A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty.

On cluster analysis of complex and heterogeneous data

3rd SMTDA Conference Proceedings, 11-14 June 2014, Lisbon Portugal.

Clinicopathologic analysis of acute myeloid leukemia arising from chronic myelomonocytic leukemia.

Acute myeloid leukemia arising from chronic myelomonocytic leukemia is currently classified as acute myeloid leukemia with myelodysplasia-related changes, a high-risk subtype. However, the specific features of these cases have not been well described. We studied 38 patients with chronic myelomonocytic leukemia who progressed to acute myeloid leukemia. We compared the clinicopathologic and genetic features of these cases with 180 patients with de novo acute myeloid leukemia and 34 patients with acute myeloid leukemia following myelodysplastic syndromes. We also examined features associated with progression from chronic myelomonocytic leukemia to acute myeloid leukemia by comparing the progressed chronic myelomonocytic leukemia cases with a cohort of chronic myelomonocytic leukemia cases that did not transform to acute myeloid leukemia. Higher white blood cell count, marrow cellularity, karyotype risk score, and Revised International Prognostic Scoring System score were associated with more rapid progression from chronic myelomonocytic leukemia to acute myeloid leukemia. Patients with acute myeloid leukemia ex chronic myelomonocytic leukemia were older (P<0.01) and less likely to receive aggressive treatment (P=0.02) than de novo acute myeloid leukemia patients. Most cases showed monocytic differentiation and fell into the intermediate acute myeloid leukemia karyotype risk group; 55% had normal karyotype and 17% had NPM1 mutation. Median overall survival was 6 months, which was inferior to de novo acute myeloid leukemia (17 months, P=0.002) but similar to post myelodysplastic syndrome acute myeloid leukemia. On multivariate analysis of all acute myeloid leukemia patients, only age and karyotype were independent prognostic variables for overall survival. Our findings indicate that acute myeloid leukemia following chronic myelomonocytic leukemia displays aggressive behavior and support placement of these cases within the category of acute myeloid leukemia with myelodysplasia-related changes. The poor prognosis of these patients may be related to an older population and lack of favorable-prognosis karyotypes that characterize many de novo acute myeloid leukemia cases.

Existential behavioural therapy for informal caregivers of palliative patients: a randomised controlled trial.

BACKGROUND: Existential behavioural therapy (EBT) was developed to support informal caregivers of palliative patients in the last stage of life and during bereavement as a manualised group psychotherapy comprising six sessions. We tested the effectiveness of EBT on mental stress and quality of life (QOL). METHODS: Informal caregivers were randomly assigned (1:1) to EBT or a treatment-as-usual control group using computer-generated numbers in blocks of 10. Primary outcomes were assessed with the Brief Symptom Inventory (subscales somatisation, anxiety and depression), the Satisfaction with Life Scale (SWLS), the WHOQOL-BREF and a numeric rating scale for QOL (QOL-NRS, range 0-10). Data were collected at baseline, pre-treatment, post-treatment and follow-ups after 3 and 12âeuro0/00months. Treatment effects were assessed with a multivariate analysis of covariance. RESULTS: Out of 160 relatives, 81 were assigned to EBT and 79 to the control group. Participants were 54.5âeuro0/00±âeuro0/0013.2âeuro0/00years old; 69.9% were female. The multivariate model was significant for the pre-/post-comparison (pâeuro0/00=âeuro0/000.005) and the pre-/12-month comparison (pâeuro0/00=âeuro0/000.05) but not for the pre-/3-month comparison. Medium to large effects on anxiety and QOL (SWLS, WHOQOL-BREF, QOL-NRS) were found at post-treatment; medium effects on depression and QOL (QOL-NRS) emerged in the 12-month follow-up. No adverse effects of the intervention were observed. CONCLUSION: Existential behavioural therapy appears to exert beneficial effects on distress and QOL of informal caregivers of palliative patients. Further longitudinal evidence is needed to confirm these findings. Copyright © 2013 John Wiley & Sons, Ltd.

Clinical relevance of CD44 cell-surface expression and N-myc gene amplification in a multicentric analysis of 121 pediatric neuroblastomas.

