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Measurement of carbonaceous aerosols: validation and comparison of a solvent extraction-gas chromatographic method and a thermal optical transmittance method.

A solvent extraction-gas chromatographic method was developed for the measurement of four classes of solvent-extractable organic compounds (SEOC), viz., aliphatic hydrocarbons, polynuclear aromatic hydrocarbons, fatty acids and alkanols, in ambient carbonaceous aerosols. The selectivity and recovery of the method using different solvents commonly used in the analysis of SEOC was evaluated. The composition of SEOC in aerosol and urban dust samples was found to vary with the choice of solvent. Such variation was not observed in filters spiked with standards of SEOC. The developed method was validated by the analysis of reference urban dust SRM 1649a from the National Institute of Standards and Technology. The concentrations of selected polynuclear aromatic hydrocarbons in the reference dust were found to fall within the certified and reference concentrations. The thermal characteristics of aerosol samples collected in an urban area of Hong Kong and the four classes of identified SEOC were also studied using a thermal optical transmittance (TOT) method as specified in NIOSH Method 5040. Correlations were made to compare the method-dependent SEOC content obtained by the solvent extraction method and the results for total carbon, organic carbon and elemental carbon obtained by the TOT method.

Aerosols↗

EU Drinking Water Directive reference methods for enumeration of total coliforms and Escherichia coli compared with alternative methods.

AIMS: The reference methods for enumeration of total coliforms and Escherichia coli as stated in the European Drinking Water Directive were compared with alternative methods. METHODS AND RESULTS: Laboratories used the reference method on Lactose TTC agar (LTTC), the Colilert/18 system, Laurysulphate Agar (LSA), Chromocult Coliform Agar and the E. coli Direct Plating (DP) method. They enumerated more total coliforms on LTTC than on LSA. CONCLUSIONS: LTTC is suitable for analysis of very clean water samples only, due to heavy background growth. Colilert/18 is a good alternative but it enumerates a broader group of total coliforms, resulting in higher counts. The DP method appeared to be the best choice for enumeration of E. coli because Colilert/18 produces lower counts and false-negative results. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows the limitations of the EU reference method on LTTC due to lack of selectivity and suggests alternative methods for the enumeration of total coliforms and E. coli.

Colony Count, Microbial↗

Validation of a simple, manual urinary iodine method for estimating the prevalence of iodine-deficiency disorders, and interlaboratory comparison with other methods.

The measurement of urinary iodine in population-based surveys provides a biological indicator of the severity of iodine-deficiency disorders. We describe the steps performed to validate a simple, inexpensive, manual urinary iodine acid digestion method, and compare the results using this method with those of other urinary iodine methods. Initially, basic performance characteristics were evaluated: the average recovery of added iodine was 100.4 +/- 8.7% (mean +/- SD), within-assay precision (CV) over the assay range 0-0.95 mumol/L (0-12 micrograms/dL) was < 6%, between-assay precision over the same range was < 12%, and assay sensitivity was 0.05 mumol/L (0.6 microgram/dL). There were no apparent effects on the method by thiocyanate, a known interfering substance. In a comparison with five other methods performed in four different laboratories, samples were collected to test the method performance over a wide range of urinary iodine values (0.04-3.7 mumol/L, or 0.5-47 micrograms/dL). There was a high correlation between all methods and the interpretation of the results was consistent. We conclude that the simple, manual acid digestion method is suitable for urinary iodine analysis.

Arsenic↗

Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics.

Recent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales. It has been proposed that the use of structural information may offer advantages over sequences in phylogenetic reconstruction, due to their slower rate of evolution and direct correlation to function. Here, we examined how recently developed methods for structure-based homology search and tree reconstruction compare with current state-of-the-art sequence-based methods in reconstructing genome-wide collections of gene phylogenies (i.e. phylomes). While structure-based methods can be useful in specific scenarios, we found that their current performance does not justify using the newly developed structure-based methods as a default choice in large-scale phylogenetic studies. On the one hand, the best performing sequence-based tree reconstruction methods still outperform structure-based methods for this task. On the other hand, structure-based homology detection methods provide larger lists of candidate homologs, as previously reported. However, this comes at the expense of missing hits identified by sequence-based methods, as well as providing sets of homolog candidates with higher fractions of false positives. These insights help to guide the use of structural data in comparative genomics and highlight the need to continue improving structure-based approaches. Our pipeline is fully reproducible and has been implemented in a Snakemake workflow. This will facilitate a continuous assessment of future improvements of structure-based tools in the AlphaFold era.

