Analysis of Medication Off-odors Using an Electronic Nose

Packaging materials have been implicated as a source for off-odorsin pharmaceutical products. A new instrumentation method employingan array of conducting polymer gas sensors was used to identifythe offending packaging components in the canister of a pharmaceuticalinhalant. A case study is described in which tainted inhalersas well as elastomeric components of the canisters were ‘sniffed’by the electronic nose. The electronic nose was able to differentiatebetween tainted and untainted canisters. Signal processing algorithmsperformed on the raw data from the sensors suggested that specificelastomeric components were responsible for the off-odor. Afurther experiment suggested that the propellant (Freon) extractedthe odor from the elastomeric components as the medication wasexpelled from the canister. These data indicate that the electronicnose is a potential tool to solve odor problems in which humanodor assessment is not feasible due to excess exposure to themedically active ingredient. Chem. Senses 22: 119–128,1997.     

A separation-free amperometric immunosensor for vitellogenin based on screen-printed carbon arrays modified with a conductive polymer

A disposable amperometric immunosensor was studied for the rapid detection of carp (Carassius auratus) Vitellogenin (Vtg). The sensor was fabricated based on screen-printed carbon arrays (SPCAs) containing eight carbon working and an integrated carbon counter electrodes. To construct the sensor, a conducting polymer (poly-terthiophene carboxylic acid) was electropolymerized on the surface of working electrodes and the polymer-coated SPCAs was characterized by SEM. Horseradish peroxidase (HRP) and a monoclonal antibody (anti-Vtg) specific to carp Vtg were covalently attached onto the polymer modified SPCAs. The immobilization of HRP and anti-Vtg onto the polymer-coated SPCAs was examined using cyclic voltammetry and quartz crystal microbalance studies. In order to detect the amount of Vtg, glucose oxidase (GOx)-labelled Vtg bound to the sensor surface under competition with the Vtg analyte was quantified amperometrically using glucose as a substrate. The performance of the eight sensors in arrays was evaluated by obtaining the calibration plots for Vtg. The sensor arrays exhibit a linear range of the Vtg concentration from 0.25 to 7.8 ng/ml and the detection limit was determined to be 0.09 ng/ml. Furthermore, the performance of the immunosensor for the determination of Vtg was evaluated by a standard addition method performed in fish serum samples.     

Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays

Motivation: High-density DNA microarrays provide us with usefultools for analyzing DNA and RNA comprehensively. However, thebackground signal caused by the non-specific binding (NSB) betweenprobe and target makes it difficult to obtain accurate measurements.To remove the background signal, there is a set of backgroundprobes on Affymetrix Exon arrays to represent the amount ofnon-specific signals, and an accurate estimation of non-specificsignals using these background probes is desirable for improvementof microarray analyses. Results: We developed a thermodynamic model of NSB on shortnucleotide microarrays in which the NSBs are modeled by duplexformation of probes and multiple hypothetical targets. We fittedthe observed signal intensities of the background probes withthose expected by the model to obtain the model parameters.As a result, we found that the presented model can improve theaccuracy of prediction of non-specific signals in comparisonwith previously proposed methods. This result will provide auseful method to correct for the background signal in oligonucleotidemicroarray analysis. Availability: The software is implemented in the R languageand can be downloaded from our website (http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/MSNS/). Contact: furusawa{at}ist.osaka-u.ac.jp Supplementary information: Supplementary data are availableat Bioinformatics online. The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. Associate Editor: Trey Ideker     

Enzymatically and combinatorially generated array-based polyphenol metal ion sensor

Phenolic polymers were synthesized via soybean hull peroxidase catalysis and used as metal-based sensor components in a polymer array. A sensor array for Fe(3+), Cu(2+), Co(2+), and Ni(2+) has been developed consisting of 15 phenolic homopolymers and copolymers generated from five phenolic monomers by peroxidase-catalyzed oxidative polymerization. Sensing was based on the change of intrinsic polyphenol fluorescence upon addition of a metal ion or a metal ion mixture to an aqueous suspension of a polyphenol. Importantly, the fluorescence response of copolymers differed, in some cases dramatically, from the constituent homopolymers and was dependent upon the relative ratio of monomers that comprise the polymer. This finding suggests that an extremely broad range of sensor arrays can be generated from a limited number of phenolic monomers. Using a statistical analysis, histograms constructed for the four different metal ions yielded unique fingerprints of the array response and can be used to identify specific metal ions.     

Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome

Motivation: Quick and easy gene mapping by the use of a panelof cytogenetically characterized somatic cell hybrids is possible,even if some discordant experimental results arise. Results: An interactive program is proposed and is made availableon a WWW site to users of a somatic cell hybrid panel. Assignmentsto chromosomes and subchromosomal regions are based on likelihoodcalculations and Bayes' theorem, and a confidence level is provided.The method is illustrated in the case of the pig genome. Availability: The program can be accessed free of charge atURL http:/ /www. toulouse. inra.fr/lgc/lgc.html. Contact: E-mail: chevalet{at}toulouse.inra.fr     

Mitigation of Heavy Metal Contamination in Soil via Successive Pig Slurry Application

This study evaluates heavy metal removal associated with phytomass management in a Typic Hapludox after three applications of pig slurry. Like humic acids in pig slurry were characterized through physics and chemical spectroscopy technics. Heavy metal levels were determined in ration that was offered to pigs, anaerobically digested pig slurry, and plant tissues from pig slurry-fertilized black oat (Avena strigosa Schreb.) and ryegrass (Lolium multiflorum Lam.) intercrop. Soil contamination was evaluated by the pseudo-total heavy metal levels in six soil layers and the bioavailable levels in the top soil layer. Results indicate that the ration is the origin of heavy metals in the pig slurry. The approximate levels in the ration were as follows (mg kg^?1): Cu 23.9, Zn 92.02, 153.15, Mn 30.98, Ni 0.23, Pb 10.75, Cr 0.34, Co 0.08, and Cd 0.05. The approximate levels of these metals in the pig slurry were as follows (mg kg^?1): Cu 71.08, Zn 345.67, Fe 83.02, Mn 81.71, Ni 1.13, Pb 4.35, Co 0.28, and Cd 0.16. Like humic acids contained 55% aliphatic chains, 14% oxygenated aliphatic chains, and 15% carboxyls, demonstrating their high capacity for interaction with heavy metals by forming soluble complexes. Soil contamination was indicated by the accumulation of heavy metals in the six soil layers in relation to the applied pig slurry dose (ranged as follows (mg kg^?1): Cu 110 to 150, Zn 50 to 120, Ni 20 to 40, and Pb 12 to 16) and as bioavailable forms (levels ranged as follows (mg kg^?1): Cu < 1, Zn 1.0–1.5, Ni 0.1–1.5, and Pb 1.9–6.3). The positive correlation between heavy metal accumulation in the plants and soil bioavailable heavy metal levels and the lowest heavy metal levels under higher intensity of phytomass removal demonstrate the ability of phytomass management to reduce soil contamination.     

Electrochemical analysis of copper ion using a Gly–Gly–His tripeptide modified poly(3-thiopheneacetic acid) biosensor