PURPOSE: In contrast to other human tumors, a repression of the cell-surface glycoprotein CD44 on neuroblastoma is a marker of aggressiveness that usually correlates to N-myc amplification. We thus compared the prognostic value of both markers in the initial staging of 121 children treated for neuroblastoma in collaborative institutions. METHODS: Frozen samples were analyzed by a rapid and well-standardized technique of immunostaining with monoclonal antibodies (MoAbs) against epitopes in the CD44 constant region. RESULTS: In this retrospective series, CD44 was expressed on 102 specimens and strongly correlated with favorable tumor stages and histology, younger age, and normal N-myc copy numbers. In univariate analysis, CD44 expression and normal N-myc were the most powerful markers of favorable clinical outcome (P < 10(-6) and chi 2 = 65.40 and P < 10(-6) and chi 2 = 42.56, respectively), but analysis of CD44 affords significant prognostic discrimination in subgroups of patients with or without N-myc-amplified tumors. In the subgroup of stage IV neuroblastomas, CD44 was the only significant prognostic marker (P < .02, chi 2 = 5.76), whereas N-myc status was not discriminant. In multivariate analysis of five factors, ie, N-myc amplification, CD44 expression, age, tumor stage, and histology, the only independent prognostic factors of event-free survival were CD44 expression and tumor stage. CONCLUSION: The analysis of CD44 cell-surface expression must be recommended as an additional biologic marker in the initial staging of the disease.

Persistence of cognitive impairment and its negative impact on psychosocial functioning in lithium-treated, euthymic bipolar patients: a 6-year follow-up study.

BACKGROUND: Previous cross-sectional studies report that cognitive impairment is associated with poor psychosocial functioning in euthymic bipolar patients. There is a lack of long-term studies to determine the course of cognitive impairment and its impact on functional outcome. Method A total of 54 subjects were assessed at baseline and 6 years later; 28 had DSM-IV TR bipolar I or II disorder (recruited, at baseline, from a Lithium Clinic Program) and 26 were healthy matched controls. They were all assessed with a cognitive battery tapping into the main cognitive domains (executive function, attention, processing speed, verbal memory and visual memory) twice over a 6-year follow-up period. All patients were euthymic (Hamilton Rating Scale for Depression score lower than 8 and Young mania rating scale score lower than 6) for at least 3 months before both evaluations. At the end of follow-up, psychosocial functioning was also evaluated by means of the Functioning Assessment Short Test. RESULTS: Repeated-measures multivariate analysis of covariance showed that there were main effects of group in the executive domain, in the inhibition domain, in the processing speed domain, and in the verbal memory domain (p<0.04). Among the clinical factors, only longer illness duration was significantly related to slow processing (p=0.01), whereas strong relationships were observed between impoverished cognition along time and poorer psychosocial functioning (p<0.05). CONCLUSIONS: Executive functioning, inhibition, processing speed and verbal memory were impaired in euthymic bipolar out-patients. Although cognitive deficits remained stable on average throughout the follow-up, they had enduring negative effects on psychosocial adaptation of patients.

Analysis of time-related metabolic fluctuations induced by ethionine in the rat

The time-course of metabolic events following response to a model hepatotoxin ethionine (800 mg/kg) was investigated over a 7 day period in rats using high-resolution (1)H NMR spectroscopic analysis of urine and multivariate statistics. Complementary information was obtained by multivariate analysis of (1)H MAS NMR spectra of intact liver and by conventional histopathology and clinical chemistry of blood plasma. (1)H MAS NMR spectra of liver showed toxin-induced lipidosis 24 h postdose consistent with the steatosis observed by histopathology, while hypertaurinuria was suggestive of liver injury. Early biochemical changes in urine included elevation of guanidinoacetate, suggesting impaired methylation reactions. Urinary increases in 5-oxoproline and glycine suggested disruption of the gamma-glutamyl cycle. Signs of ATP depletion together with impairment of the energy metabolism were given from the decreased levels in tricarboxylic acid cycle intermediates, the appearance of ketone bodies in urine, the depletion of hepatic glucose and glycogen, and also hypoglycemia. The observed increase in nicotinuric acid in urine could be an indication of an increase in NAD catabolism, a possible consequence of ATP depletion. Effects on the gut microbiota were suggested by the observed urinary reductions in the microbial metabolites 3-/4-hydroxyphenyl propionic acid, dimethylamine, and tryptamine. At later stages of toxicity, there was evidence of kidney damage, as indicated by the tubular damage observed by histopathology, supported by increased urinary excretion of lactic acid, amino acids, and glucose. These studies have given new insights into mechanisms of ethionine-induced toxicity and show the value of multisystem level data integration in the understanding of experimental models of toxicity or disease.

