Discriminant analysis of volatile fatty acids produced in culture medium: a novel approach to the identification of Pseudomonas species

The volatile fatty acids produced in culture medium by 357 Pseudomonas strains belonging to eight species were determined quantitatively by GLC. The resultant chromatograms were submitted to discriminant analysis. Stable discriminant functions were computed and included in a computerized identification system which also involved some distinctive volatile fatty acids regarded as two-state qualitative characters (presence or absence characters). Using a test group of 249 strains belonging to the studied species, more than 89% of the identifications made by this system agreed with those made by conventional biochemical methods despite the relatively poor differentiation between P. putida and P. fluorescens. When the individual species within the matrices were weighted with prior probabilities reflecting results given by two simple biochemical tests, 96% of the 249 strains were correctly identified.     

Morphometric discrimination among females of sibling species of Aconophorini (Homoptera: Membracidae)

Abstract. Keys to species of auchenorrhynchous Homoptera are often based on male features, leaving no means for identifying females other than association with males. As a possible solution to this problem, we examined the use of linear discriminant functions derived from morphometric data (ten linear measurements among homologous body landmarks) for distinguishing females in two groups of sibling species in the Neotropical treehopper tribe Aconophorini (Membracidae: Membracinae): (1) Calloconophora caliginosa (Walker) and C.pinguis (Fowler); and (2) Guayaquila minuta (Fowler), G.venezuelensis Dietrich, and Central and South American populations of G.pallescens (Stål). Samples of female specimens identified by association with males were used to derive the discriminant functions. Performance of these discriminant functions as evaluated by jackknifing the data was as follows: 98.11% of the specimens in the first group correctly identified using a combination of three measurements, and 94.94% of the specimens in the second group correctly identified using a combination of ten measurements.     

Possibilities of using non-invasive techniques to predict pulmonary arterial pressure in chronic respiratory diseases]

The value of non-invasive procedures for predicting pulmonary arterial pressure (PAP) was assessed in 297 patients with chronic obstructive lung disease (COLD) and in 73 patients with alveolitis in multicenter trials at 9 centres in 6 European countries. FEV1, blood gases, ECG, radiographic dimensions of the pulmonary artery, right ventricle dimensions measured with M-mode echocardiography, and 201Ta heart scintigraphy together with clinical examinations served the purpose. No single variable was correlated closely enough to allow precise prediction of PAP. In patients with COLD multiple stepwise analysis of regression explained 49% of the variance in PAP but was not useful for prediction. Discriminant analysis allowed patients allocation to PAP bands similarly to 2 non-parametric procedures in which decision trees were established with the aid of either Kolmogoroff-Smirnoff statistics or Fishers' exact test. Patients with PAP of 30 mm Hg or higher were identified with sensitivity of 83% and specificity of 91%. Non-parametric tests produced better results than discriminant functions. Additional 54 patients were tested to validate these functions. Ninety percent of them with PAP > 20 mm Hg, and 80% with PAP > 29 mm Hg were identified correctly. Similar results were achieved in patients with fibrosing alveolitis. These mathematical functions allow the use of non-invasive procedures combinations to select those individuals out the populations at risk of pulmonary hypertension in whom direct PAP measurements are required. These mathematical functions may further be widen by addition of other variables obtained from newer non-invasive techniques.     

FT-IR microspectroscopy: a promising method for the rapid identification of Listeria species

This work presents a pilot study to investigate the potential of fourier transform infrared (FT-IR) microspectroscopy for rapid identification of Listeria at the species level. Using this technique, FT-IR spectra were acquired from 30 strains from five Listeria species. The FT-IR spectra were analysed using stepwise canonical discriminant analysis and partial least-squares regression in a stepwise identification scheme. The results showed that 93% of all the samples were assigned to the correct species, and that 80% of the Listeria monocytogenes strains were correctly identified. In comparison, 100% of the samples, including the L. monocytogenes samples, were correctly identified using spectra acquired by FT-IR macrospectroscopy. The results show that FT-IR microspectroscopy has potential as a rapid screening method for Listeria, which is especially valuable for the food industry.     