Phylogeny↗

Phonomyography as a novel method to determine neuromuscular blockade at the laryngeal adductor muscles: comparison with the cuff pressure method.

BACKGROUND: Neuromuscular blockade at the laryngeal adductor muscles may be measured using the cuff of a endotracheal tube placed between the vocal cords. Phonomyography is an alternative method of neuromuscular monitoring. In this study, phonomyography is applied to determine blockade at the larynx and compared with the cuff pressure method. METHODS: After the authors obtained approval from the ethics committee and informed consent, 28 patients were entered in the study. After induction of anesthesia, a endotracheal tube was inserted. Its cuff was placed in the trachea in routine fashion (n = 14) or between the vocal cords (n = 14). In all patients, a small condenser microphone was placed in the vestibular fold, just lateral to the tube, next to the laryngeal adductor muscles. The recurrent laryngeal nerve was stimulated supramaximally with single twitch stimulation (0.1 Hz) for onset, and train-of-four stimulation every 12 s during offset of neuromuscular blockade was produced by 0.1 mg/kg mivacurium. Onset and recovery of neuromuscular blockade measured by the two methods were compared using the test (P < 0.05), and a Bland-Altman test was performed to define agreement between the two methods. Onset and recovery of neuromuscular blockade measured by phonomyography with the cuff placed between the vocal cords or in the trachea were compared using the test (P < 0.05). RESULTS: Mean onset, maximum effect, and time to reach 25% and 75% of control twitch response for phonomyography cuff pressure method were 145 s (SD, 25) 156 s (SD, 33), 89% (SD, 4) 91% (SD, 4), 9 min (SD, 4) 10 min (SD, 3), and 27 min (SD, 4) 29 min (SD, 4), respectively, without being significantly different. Mean bias was -2%, with limits of agreement of -20 and +18% for all signals (cuff method minus phonomyography). There was no significant difference in onset and offset of neuromuscular blockade measured using phonomyography with the cuff placed between the vocal cords or in the trachea. CONCLUSIONS: Both methods can be used interchangeably to determine neuromuscular blockade of the laryngeal adductor muscles. Phonomyography allows measurement of laryngeal blockade with the endotracheal tube in the normal position.

Blood Pressure↗

Combination of improved multibondic method and the Wang-Landau method.

We propose a method for Monte Carlo simulation of statistical physical models with discretized energy. The method is based on several ideas including the cluster algorithm, the multicanonical Monte Carlo method and its acceleration proposed recently by Wang and Landau. As in the multibondic ensemble method proposed by Janke and Kappler, the present algorithm performs a random walk in the space of the bond population to yield the state density as a function of the bond number. A test on the Ising model shows that the number of Monte Carlo sweeps required of the present method for obtaining the density of state with a given accuracy is proportional to the system size, whereas it is proportional to the system size squared for other conventional methods. In addition, the method shows a better performance than the original Wang-Landau method in measurement of physical quantities.

Journal Article↗

A generalization of the two-dimensional prolate spheroidal wave function method for nonrectilinear MRI data acquisition methods.

The two-dimensional (2-D) prolate spheroidal wave function (2-D PSWF) method was previously introduced as an efficient method for trading off between spatial and temporal resolution in magnetic resonance imaging (MRI), with minimal penalty due to truncation and partial volume effects. In the 2-D PSWF method, the k-space sampling area and a matching 2-D PSWF filter, with optimal signal concentration and minimal truncation artifacts, are determined by the shape and size of a given convex region of interest (ROI). The spatial information in the reduced k-space data is used to calculate the total image intensity over a nonsquare ROI instead of producing a low-resolution image. This method can be used for tracking dynamic signals from non-square ROIs using a reduced k-space sampling area, while achieving minimal signal leakage. However, the previous theory is limited to the case of rectilinear sampling. In order to make the 2-D PSWF method more suitable for dynamic studies, this paper presents a generalized version of the 2-D PSWF theory that can be applied to nonrectilinear data acquisition methods. The method is applied to an fMRI study using a spiral trajectory, which illustrates the methods efficiency at tracking hemodynamic signals with high temporal resolution.

