule, Steroid

This work describes our studies on the molecular design of interfacial architectures suitable for DNA sensing which could resist non-specific binding of nanomaterials commonly used as labels for amplifying biorecognition events. We observed that the non-specific binding of bio-nanomaterials to surface-confined oligonucleotide strands is highly dependent on the characteristics of the interfacial architecture. Thiolated double stranded oligonucleotide arrays assembled on Au surfaces evidence significant fouling in the presence of nanoparticles (NPs) at the nanomolar level. The non-specific interaction between the oligonucleotide strands and the nanomaterials can be sensitively minimized by introducing streptavidin (SAv) as an underlayer conjugated to the DNA arrays. The role of the SAv layer was attributed to the significant hydrophilic repulsion between the SAv-modified surface and the nanomaterials in close proximity to the interface, thus conferring outstanding anti-fouling characteristics to the interfacial architecture. These results provide a simple and straightforward strategy to overcome the limitations introduced by the non-specific binding of labels to achieve reliable detection of DNA-based biorecognition events.

JTD Keywords: DNA/ analysis, Gold, Nanostructures/ chemistry, Oligonucleotide Array Sequence Analysis/ instrumentation, Oligonucleotides/ chemistry, Streptavidin/ chemistry, Sulfhydryl Compounds

Lately there has been an increasing interest in the development of tools that enable the high throughput analysis of combinations of surface-immobilized signaling factors and which examine their effect on stem cell biology and differentiation. These surface-immobilized factors function as artificial microenvironments that can be ordered in a microarray format. These microarrays could be useful for applications such as the study of stem cell biology to get a deeper understanding of their differentiation process. Here, the evaluation of several key process parameters affecting the cellular microarray fabrication is reported in terms of its effects on the mesenchymal stem cell culture time on these microarrays. Substrate and protein solution requirements, passivation strategies and cell culture conditions are investigated. The results described in this article serve as a basis for the future development of cellular microarrays aiming to provide a deeper understanding of the stem cell differentiation process.

JTD Keywords: Bone-marrow, Protein microarrays, Progenitor cells, Differentiation, Surfaces, Growth, Biomaterials, Commitment, Pathways, Culture media

A first step towards the multidetection of anabolic androgenic steroids by Enzyme-linked immunosorbent assays (ELISA) has been performed in this study. This proposal combines an array of classical ELISA assays with different selectivities and multivariate data analysis techniques. Data has been analyzed by principal component analysis in conjunction with a k-nearest line classifier has been used. This proposal allows to detect simultaneously four different compounds in the range of concentration from 10(-1.5) to 10(3) mM with a total rate of 90.6% of correct detection.

JTD Keywords: Immunoarray, Anabolic androgenic steroid, Multidetection, Pattern recognition, K-nearlest line

Novel medical and biological applications are driving increased interest in the fabrication of micropipette or micro-dispensers. Reduced volume samples and drug dosages are prime motivators in this effort. We have combined microfabrication technology with ion beam milling techniques to successfully produce cantilever-type polysilicon micro-dispensers with 3D enclosed microchannels. The microfabrication technology described here allows for the designing of nozzles with multiple shapes. The contribution of ion beam milling has had a large impact on the fabrication process and on further customizing shapes of nozzles and inlet ports. Functionalization tests were conducted to prove the viability of ion beam-fabricated micro-dispensers. Self-assembled monolayers were successfully formed when a gold surface was patterned with a thiol solution dispensed by the fabricated micro-dispensers.

JTD Keywords: Dip-pen nanolithography, Silicon, Deposition, Microneedles, Delivery, Arrays, Polysilicon, Capillary, Systems, Gene