Sex determination of Antarctic Petrels Thalassoica antarctica by discriminant analysis of morphometric characters

We present data on sexual dimorphism in some morphological measurements (wing length, head length, bill depth and bill length) in the Antarctic Petrel Thalassoica antarctica. Males were on average larger than females for all measurements. Sexual dimorphism was on average largest for bill depths whereas wing lengths discriminated least between the sexes. A discriminant function including bill depth, head length and wing length correctly sexed 92% of the sample. Due to between-measurer variation it is recommended that morphometric measurements obtained by others on sexed birds are compared with ours before proceeding with the use of the discriminant function on unsexed individuals.Publication No. 116 of the Norwegian Antarctic Research Expeditions (1991/92)     

A Side by Side Comparison of Bruker Biotyper and VITEK MS: Utility of MALDI-TOF MS Technology for Microorganism Identification in a Public Health Reference Laboratory

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid, highly accurate, and cost-effective method for routine identification of a wide range of microorganisms. We carried out a side by side comparative evaluation of the performance of Bruker Biotyper versus VITEK MS for identification of a large and diverse collection of microorganisms. Most difficult and/or unusual microorganisms, as well as commonly encountered microorganisms were selected, including Gram-positive and negative bacteria, mycobacteria, actinomycetes, yeasts and filamentous fungi. Six hundred forty two strains representing 159 genera and 441 species from clinical specimens previously identified at the Laboratoire de santé publique du Québec (LSPQ) by reference methods were retrospectively chosen for the study. They included 254 Gram-positive bacteria, 167 Gram-negative bacteria, 109 mycobacteria and aerobic actinomycetes and 112 yeasts and moulds. MALDI-TOF MS analyses were performed on both systems according to the manufacturer’s instructions. Of the 642 strains tested, the name of the genus and / or species of 572 strains were referenced in the Bruker database while 406 were present in the VITEK MS IVD database. The Biotyper correctly identified 494 (86.4%) of the strains, while the VITEK MS correctly identified 362 (92.3%) of the strains (excluding 14 mycobacteria that were not tested). Of the 70 strains not present in the Bruker database at the species level, the Biotyper correctly identified 10 (14.3%) to the genus level and 2 (2.9%) to the complex/group level. For 52 (74.2%) strains, we obtained no identification, and an incorrect identification was given for 6 (8.6%) strains. Of the 178 strains not present in the VITEK MS IVD database at the species level (excluding 71 untested mycobacteria and actinomycetes), the VITEK MS correctly identified 12 (6.8%) of the strains each to the genus and to the complex/group level. For 97 (54.5%) strains, no identification was given and for 69 (38.7%) strains, an incorrect identification was obtained. Our study demonstrates that both systems gave a high level (above 85%) of correct identification for a wide range of microorganisms. However, VITEK MS gave more misidentification when the microorganism analysed was not present in the database, compared to Bruker Biotyper. This should be taken into account when this technology is used alone for microorganism identification in a public health laboratory, where isolates received are often difficult to identify and/or unusual microorganisms.     

上肢长骨的性别判别分析研究

本文对100例(男女各50)国人上肢骨进行了36项测量。统计结果显示所有测量项目均值男性都大于女性并具有显著性的差异。本研究表明可以采用单一指标对破损严重的肢骨进行性别鉴定。36个测量项目中有23项单一指标性别判别率达75％以上,其中9项在80％以上。本文采用Fisher判别分析法建立了56项单一肢骨性别判别函数,判别率为80％—87％。为进一步提高判别效果,采用逐步判别分析法建立了四项逐步性别判别函数,判别率达90％以上。     

Estimation of sex from the dimensions of foot, footprints, and shoe

This study intends to determine if the sex of an individual can be identified by foot lengths, shoe lengths, and/or footprints. For this purpose, foot length, foot breadth, and foot heel breadth of 506 subjects, comprising 253 females and 253 males ranging from 17.56 to 82.92 years of age, were taken. In addition, the footprints (length, breadth, and heel breadth) and footwear (length and breadth) of the same subjects were measured. Finally, the shoe size of the subjects was recorded. Univariate and multivariate discriminant function models were developed for sex allocations. Statistical analyses indicated that univariate models correctly assign approximately 67-94% of individuals to their correct sex groups. Among univariate models the most reliable measurement was shoe length. The results of multivariate models were better than those of univariate ones, with an approximately 82-96% correct assignment. The best multivariate model was comprised of four variables: foot length, shoe length, shoe breadth and shoe size. It could be suggested that these discriminant functions can provide useful clues to establish personal identity whenever complete or partial feet, footprints, or footwear are recovered.     