Algorithms↗

Method specificity of non-invasive blood pressure measurement: oscillometry and finger pulse pressure vs acoustic methods.

1. The agreement of blood pressure measurements by stethoscope auscultation (SBPa, DBPa-IV and DBPa-V), oscillometry (Dinamap; SBPo, and DBPo) and digital photoplethysmography (Finapres; SBPf, and DBPf) with the graphical analysis of the analogue microphone signals of vascular wall motion sound (SBPg and DBPg) was evaluated in eight healthy subjects in the presence of responses to the intravenous infusion of 1 microgram min-1 isoprenaline. 2. In general, there was good agreement between the SBP/DBP-measurements based on auscultatory Korotkoff-I- and IV-criteria and the reference method; the average method difference in estimating the isoprenaline responses for SBPa-SBPg was: -1.1, 95% CI: -5.4 to 3.1 mm Hg with a within-subject between-method repeatability coefficient (REP) of 11.6 mm Hg and for DBPa-IV-DBPg: 3.5, 95% CI: -0.5 to 6.5 mm Hg, REP: 11.5 mm Hg. The ausculatation of Korotkoff-V substantially overestimated the isoprenaline induced reduction of DBP: method difference DBPa-V-DBPg: -11.3, 95% CI: -17.8 to -4.7 mm Hg, REP: 31.8 mm Hg. 3. Oscillometry yielded good approximations for the SBP response to isoprenaline (average method difference SBPo-SBPg: -2.9, 95% CI: -9.0 to 3.3 mm Hg, REP: 17.6 mm Hg) but was poorly sensitive with regard to the DBP responses: method difference DBPo-DBPg: 6.5, 95% CI: -1.3 to 14.3 mm Hg, REP: 25.7 mm Hg. 4. Whilst the finger pulse pressure agreed well with regard to DBP (method difference for the DBP responses to isoprenaline: DBPf-DBPg: 1.8, 95% CI: -5.1 to 8.6 mm Hg, REP: 18.5 mm Hg) it was rather unsatisfactory with regard to SBP (method difference SBPf-SBPg: -14.1, 95% CI: -28.2 to -0.1 mm Hg, REP: 49.9 mm Hg).(ABSTRACT TRUNCATED AT 250 WORDS)

Adrenergic beta-Antagonists↗

HLA-DQB1 allele typing by a new PCR-RFLP method: correlation with a PCR-SSO method.

We have developed a new PCR-RFLP method for HLA-DQB1 typing. This method was easy to follow, requiring only one DQB1 generic amplification and 5 endonucleases to assign 14 out of 15 HLA-DQB1 alleles. In addition, we determined that by using one generic amplification and two enzymes (Sau96 I and Hae III) it was possible to type the generic specificities: DQw2, DQw4, DQw5, DQw6, and DQw7, DQw8-9, providing a practical alternative for serological HLA-DQ generic typing. We also performed a side-by-side correlation with a PCR-SSO typing method and found an almost 100% concordance between the methods. The limitations of these methods were: 1) the PCR-RFLP method did not allow the differentiation between the HLA-DQB1*0602 and *0603 alleles; 2) the PCR-SSO method gave crosshybridization signals in the detection of *0302 or *0303 alleles. Our results suggested that both methods, PCR-RFLP and PCR-SSO, are useful alternatives for HLA-DQB1 typing.

Alleles↗

Sterility testing of cell therapy products: parallel comparison of automated methods with a CFR-compliant method.