Analysis of various conditions in order to measure electromyography of isometric contractions in water and on air

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Comparing the tadpoles of Hyla geographica and Hyla semilineata

External morphology, internal oral anatomy, and chondrocranial anatomy were examined for tadpoles of Hyla geographica from the Amazon rainforest, Brazil, and Hyla semilineata from the Atlantic rainforest, Brazil. Here, we provide morphological larval data to help diagnose these closely related species. Scanning electron microscopy analysis of buccal morphology showed the most distinctive features between these species: the distance between the lingual papillae in the buccal floor of H. geographica is three times greater than that distance in H. semilineata, and the relative size of the lingual papillae in H. geographica is less than half their size in H. semilineata. Although the chondrocranium of both species is identical, and the external morphology of the larvae of both taxa is very similar, they differ greatly in size at most developmental stages. A multivariate analysis of covariance, corrected for stage and size, also showed a significant difference between morphometric measurements of the two species. These differences support the existence of two separate taxa.

Surface roughness of packable composite resins polished with various systems

Purpose: The aim of this study was to evaluate the surface roughness of four packable composite resins, SureFil™ (Dentsply, Petrópolis, Rio de Janeiro, Brazil), Prodigy Condensable™ (Kerr Co., Orange, CA, USA), Filtek P60™ (3M do Brasil, São Paulo, Brazil), and ALERT® (Jeneric/Pentron, Inc., Wallingford, CT, USA) and one microhybrid composite resin (Filtek Z250™, 3M do Brasil) after polishing with four finishing systems. Materials and Methods: Twenty specimens were made of each material (5 mm in diameter and 4 mm high) and were analyzed with a profilometer (Perthometer® S8P, Perthen, Mahr, Germany) to measure the mean surface roughness (Ra). The specimens were then divided into four groups according to the polishing system: group 1 - Sof-Lex™ (3M do Brasil), group 2 - Enhance™ (Dentsply), group 3 - Composite Finishing Kit (KG Sorensen, Barueri, São Paulo, Brazil), and group 4 - Jiffy Polisher Cups® (Ultradent Products, Inc., South Jordan, UT, USA). The specimens were polished and then evaluated for Ra, and the data were subjected to analysis of variance, analysis of covariance, and Tukey's test (p = .05). Results: The mean Ra of SureFil polished with Sof-Lex was significantly lower than that of KG points. Prodigy Condensable polished with Enhance showed a significantly less rough surface than when polished with Sof-Lex. Filtek P60 did not exhibit a significant difference with the various polishing systems. For ALERT the lowest mean Ra was obtained with Sof-Lex and the highest mean Ra with KG points. Regarding Filtek Z250, polishing with KG and Jiffy points resulted in a significantly lower mean Ra than when polished with Enhance. Conclusions: Packable composite resins display variable roughness depending on the polishing system used; the Sof-Lex disks and Jiffy points resulted in the best Ra values for the majority of the materials tested.

Morphometric analysis of a population of diplopods of the genus Rhinocricus Karsch, 1881

Diplopods belonging to the subclass Helminthomorpha may present one or both leg pairs of the seventh diplosegment modified into structures that aid copulation, called gonopods. These structures are used as a taxonomic trait for the description of most species. In the genus Rhinocricus these structures are closely similar, so that it is difficult to distinguish species only on the basis of this trait. Two species, R. padbergi and R. varians, are found in the same habitat and present gonopods practically identical in shape; together they present a broad colour gradient, ranging from dark brown to light beige. Morphometric data for individuals of the experimental group were submitted to ANOVA and MANOVA, using Hotelling-Lawley Trace and generalized Mahalanobis distances (D 2) tests. The results demonstrated a relationship between size and colour, with darker individuals being larger. On the basis of this preliminary analysis, we may suggest that the two species are distinct since dark individuals are distant from medium- and light-coloured individuals according to the D 2 values. This seems to indicate a possible polymorphism of individuals belonging to R. padbergi which present close proximity in the values obtained. In all analyses, we observed that the main variables were diameter, length and telson size.