Multiple discriminant function analysis of sex and race in the postcranial skeleton

Terry Collection femora and innominates of 260 American Whites and Blacks (65 males and 65 females of each race) were analyzed by multiple discriminant function analysis. A stepwise procedure produced three optimal discriminant functions using 15 of our 32 measurements. These functions correctly identified 95% of the sample. The first two-one for sex and one for race-are statistically and biologically significant and form the basis of our analysis. The sexing function manifested both size and shape elements. Prominent among the former was joint size--acetabular diameter and epicondylar diameter of the femur. The shape elements included form of the greater sciatic notch and of the inferomedial aspect of the pubic body. The racing function highlighted a pattern of greater innominate dimensions, exclusive of the acetabular joint, in Whites. This was in contrast to the greater length of the Black femur. Overall, the function seems to express the established differences between the races in the ratio of lower limb length to torso length. While these functions have been applied successfully to forensic cases with confirmed identifications, questions regarding the breadth of applicability of discriminant functions make it desirable to validate our results on new material from the Terry and other collections.     

Within-centre evaluation of hypercalcaemia discriminant functions 5 years after their development

Diagnostic hypercalcaemia discriminant functions, discriminating between clinically significant and non-significant hypercalcaemia, were tested 5 years after their development in order to evaluate the impact of time on their diagnostic capacity. Two populations, consisting of 257 and 129 patients with hypercalcaemia, were consecutively recorded, during six and three months respectively, 5 years apart under similar circumstances. The prevalence of hypercalcaemia was comparable in both populations, being 2.57 and 2.38% respectively (non-significant) (NS). The female/male ratio was 1.9 and 1.7 (NS). The discriminant functions correctly classified 81 and 80% of the women, respectively (NS) and respectively 75% and 64% of the men (NS) in the first and second recorded populations.     

A few characteristics of mouse having high sensibility to anaphylatic shock separated from El mouse (author's transl)]

During an experiment of shaking in El mice, a strain which was less susceptible to convulsion was found out. In this strain (ASK), the mortality to anaphylactic shock and susceptibility to audiogenic seizure were compared with five other strains of mice. Six strains of mice (ASK, EL, IDT, JCC-ICR, dd, C57BL/6J) were sensitized by two subcutaneous injections with 2 mg/head of crystalline egg albumin at five and six weeks of age, and then challenged by the intravenous injection of 0.125, 1, 8, 64, 512 and 4096 mug/head at seven weeks of age. In both sexes of ASK strain, the mortality was the maximum (75--95%) after the challenge of 8--4096 mug egg albumin. The mortality of the female El and IDT and the both sexes of JCL-ICR strains was middle (55--70%) after the challenge with 64 mug egg albumin, while that of other strains (dd and C57BL/6J) was very low (0--20%). The susceptibility of 3-weeks-old mice of ASK, El, IDT, JCL-ICR and dd strains was low (1.9--19.0%), whereas mice of DBA/2 strain showed a very high susceptibility (80%) to 110 phons.     

Feasibility of automating the micronucleus assay

The results of a feasibility study on the automation of the micronucleus assay in whole blood cultures of human lymphocytes are reported. The assay requires determination of the number of lymphocytes with micronuclei among the proliferating population. Using an in-house-assembled image analysis system, a prototype software package was developed that addressed two problems: micronuclei identification and discrimination of nonproliferating cells from proliferating lymphocytes (the only ones that can give rise to micronuclei). The results of manual verification of automated micronucleus scoring showed that 70% of all digitized micronuclei were extracted from the images and 90% of them were correctly classified and paired with a parent nucleus by an "affinity function". The discrimination between proliferating and nonproliferating cells was carried out by linear discriminant analysis of simple nuclear features extracted from Feulgen-stained cells. Among the Feulgen-stained nuclei that were identified by autoradiography as proliferating or not, 85% were correctly classified by a six-feature discriminant function.     

Discrimination of intact mycobacteria at the strain level: a combined MALDI-TOF MS and biostatistical analysis

New methodologies for surveillance and identification of Mycobacterium tuberculosis are required to stem the spread of disease worldwide. In addition, the ability to discriminate mycobacteria at the strain level may be important to contact or source case investigations. To this end, we are developing MALDI-TOF MS methods for the identification of M. tuberculosis in culture. In this report, we describe the application of MALDI-TOF MS, as well as statistical analysis including linear discriminant and random forest analysis, to 16 medically relevant strains from four species of mycobacteria, M. tuberculosis, M. avium, M. intracellulare, and M. kansasii. Although species discrimination can be accomplished on the basis of unique m/z values observed in the MS fingerprint spectrum, discrimination at the strain level is predicted on the relative abundance of shared m/z values among strains within a species. For the 16 mycobacterial strains investigated in the present study, it is possible to unambiguously identify strains within a species on the basis of MALDI-TOF MS data. The error rate for classification of individual strains using linear discriminant analysis was 0.053 using 37 m/z variables, whereas the error rate for classification of individual strains using random forest analysis was 0.023 using only 18 m/z variables. In addition, using random forest analysis of MALDI-TOF MS data, it was possible to correctly classify bacterial strains as either M. tuberculosis or non-tuberculous with 100% accuracy.     