A novel biosensor harnessing a conducting polymer functionalized with a copper ion specific peptide proved to be highly effective for electrochemical analysis of copper ions. The developed sensor comprised a transducer based on a conducting polymer (poly(3-thiopheneacetic acid)) electrode and a probe (tripeptide, Gly–Gly–His) selectively cognitive of copper ions. For functionalization of the electrode, the carboxylic group of the polymer was covalently coupled with the amine group of the tripeptide, and its structural features were confirmed by X-ray photoelectron spectroscopy (XPS) and attenuated total reflection infrared (ATR-IR) spectroscopy. The peptide modified polythiophene biosensor was used for the electrochemical analysis of various trace metal ions by square wave voltammetry. The electrode was found to be highly sensitive and selective to Cu²⁺ in the range of 0.02–20 μM with almost no cross binding to other metal ions such as Ni²⁺ and Pb²⁺. Furthermore, the developed sensor exhibited a high stability and reproducibility despite the repeated use of the sensor electrode and probe. With the advent of more diverse affinity bioprobes specific towards a broad range of analytes, the demonstrated strategy harnessing peptide modified polythiophene biosensor is likely to provide an excellent platform for the selective determination of trace amount of analytes whose detection is otherwise cumbersome.     

Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry

The bacterial community assembly patterns and processes are poorly understood in pig manure slurry. We collected pig manure slurry samples during the winter and summer seasons from eight commercial pig farms in South Korea. The V3 region of 16S rRNA genes was PCR amplified and sequenced using paired-end Illumina technology for in-depth characterization of bacterial community. Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Tenericutes were the predominant bacterial phyla present in slurry samples. Bacterial taxonomic community composition was not influenced by the season; however, phylogenetic community composition was affected by seasonal variations. The community composition and diversity patterns were strongly influenced by pH. The bacterial diversity indices showed a unimodal relationship with pH. Phylogenetic signals were detected over only short phylogenetic distances, revealing that closely related bacterial operational taxonomic units (OTUs) tend to co-occur in the same environment; hence, they are ecologically similar. Across all samples, a niche-based process, through strong environmental filtering imposed by pH, primarily governed bacterial community assembly; however, in samples close to the neutral pH range, the role of environmental filtering was decreased due to neutral community assembly. In summary, pH emerged as the major physico-chemical variable in pig manure slurry that regulates the relative importance of niche-based and neutral processes in shaping the community assembly of bacteria.     

Conditional random pattern algorithm for LOH inference and segmentation

Motivation: Loss of heterozygosity (LOH) is one of the mostimportant mechanisms in the tumor evolution. LOH can be detectedfrom the genotypes of the tumor samples with or without pairednormal samples. In paired sample cases, LOH detection for informativesingle nucleotide polymorphisms (SNPs) is straightforward ifthere is no genotyping error. But genotyping errors are alwaysunavoidable, and there are about 70% non-informative SNPs whoseLOH status can only be inferred from the neighboring informativeSNPs. Results: This article presents a novel LOH inference and segmentationalgorithm based on the conditional random pattern (CRP) model.The new model explicitly considers the distance between twoneighboring SNPs, as well as the genotyping error rate and theheterozygous rate. This new method is tested on the simulatedand real data of the Affymetrix Human Mapping 500K SNP arrays.The experimental results show that the CRP method outperformsthe conventional methods based on the hidden Markov model (HMM). Availability: Software is available upon request. Contact: xzhou{at}tmhs.org Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Alex Bateman     

Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management

The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.     

Prevalence and Identity of Cryptosporidium spp. in Pig Slurry

Cryptosporidium spp. were detected in 25 of 56 pig slurry samples from 33 Irish farms by PCR and DNA sequencing. The organisms detected included C. suis, Cryptosporidium pig genotype II, and C. muris. We concluded that Cryptosporidium oocysts can persist in treated slurry and potentially contaminate surface water through improper discharge or uncontrolled runoff.     