BACKGROUND: Automated blood culture systems are not FDA-approved for sterility testing of human cells, tissues, or cellular- or tissue-based products. It was previously demonstrated that BacT/ALERT (bioMérieux) and Bactec (Becton Dickinson) were superior to the manual CFR method described in the general biologics regulations, in rates of detection and time to detection of organisms seeded into mock mononuclear cell products with a variety of background media and antibiotics. In this study, the two automated systems were compared to the CFR method for sterility testing of actual cell therapy products manufactured in our facility. STUDY DESIGN AND METHODS: Over a 36-month period, in-process and final product samples from all cell therapy products manufactured in our facility were tested for sterility both by the CFR method and by either BacT/ALERT or Bactec. Products were categorized according to collection and processing variables for analysis of results. RESULTS: For 1617 samples of a broad range of cell therapy products, rates of true-positive tests were comparable for the automated and CFR methods (2.3% vs. 2.1%), but the CFR method had higher rates of false-positive results (7.3% vs. 0.2%). For automated systems, time to detection of organisms was equivalent to, or faster than, the CFR method. CONCLUSION: Compared to the CFR method, both BacT/ALERT and Bactec are more sensitive, faster in time to detection, less prone to false-positive results, and less labor-intensive. Both of these automated systems are suitable for sterility testing of cell therapy products after site-specific validation has been performed.

Automation↗

Cutaneous immunohistochemistry. The direct immunoperioxidase and immunoglobulin-enzyme bridge methods compared with the immunofluorescence method in dermatology.

Two immunohistochemical methods, using the enzyme horseradish peroxidase, the direct immunoperoxidase (DIP) and the immunoglobulin-enzyme bridge (IEB) method were applied on 129 skin specimens of 81 patients with lupus erythematosus, bullous pemphigoid, pemphigus vulgaris and rosacea. These methods were compared with each other and with the immunofluorescence (IF) method. The DIP method was preferred to the IEB method because of the greater contrast between the specific staining and the nonspecific staining of the former. The results obtained with both peroxidase methods were comparable with those of the IF method.

Fluorescent Antibody Technique↗

Pulse pressure method and the area method for the estimation of total arterial compliance in dogs: sensitivity to wave reflection intensity.

We estimated total arterial compliance (C) in eight anesthetized mongrel dogs with (i) the area method (AM), (ii) the pulse pressure method (PPM), and (iii) the stroke volume-to-pulse pressure ratio (SV/PP). Average compliance was C(AM)=1.1+/-0.73 ml mm Hg(-1) using AM; C(PPM)=0.60+/-0.31 ml mm Hg(-1) using PPM and C(SV/PP)=0.87+/-0.49 ml mm Hg(-1) using SV/PP. Mean aortic pressure was 64+/-23 mm Hg. The overall agreement between C(AM) and C(PPM) was relatively poor (C(AM)=0.15+/-1.61 C(PPM); r2=0.48), with a consistent overestimation of the area method with respect to the pulse pressure method. There was a significant correlation (r=-0.78) between the relative difference between PPM and AM, and the modulus of the first harmonic of the wave reflection coefficient [gamma] which was low in our dog population (0.37+/-0.18). SV/PP overestimated PPM, but both methods were highly correlated (C(SV/PP)=0.06+/-1.60C(PPM); r2=0.97). C(SV/PP) and C(AM) were similar only for [gamma]>0.4. The effect of isolated changes of [gamma] on PPM, AM, and SV/PP was studied using the linear wave separation technique. The area method appeared very sensitive to the wave reflection intensity. For low reflection coefficients, the diastolic wave profile was flattened and compliance was overestimated. PPM and SV/PP were relatively independent of [gamma] and remained even applicable for [gamma]=0. We believe that the pulse pressure method is the most consistent method for the estimation of total arterial compliance in hemodynamic conditions characterized by a low wave reflection intensity.

Animals↗

Comparison of the BAX for screening/E. coli O157:H7 method with conventional methods for detection of extremely low levels of Escherichia coli O157:H7 in ground beef.

Escherichia coli O157:H7 is an important food-borne pathogen. Often E. coli O157:H7 is difficult to detect, because it is present sporadically at very low levels together with very high levels of competitor organisms which can be difficult to distinguish phenotypically. Cultural methods are time-consuming and give variable results in the detection of E. coli O157:H7. This study examined the performance of BAX for Screening/E. coli O157:H7, a new rapid method for the detection of E. coli O157:H7, against traditional and improved cultural methods and an immunodiffusion assay. All cultural methods demonstrated inadequacy in detecting the presence of E. coli O157:H7 in inoculated samples. The limitations of these cultural methods further complicate evaluation of screening methodologies. The BAX for Screening/E. coli O157:H7 assay outperformed the other methods, with a detection rate of 96.5%, compared to 39% for the best cultural method and 71.5% for the immunodiffusion method. The BAX for Screening/E. coli O157:H7 assay proved to be a rapid, highly sensitive test for the detection of low levels of E. coli O157:H7 in ground beef.