Evaluation of the use of the bioMerieux Rapid ID32 A for the identification of Clostridium botulinum

The neurotoxins produced by Clostridium botulinum are amongst the most potent known to man. Toxin production is detected by a mouse bioassay, which requires several days for a result and is not acceptable for routine use unless there is a high level of suspicion. The Rapid ID32 A kit produced by bioMerieux gives an identification of an isolate within 4 h. The aim of this study was to examine the efficiency of the identification of Cl. botulinum using the Rapid ID32 A. Forty-two strains of Cl. botulinum , one strain each of botulinum toxin-producing Cl. butyricum and Cl. baratii , and four strains of Cl. sporogenes , were tested. One strain of Group I Cl. botulinum gave a presumptive identification of Group II Cl. botulinum , six strains of Cl. botulinum were identified as 50–98% Cl. botulinum in some tests, and 17 strains of Cl. botulinum were identified as <50% Cl. botulinum. Thirteen strains of Cl. botulinum were identified as >99% Cl. sporogenes or 86% Cl. histolyticum , and five strains gave a combination of these results. All strains of Cl. sporogenes were correctly identified. These results show that some strains of Cl. botulinum may not be correctly identified using the Rapid ID32 A.     

Sexing terns using biometrics: the advantage of within-pair comparisons

Capsule Within-pair comparisons substantially improve the accuracy of sexing from biometrics for two congeneric species of seabird with monomorphic plumage and soft-tissue colouration.

Aims To examine the extent to which statistical limitations of sexing birds from biometrics using sample-level analysis could be overcome by sexing Common and Arctic Terns (Sterna hirundo and S. paradisaea) using measurements obtained from breeding pairs.

Methods Incubating adults were caught at the nest using walk-in traps and wing, tarsus, head-plus-bill, tail length, tail fork, and body mass measured. Each bird was individually colour-ringed and dyed with picric acid, enabling subsequent sexing by behavioural observations of copulation and courtship feeding. Birds were sexed using biometrics and the proportion of birds sexed correctly this way at the sample level was compared with the accuracy achieved if, within a pair, the larger bird was classified as male.

Results Head-plus-bill length was the single most accurate measurement for sexing individuals of both species, and correctly classified 72% of Arctic Terns and 73% of Common Terns. Combinations of measurements derived from discriminant analysis achieved slightly higher accuracy (73% and 78% respectively). Within-pair comparisons were more accurate than sample-level analysis for both single measurements and discriminant functions, and were able to sex 84% of Arctic Terns and 86% of Common Terns correctly.

Conclusion Comparing birds within pairs improves accuracy and can eliminate the need to calculate cut points or discriminant functions from a sample of birds of known sex for each particular study. We strongly advocate such comparisons wherever possible to increase accuracy and simplify computational procedures for predicting sex, thus reducing associated sources of error.     

Morphological variability between wild populations and inbred stocks of a Chinese minnow, Gobiocypris rarus

Gobiocypris rarus, a small, native cyprinid fish, is currently widely used in research on fish pathology, genetics, toxicology, embryology, and physiology in China. To develop this species as a model laboratory animal, inbred strains have been successfully created. In this study, to explore a method to discriminate inbred strains and evaluate inbreeding effects, morphological variation among three wild populations and three inbred stocks of G. rarus was investigated by the multivariate analysis of eight meristic and 30 morphometric characters. Tiny intraspecific variations in meristic characters were found, but these were not effective for population distinction. Stepwise discriminant analysis and cluster analysis of conventional measures and truss network data showed considerable divergence among populations, especially between wild populations and inbred stocks. The average discriminant accuracy for all populations was 82.1% based on conventional measures and 86.4% based on truss data, whereas the discriminant accuracy for inbred strains was much higher. These results suggested that multivariate analyses of morphometric characters are an effective method for discriminating inbred strains of G. rarus. Morphological differences between wild populations and inbred strains appear to result from both genetic differences and environmental factors. Thirteen characters, extracted from stepwise discriminant analysis, played important roles in morphological differentiation. These characters were mainly measures related to body depth and head size.     