DNA hybridization electrochemical sensor using conducting polymer

We report the use of poly(thiophen-3-yl-acetic acid 1,3-dioxo-1,3-dihydro-isoindol-2-yl ester (PTAE) for application to electrochemical hybridization sensor. A synthetic route for the thiophen-3-yl-acetic acid 1,3-dioxo-1,3-dihydro-isoindol-2-yl ester (TAE) is described, which is used as a monomer of conducting polymer sensor. A direct chemical substitution of probe oligonucleotide to good leaving group site in the PTAE is carried out on the conducting polymer film. A biological recognition can be monitored by comparison with the electrochemical signal (cyclic voltammogram) of single and double strand state oligonucleotide. The sensitivity of the electrochemical sensor is 0.62 microA/nmole and the detection limit is 1 nmole. The oxidation current of double strand state oligonucleotide is a half of that of single strand, that is corresponding to the decrease of electrochemical activity of conducting polymer with increase of stiffness of side group of the polymer. The oxidation current decreasing ratios of perfect matched and single nucleotide mismatched samples are 52 and 25-30%, respectively. The more decreasing ratio is attributable to the more steric hindrance of single nucleotide mismatched sample.     

Microbial activity in pig slurry-amended soils under aerobic incubation

A 120-day aerobic incubation experiment was conducted to study the effects of pig slurry application on soil microbial activity. Pig slurry was added to soil at rates of 0 (control treatment), 150 and 300 m³ ha⁻¹. Soil samples were taken after 0, 7, 14, 30, 45, 60, and 120 days of incubation and analyzed for total organic C and microbial biomass C contents, and basal respiration. Most of the organic C applied to soil with pig slurry was readily decomposed within 30 days. During the first phase (0 to 14–30 days), the addition of pig slurry to the soil, especially at the larger rate, increased microbial biomass C content, microbial biomass C/total organic C ratio, basal respiration, and metabolic quotient. The microbial growth and the increase of their activity that these results reflected were not persistent, since the initially measured values in pig slurry-amended soils decreased and reached those of the control soil in a relatively short time.     

Label-free detection of kanamycin based on the aptamer-functionalized conducting polymer/gold nanocomposite

Highly sensitive label-free detection of kanamycin is achieved with an aptamer sensor based on a conducting polymer/gold self-assembled nanocomposite. The sensor probe is fabricated by covalently immobilizing an in vitro selected DNA aptamer for kanamycin onto gold nanoparticle (AuNP)-comprised conducting polymer, poly-[2, 5-di-(2-thienyl)-1H-pyrrole-1-(p-benzoic acid)] (poly-DPB). The self-assembling of DPB on AuNP is investigated by TEM and UV-vis spectroscopy and the modification of the aptamer sensor is characterized using XPS and electrochemical impedance spectroscopy. The probe is applied to detect kanamycin by using voltammetric techniques. The sensor shows a pair of redox peaks around 0.26/ 0.08 V (vs. Ag/AgCl) for kanamycin captured by the aptamer-immobilized probe. The parameters that can affect the response, such as aptamer concentration, incubation time, temperature, and pH are optimized. The calibration plot shows a linear range from 0.05 μM to 9.0 μM kanamycin with a detection limit of 9.4±0.4 nM. The proposed aptamer sensor is examined with a real sample.     

Comparison of N losses (NO − 3, N 2O, NO) from surface applied, injected or amended (DCD) pig slurry of an irrigated soil in a Mediterranean climate

Nitrous oxide (N ₂O), nitric oxide (NO), denitrification losses and NO^–₃ leaching from an irrigated sward were quantified under Mediterranean conditions. The effect of injected pig slurry (IPS) with and without the nitrification inhibitor dicyandiamide (DCD) was evaluated and also compared with that of a surface pig slurry application (SPS) and a control treatment (Control) without fertiliser. After application, fluxes of NO and N ₂O peaked from SPS (3.06 mg NO-N m ^–2 d ^–1 and 108 mg N ₂O-N m ^–2 d ^–1) and IPS (3.50 mg NO-N m ^–2 d ^–1 and 105 mg N ₂O-N m ^–2 d ^–1). However, when irrigation was applied, N ₂O and NO emissions declined. The total N ₂O and denitrification losses were slightly large from IPS than from SPS, although the differences were not significant (P < 0.05). Emission of NO was not affected by the method of pig slurry application. DCD inhibited nitrification during the first 20–30 days and reduced N ₂O and NO emissions from pig slurry by at least 46% and 37%, respectively. Considering the 215 days following pig slurry application, the emission factor of N ₂O based on N fertiliser was 1.60% (SPS), 2.95% (IPS), and 0.50% (IPS + DCD). The emission factor for NO was 0.14% (SPS), 0.12% (IPS), and 0.02% (IPS + DCD). Environmental conditions of the crop favoured the denitrification process as the most important source of N ₂O during the experimental period. The differences in the denitrification rate between treatments could be explained by the pattern of water soluble carbon (WSC), that was the highest value in injected pig slurry (with and without DCD). Due to low drainage (5% of water applied), leaching losses of NO₃^– were lower than those of denitrification from the upper soil layer (0–10 cm) in all treatments and especially with IPS + DCD, where the nitrification inhibitor was very efficient in reducing leaching losses.     