Animals↗

Comparison of an established antibody sandwich method with an inhibition method of Histoplasma capsulatum antigen detection.

The Histoplasma antigen immunoassay utilizes an antibody sandwich method that provides a rapid and reliable means of diagnosing the more severe forms of histoplasmosis. Inhibition assays have been developed for antigen detection and offer at least one potential advantage, namely, reduced antibody requirements. We have developed an inhibition assay using the polyclonal antibody employed in our standard sandwich assay. Urine and serum specimens from patients with culture-proven histoplasmosis and controls were tested using both methods. The two methods had similar sensitivities for detection of antigen in urine (antibody sandwich = 92.5% versus inhibition = 87.5%, P = 0.500) and serum (82.5% versus 80.0%, P = 1. 000). With serum, the specificities of both methods were similar (antibody sandwich assay = 95.0% versus inhibition assay = 92.5%, P = 1.000), and with urine, the specificity of the antibody sandwich method was superior (97.5% versus 80.0%, P = 0.039). While the overall reproducibility of both methods was excellent (with urine, antibody sandwich assay intraclass correlation coefficient = 0.9975 and with serum = 0.9949; correlation coefficient of the inhibition assay with urine = 0.9736 and with serum = 0.9850), that of the inhibition method was only fair to poor for the controls: urine = -0. 0152, serum = 0.5595. Reproducibility was good for the controls using the sandwich method: urine = 0.7717, serum = 0.9470. Cross-reactivity was observed in specimens from patients infected with Blastomyces dermatitidis, Paracoccidioides brasiliensis, and Penicillium marneffei. In conclusion, the decreased specificity and inferior reproducibility with control specimens suggest that the inhibition assay has poorer precision toward the lower end of the detection range.

Antibodies, Fungal↗

Comparison of NCCLS and 3-(4,5-dimethyl-2-Thiazyl)-2, 5-diphenyl-2H-tetrazolium bromide (MTT) methods of in vitro susceptibility testing of filamentous fungi and development of a new simplified method.

The susceptibility of 30 clinical isolates belonging to six different species of filamentous fungi (Aspergillus fumigatus, Aspergillus flavus, Scedosporium prolificans, Scedosporium apiospermum, Fusarium solani, and Fusarium oxysporum) was tested against six antifungal drugs (miconazole, voriconazole, itraconazole, UR9825, terbinafine, and amphotericin B) with the microdilution method recommended by the National Committee for Clinical Laboratory Standards (NCCLS) (M38-P). The MICs were compared with the MICs obtained by a colorimetric method measuring the reduction of the dye 3-(4,5-dimethyl-2-thiazyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) to formazan by viable fungi. The levels of agreement between the two methods were 96 and 92% for MIC-0 (clear wells) and MIC-1 (75% growth reduction), respectively. The levels of agreement were always higher for Aspergillus spp. (97% +/- 2.5%), followed by Scedosporium spp. (87% +/- 10.3%) and Fusarium spp. (78% +/- 7.8%). The NCCLS method was more reproducible than the MTT method: 98 versus 95% for MIC-0 and 97 versus 90% for MIC-1. However, the percentage of hyphal growth as determined visually by the NCCLS method showed several discrepancies when they were compared with the percentages of MTT reduction. A new simplified assay that incorporates the dye MTT with the initial inoculum and in which the fungi are incubated with the dye for 48 h or more was developed, showing comparable levels of agreement and reproducibility with the other two methods. Furthermore, the new assay was easier to perform and more sensitive than the MTT method.

Antifungal Agents↗

A new method for direct detection of heparin on surface-modified intraocular lenses. A modification of Jaques' toluidine blue staining method.