Discriminant analysis of neuromuscular variables in chronic low back pain

Background: Investigation and discrimination of neuromuscular variables related to the complex aetiology of low back pain could contribute to clarifying the factors associated with symptoms. Objective: Analysing the discriminative power of neuromuscular variables in low back pain. Methods: This study compared muscle endurance, proprioception and isometric trunk assessments between women with low back pain (LBP, n=14) and a control group (CG, n=14). Multivariate analysis of variance and discriminant analysis of the data were performed. Results: The muscle endurance time (s) was shorter in the LBP group than in the CG (p=0.004) with values of 85.81 (37.79) and 134.25 (43.88), respectively. The peak torque (Nm/kg) for trunk extension was 2.48 (0.69) in the LBP group and 3.56 (0.88) in the GG (p=0.001); for trunk flexion, the mean torque was 1.49 (0.40) in the LBP group and 1.85 (0.39) in the CG (p=0.023). The repositioning error (degrees) before the endurance test was 2.66 (1.36) in the LBP group and 2.41 (1.46) in the CG (p=0.664), and after the endurance test, it was 2.95 (1.94) in the LBP group and 2.00 (1.16) in the CG (p=0.06). Furthermore, the variables showed discrimination between the groups (p=0.007), with 78.6% of the individuals with low back pain correctly classified in the LBP group. In turn, variables related to muscle activation showed no difference in discrimination between the groups (p=0.369). Conclusion: Based on these findings, the clinical management of low back pain should consist of both resistance and strength training, particularly in the extensor muscles.

Diagnostic index of three-dimensional osteoarthritic changes in temporomandibular joint condylar morphology

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Morphological, molecular and cross-breeding analysis of geographic populations of coconut-mite associated predatory mites identified as Neoseiulus baraki: evidence for cryptic species?

Surveys were conducted in Brazil, Benin and Tanzania to collect predatory mites as candidates for control of the coconut mite Aceria guerreronis Keifer, a serious pest of coconut fruits. At all locations surveyed, one of the most dominant predators on infested coconut fruits was identified as Neoseiulus baraki Athias-Henriot, based on morphological similarity with regard to taxonomically relevant characters. However, scrutiny of our own and published descriptions suggests that consistent morphological differences may exist between the Benin population and those from the other geographic origins. In this study, we combined three methods to assess whether these populations belong to one species or a few distinct, yet closely related species. First, multivariate analysis of 32 morphological characters showed that the Benin population differed from the other three populations. Second, DNA sequence analysis based on the mitochondrial cytochrome oxidase subunit I (COI) showed the same difference between these populations. Third, cross-breeding between populations was unsuccessful in all combinations. These data provide evidence for the existence of cryptic species. Subsequent morphological research showed that the Benin population can be distinguished from the others by a new character (not included in the multivariate analysis), viz. the number of teeth on the fixed digit of the female chelicera.

A multi-center retrospective analysis of treatment effects and quality of life in adult patients with cranial ependymomas

Long term quality of life data of adult patients harboring intracranial ependymomas have not been reported. The role of adjuvant radiation therapy in Grade II ependymomas is unclear and differs from study to study. We therefore sought to retrospectively analyze outcome and quality of life of adult patients that were operated on intracranial ependymomas at four different surgical centers in two countries. All patients were attempted to be contacted via telephone to assess quality of life (QoL) at the time of the telephone interview. The standard EORTC QoL Questionnaire C30 (EORTC QLQ-C30) and the EORTC QLQ-Brain Cancer Module (QLQ-BN20) were used. 64 adult patients with intracranial ependymomas were included in the study. The only factor that was associated with increased survival was age <55 years (p < 0.001). Supratentorial location was correlated with shorter progression free survival than infratentorial location (PFS; p = 0.048). In WHO Grade II tumors local irradiation did not lead to increased PFS (p = 0.888) or overall survival (p = 0.801). Even for incompletely resected Grade II tumors local irradiation did not lead to a benefit in PFS (p = 0.911). In a multivariate analysis of QoL, irradiated patients had significantly worse scores in the item "fatigue" (p = 0.037) than non-irradiated patients. Here we present QoL data of adult patients with intracranial ependymomas. Our data show that local radiation therapy may have long-term effects on patients' QoL. Since in the incompletely resected Grade II tumors local irradiation did not lead to a benefit in PFS in this retrospective study, prospective randomized studies are necessary. In addition to age, supratentorial tumor location is associated with a worse prognosis in adult ependymoma patients.