A comparison of models for predicting slurry production on a pig farm

Three methods of predicting slurry production were compared with the volumes actually produced on a 150 sow breeding and fattening pig unit. The methods were based on (a) feed, water and slurry relationships measured in crated and penned pigs; (b) values given in the literature and used by ADAS to predict slurry outputs from pigs; (c) a method based on the digestibility of feed and of water measured at the actual piggery. Method (a) was not found appropriate because of the high overall water:meal ratio found in the unit (13:1). Method (b) was able to predict dry matter production accurately but underestimated the volume produced unless the ADAS allowance of 0·5 litres pig⁻¹ day⁻¹ for washing water and leaking drinkers was increased to 10 litres. Method (c) was the best method for estimating volume but underestimated dry matter production. Combining the better aspects of methods (b) and (c) allows volume, dry matter production and dry matter concentration to be predicted satisfactorily. The daily movements of slurry from the reception pit were very variable. The use of water meters on pig units is recommended to identify wastage.     

猪场废水施用对直播稻磷素吸收利用与氮磷生态化学计量的影响

以直播稻为对象,在上海农场进行了猪场处理废水基肥和穗肥不同用量组合的田间试验,研究猪场废水对水稻磷养分吸收利用与氮磷生态化学计量的影响。结果表明:施用猪场处理废水对直播水稻干物质积累、植株磷含量有显著影响。水稻拔节期、齐穗期和成熟期干物质积累量以及产量随废水施用量增加而增加;拔节期、齐穗期和成熟期植株、秸秆及籽粒含磷量与废水用量皆呈显著正相关;不同施肥处理在整个生育期水稻植株N∶P为3.13~5.10,在拔节期、齐穗期、成熟期分别为3.13~4.83、3.42~4.35、3.98~5.10,总体上以齐穗期N∶P值较低;成熟期秸秆N∶P值变动较大(4.30~6.57),而籽粒变化较小(3.85~4.37);齐穗期植株、成熟期秸秆、籽粒和植株的N∶P值与废水施用总量皆呈显著正相关,表明废水施用对直播稻氮素吸收的促进作用大于磷素。     

Effect of biofuel co-products in pig diets on the excretory patterns of N and C and on the subsequent ammonia and methane emissions from pig effluent