BACKGROUND: Examination of surface-bound heparin on synthetic polymers can only be performed by few staining methods. These methods are limited by an only approximate detection of heparin visible at high magnification. Other methods only measure heparin quantitatively (per square dimension) and are rather sensitive to artifacts. Due to its homogeneous staining pattern, the modified toluidine blue staining technique, using a non-protein-based substance, allows examination and analysis of the homogeneity of the monomolecular heparin layer even under critical conditions like scanning electron microscopy. MATERIALS AND METHODS: For critical examination of the heparin layer, this method was used for 5 sterile heparin surface-modified (HSM) monofocal (Pharmacia, 809C, 5 mm optical zone), 2 multifocal PMMA (Pharmacia, 811E, 6 mm optical zone) and 1 standard PMMA intraocular lenses (IOLs; Pharmacia, 809P, 5 mm optical zone). A special mixture containing a sodium borate buffer was used to avoid cross-reactions of toluidine with phenylimines, which permit a covalent surface linkage of heparin to synthetic polymeric materials via reductive amination. This resulted in less coarse-grained complex agglutination. After light and spectral microscopy of the surface of stained IOLs, scanning electron microscopy was performed to investigated the reliability and validity of this modified staining method. RESULTS: All HSM IOLs showed a homogeneous heparin structure and coating, which could be demonstrated even under critical photographic circumstances. CONCLUSIONS: The modification of the original toluidine blue staining method introduced by Jaques in 1943 is a reliable and reproducible technique for the detailed in vitro analysis of surface-bound heparin with a low artifact rate. Because of the detailed detection of heparin on polymeric surfaces, this staining method is recommended for special problems, e.g. in cataract surgery.

Coloring Agents↗

Ear oximetry: a noninvasive method for detection of patent foramen ovale: a study comparing dye dilution method and oximetry with contrast transesophageal echocardiography.

BACKGROUND AND PURPOSE: Patent foramen ovale (PFO) may play an important role as a risk factor for ischemic stroke and some other neurological conditions. There is a need for low-cost and noninvasive methods for the detection of PFO. This study evaluates the accuracy of two simple bedside tests, the dye dilution method and ear oximetry, in the detection of PFO. METHODS: Dye dilution curves and ear oximetry recordings with a noninvasive ear densitometer were obtained from consecutive cryptogenic stroke patients referred for contrast transesophageal echocardiography (TEE). All test results were blindly assessed for the presence of PFO. Sensitivity and specificity were calculated with TEE used as a reference method. kappa statistics were used to measure interrater agreement. RESULTS: Dye dilution curves were obtained from 67 patients. Dye dilution correctly diagnosed 35 of the 46 patients who had PFO in TEE and all the 21 patients without PFO. Thus, the sensitivity (95% CI) of the dye dilution method was 76% (61% to 87%) and its specificity 100% (84% to 100%). Ear oximetry was done on 83 patients. Oximetry correctly diagnosed 45 of the 53 patients who had PFO in TEE and all of the 30 patients without PFO. Thus, the sensitivity of ear oximetry was 85% (72% to 93%) and its specificity 100% (88% to 100%). The interrater agreement was excellent (kappa value 0.94 for dye dilution and 0.90 for oximetry). CONCLUSIONS: Dye dilution and oximetry are both sensitive and specific methods for the detection of PFO. Oximetry has the following primary advantages over the currently available diagnostic methods: it is noninvasive, safe, and inexpensive and causes no discomfort for the patient. We suggest that oximetry could be used as a first-line screening method for PFO in patients with cryptogenic stroke. Ear oximetry also has potential use in epidemiological studies.

Adult↗

The unlabeled antibody method: comparison of peroxidase-antiperoxidase with avidin-biotin complex by a new method of quantification.

Upon plotting of areas against optical densities in immunocytochemically stained tissue sections, hyperbolic curves were obtained which could be reduced to two straight lines, one representing variations in stained structures, and the other variations in background. The slopes of the stained structure lines reflected staining intensity independently of total area of stained structure in a section. The ratio of slopes of the stained structure and background lines reflected immunocytochemical sensitivity. A comparison of the peroxidase-antiperoxidase (PAP) method with the avidin-biotin complex (ABC) method showed that at usual antibody dilutions the PAP method was much more sensitive than the ABC method, while at impractically high antibody dilutions it was moderately more sensitive. Once sufficient dilutions of antibodies were reached, staining intensities dropped sharply with the PAP method. On the other hand, the dilution curves were flat with the ABC method. The ABC method consequently appeared unsuitable for estimating variations in concentration of antigen or for distinguishing high or low concentrations of antigen. The ABC method provided a stain for myelin even in the absence of any antibodies.

Animals↗