Classification and ordination of profundal macroinvertebrate communities in nutrient poor, oligo-mesohumic lakes in relation to environmental data

SUMMARY. 1. Profundal macroinvertebrates and water chemistry of sixty-eight nutrient poor, poorly buffered lakes were sampled in 1983 or 1986. Assemblages of profundal zoobenthos were classified using two-way indicator species analysis (TWINSPAN), ordinated by canonical correspondence analysis (CCA), and related to physico-chemical factors using CCA. discriminant analysis, and regression.
2. 90% of zoobenthos (TWINSPAN) groups were classified correctly using discriminant analysis. Depth (Function 1), soluble reactive Si(OH)₄ and HCO₃, -(2), and phytoplankton biovolume and pH (3) were the strongest correlates with the three discriminant functions.
3. Regression analysis showed that depth, KmnO₄, consumption, and phytoplankton biovolume were the best estimators of zoobenthos biomass in the profundal.
4. Multivariate analyses showed species assemblages amongst the profundal zoobenthos to be good indicators of lake type, particularly depth, pH, and phytoplankton biovolume.     

Immunofluorescence Staining of Group B Coxsackieviruses

Studies were conducted on the sensitivity and specificity of indirect fluorescent-antibody (FA) staining for identification of group B coxsackieviruses. Antisera produced in four different species (monkeys, rabbits, horses, hamsters) and immune ascitic fluids prepared in mice were compared for suitability in FA staining. The horse antisera showed high titers of nonspecific staining, and the rabbit antisera showed relatively low homologous FA titers. Immune reagents from monkeys, hamsters, and mice were used for homologous and heterologous testing against cell cultures infected with the various group B coxsackieviruses. Antisera or immune ascitic fluids produced in these three species showed some heterotypic and nonspecific staining at low dilutions, with the monkey antisera showing the highest heterotypic titers. However, the immune reagents could be diluted to a point where they gave no heterotypic reactivity, but still showed characteristic homotypic staining. Heterotypic staining appeared as diffuse, low-level staining of the cells, whereas homotypic staining revealed characteristic, brightly staining aggregates of viral antigen in the cytoplasm of the infected cells. By using hamster immune sera, appropriately diluted to eliminate heterotypic staining and yet give strong homotypic staining, it was possible to identify correctly 79 (93%) of 85 field strains of group B coxsackieviruses at the first passage level in BS-C-1 cells; the remainder of the strains were identified after two passages in BS-CS-1 cells. No incorrect identifications were made. A limited number of field strains of group B coxsackieviruses were passed into rhesus monkey kidney and human fetal diploid kidney cells, and these were all correctly identified by FA staining, even the strains which failed to produce a cytopathic effect in the human fetal diploid kidney cells. Two human heart and brain tissues from which coxsackievirus type B4 had been isolated failed to show homotypic FA staining in excess of nonspecific or heterotypic staining.     

Sex determination of African Penguins Spheniscus demersus using bill measurements: method comparisons and implications for use

African Penguins Spheniscus demersus are sexually dimorphic; on average, males are larger than females but measurements overlap making sex determination difficult through observations alone. We developed a discriminant function, using bill length and depth from a sample of birds sexed from gonad visualisation during post-mortem, which correctly classified 93% of the individuals. Cross-validation correctly assigned 90% of DNA-sexed birds and 91% of birds sexed by partner measurement comparisons. The use of discriminant function score cutpoints, while leaving 16% and 29% of birds unclassified, improved accuracy of birds sexed by DNA to 97% and of those sexed by partner comparison to 99%. Bill depth was found to be a discriminating variable. However, two techniques for measuring bill depth are currently in use for African Penguins. While these measurements are correlated (r = 0.85), they differ on average by 1.4?mm hindering accuracy of sex determination when using a discriminant function developed from the other bill depth measurement. Exploration of adult bill morphology of birds sexed from DNA at different colonies suggests the discriminant functions can be applied throughout the African Penguins’ South African range.     

SEX DETERMINATION OF THE CALIFORNIA SEA LION (ZALOPHUS CALIFORNIANUS CALIFORNIANUS) FROM CANINE TEETH

Size of canine teeth from California sea lion ( Zalophus californianus californianus ) carcasses is shown to be useful in determining the sex of animals which have missing genitalia or which are otherwise of unknown sex. A total of 267 canine teeth from carcasses of 68 males and 43 females were measured along five axes. Of root and crown measurements of upper and lower canines, males and females overlapped only in root thickness of upper canines. A multivariate ANOVA showed a significant difference in the size of canines between upper and lower canines, and between males and females. Stepwise discriminant analysis produced discriminant functions for upper and lower canines for determining sex of unknown-sexed California sea lions. A separate set of canine teeth from 39 male and 49 female California sea lions was correctly classified without prior knowledge of sex by visual inspection and by the two discriminant functions.