This study was conducted to investigate the effects of incorporation into pig diets of 20% of different co-products from the biofuel industries, which are rich in fibre, on animal growth performance, on nitrogen (N) and carbon (C) excretions, and on the subsequent ammonia volatilisation and methane production during the storage of slurry. Five experimental diets mainly based on wheat and soyabean meal were formulated: two control diets, a control high-protein (CHP) diet with 17.5% of crude protein (CP) and a control low-protein (CLP) diet with 14.0% of CP and three experimental diets with 20% of (i) dried distiller's grain with solubles (DDGS), (ii) sugar beet pulp (SBP) or (iii) fatty rapeseed meal (FRM). The animals used (20 castrated males) were housed individually in metabolism cages and fed one of the five diets (i.e. four pigs per diet). Urine and faeces were collected separately from each pig in order to measure nutrient digestibility and the excretory patterns of N and C. For each diet, ammonia volatilisation was measured from samples of slurry subsequently produced, over a 16-day storage period in a laboratory pilot scale system. The ultimate methane potential (B0, expressed in litres CH4/kg organic matter (OM)) was measured from the same slurry, for each diet, in anaerobic storage conditions over 100 days. The addition of sources of fibres to the diet decreased (P < 0.05) the animal growth performance by 13% and increased (P < 0.05) the amount of faeces excreted by 100%, whereas the amount of urine was not affected. For the high-fibre diets, there was a shift of N partitioning from urine to faeces, resulting in a much higher faecal N excretion (10 v. 5 g N/pig per day). Concurrently, the fibre enrichment in diets significantly increased (P < 0.05) the C content of the faeces by 68%. Ammonia emission from slurry was significantly reduced (P < 0.05) by 19% to 33% for the high-fibre diets, compared to the CHP diet. Ammonia emission was also reduced (P < 0.05) by 33% for the CLP compared to the CHP diet. B0 values ranged from 428 to 484 l CH4/kg OM. When these are expressed per pig and per day, the B0 from slurry was, on average, 70 l for the two control diets, and 121, 91 and 130 l for the slurry originating from the DDGS, SBP and FRM diets, respectively.     

Power enhancement via multivariate outlier testing with gene expression arrays

Motivation: As the use of microarrays in human studies continuesto increase, stringent quality assurance is necessary to ensureaccurate experimental interpretation. We present a formal approachfor microarray quality assessment that is based on dimensionreduction of established measures of signal and noise componentsof expression followed by parametric multivariate outlier testing. Results: We applied our approach to several data resources.First, as a negative control, we found that the Affymetrix andIllumina contributions to MAQC data were free from outliersat a nominal outlier flagging rate of =0.01. Second, we createda tunable framework for artificially corrupting intensity datafrom the Affymetrix Latin Square spike-in experiment to allowinvestigation of sensitivity and specificity of quality assurance(QA) criteria. Third, we applied the procedure to 507 Affymetrixmicroarray GeneChips processed with RNA from human peripheralblood samples. We show that exclusion of arrays by this approachsubstantially increases inferential power, or the ability todetect differential expression, in large clinical studies. Availability: http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.htmland http://bioconductor.org/packages/2.3/bioc/html/affyContam.htmlaffyContam (credentials: readonly/readonly) Contact: aasare{at}immunetolerance.org; stvjc{at}channing.harvard.edu The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. Associate Editor: Trey Ideker     

Biomimetic sensing layer based on electrospun conductive polymer webs

The aim of the present study is to combine a bio-inspired nanofibrous artificial epithelium to the electronic nose (e-nose) principles. The sensing device set up was an electronic nose consisting of an array of 9 micro-chemoresistors (Cr-Au, 3×3) coated with electrospun nanofibrous structures. These were comprised of doped polyemeraldine base blended with 3 different polymers: polyethylene oxide, polyvinilpyrrolidone and polystyrene, which acted as carriers for the conducting polymer and were the major responsible of the features of each fibrous overlay (electrical parameters, selectivity and sensitivity ranges). The two sensing strategies here adopted and compared consisted in the use of 2 different textural coatings: a single- and a double-overlay, where the double-overlay resulting from overdeposition of 2 different polymer blends. Such e-nose included a plurality of nanofibres whose electrical parameters were at the same time depending on each polymer exposure to analytes (NO(2), NH(3)) and on the spatial distribution of the interlacing fibres. The morphology of the coating arrangements of this novel e-nose was investigated by scanning electron microscopy (SEM) and its sensor responses were processed by multicomponent data analyses (PCA and PLS) reporting encouraging results for detection and recognition of analytes at ppb levels.