Transições reversíveis de células de leveduras entre estados viáveis, mas não cultiváveis (VBNC) e estados viáveis e cultiváveis

Pós-graduação em Biotecnologia - IQ

Influence diagnostics in Gaussian spatial linear models

Spatial linear models have been applied in numerous fields such as agriculture, geoscience and environmental sciences, among many others. Spatial dependence structure modelling, using a geostatistical approach, is an indispensable tool to estimate the parameters that define this structure. However, this estimation may be greatly affected by the presence of atypical observations in the sampled data. The purpose of this paper is to use diagnostic techniques to assess the sensitivity of the maximum-likelihood estimators, covariance functions and linear predictor to small perturbations in the data and/or the spatial linear model assumptions. The methodology is illustrated with two real data sets. The results allowed us to conclude that the presence of atypical values in the sample data have a strong influence on thematic maps, changing the spatial dependence structure.

A quantitative approach to evolution of music and philosophy

The development of new statistical and computational methods is increasingly making it possible to bridge the gap between hard sciences and humanities. In this study, we propose an approach based on a quantitative evaluation of attributes of objects in fields of humanities, from which concepts such as dialectics and opposition are formally defined mathematically. As case studies, we analyzed the temporal evolution of classical music and philosophy by obtaining data for 8 features characterizing the corresponding fields for 7 well-known composers and philosophers, which were treated with multivariate statistics and pattern recognition methods. A bootstrap method was applied to avoid statistical bias caused by the small sample data set, with which hundreds of artificial composers and philosophers were generated, influenced by the 7 names originally chosen. Upon defining indices for opposition, skewness and counter-dialectics, we confirmed the intuitive analysis of historians in that classical music evolved according to a master apprentice tradition, while in philosophy changes were driven by opposition. Though these case studies were meant only to show the possibility of treating phenomena in humanities quantitatively, including a quantitative measure of concepts such as dialectics and opposition, the results are encouraging for further application of the approach presented here to many other areas, since it is entirely generic.

Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays

Abstract Background Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies). For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard. Results We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo) against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i) ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii) reconstructed ratios derived from hybridization of each tissue against a reference RNA pool (RefPool). To evaluate the effect of the external references, reconstructed ratios were also calculated directly from intensity values of single-channel (One-Color) measurements derived from tissue sample data collected in the RefOligo experiments. We show that the average coefficient of variation of ratios between intra- and inter-slide replicates derived from RefOligo, RefPool and One-Color were similar and 2 to 4-fold higher than ratios obtained in direct hybridizations. Correlation coefficients calculated for all three tissue comparisons were also similar. In addition, the performance of all indirect methods in terms of their robustness to identify genes deemed as differentially expressed based on direct hybridizations, as well as false-positive and false-negative rates, were found to be comparable. Conclusion RefOligo produces ratios as precise and accurate as ratios reconstructed from a RNA pool, thus representing a reliable alternative in reference-based hybridization experiments. In addition, One-Color measurements alone can reconstruct expression ratios without loss in precision or accuracy. We conclude that both methods are adequate options in large-scale projects where the amount of a common reference RNA pool is usually restrictive.

Image analysis in the morphological and morphometric study of teeth

The subject of this doctoral dissertation concerns the definition of a new methodology for the morphological and morphometric study of fossilized human teeth, and therefore strives to provide a contribution to the reconstruction of human evolutionary history that proposes to extend to the different species of hominid fossils. Standardized investigative methodologies are lacking both regarding the orientation of teeth subject to study and in the analysis that can be carried out on these teeth once they are oriented. The opportunity to standardize a primary analysis methodology is furnished by the study of certain early Neanderthal and preneanderthal molars recovered in two caves in southern Italy [Grotta Taddeo (Taddeo Cave) and Grotta del Poggio (Poggio Cave), near Marina di Camerata, Campania]. To these we can add other molars of Neanderthal and modern man of the upper Paleolithic era, specifically scanned in the paleoanthropology laboratory of the University of Arkansas (Fayetteville, Arkansas, USA), in order to increase the paleoanthropological sample data and thereby make the final results of the analyses more significant. The new analysis methodology is rendered as follows: 1. Standardization of an orientation system for primary molars (superior and inferior), starting from a scan of a sample of 30 molars belonging to modern man (15 M1 inferior and 15 M1 superior), the definition of landmarks, the comparison of various systems and the choice of a system of orientation for each of the two dental typologies. 2. The definition of an analysis procedure that considers only the first 4 millimeters of the dental crown starting from the collar: 5 sections parallel to the plane according to which the tooth has been oriented are carried out, spaced 1 millimeter between them. The intention is to determine a method that allows for the differentiation of fossilized species even in the presence of worn teeth. 3. Results and Conclusions. The new approach to the study of teeth provides a considerable quantity of information that can better be evaluated by increasing the fossil sample data. It has been demonstrated to be a valid tool in evolutionary classification that has allowed (us) to differentiate the Neanderthal sample from that of modern man. In a particular sense the molars of Grotta Taddeo, which up until this point it has not been possible to determine with exactness their species of origin, through the present research they are classified as Neanderthal.

The contexts of scratching behavior and postconflict behavior in squirrel monkeys (Saimiri sciureus)

Self-directed behavior (SDB), such as scratching, is a reliable indicator of emotional arousal in non-human primates. In contrast, affiliative behavior, such as social grooming, has been shown to have a calming effect in primates and reduce arousal. In order to test whether the expression of SDB was related to arousal, the scratching behavior of eight captive squirrel monkeys (Saimiri sciureus) was compared across four social contexts (huddling, proximity to others, solitary and post-conflict). In addition,rates of scratching were examined before and after affiliative behavior during the postconflict context. I tested for this effect by using the post-conflict/matched control(PC/MC) method in which post-conflict (PC) behavior of an animal is compared to thebehavior of the same animal in a baseline, nonaggressive situation or a matched control(MC). Context and associated scratching data were obtained from a total of 98 hours of focal sample data. Scratching was significantly lower while animals were huddling thanthe other two contexts. Scratching rates while solitary were significantly higher than those occurring while animals were in proximity. Scratching was also higher in PC than MC. Following conflict, animals were significantly more likely to make contact withthird parties not involved in aggression. Most of these (79%) were a third party approaching a combatant. Further, scratching rates decreased following post-conflict third party contacts and the decrease was not due to a general decrease in scratching thatmight have been occurring after the aggressive interaction. Huddling behavior appears to reduce arousal in squirrel monkeys and may act as a tension-reduction mechanism. The elevated scratching in the solitary context may suggest that squirrel monkeys may be engaged in activities while solitary, such as vigilant behavior that may increase arousal. The third party post conflict affiliative contacts observed were the first such interactions observed in squirrel monkeys. The fact that these third contacts reduced scratching ratesin the combatants indicates that 'consolation' may have been demonstrated in this species. The overall pattern of results suggested that scratching was reliable behavioral indicator of anxiety in squirrel monkeys. These results indicate that overt behavior can be used to assess emotional states in this and other species, acting as a mediator to understanding how emotions regulate social behavior.

A Robust Parser of Czech

Mr. Kubon's project was inspired by the growing need for an automatic, syntactic analyser (parser) of Czech, which could be used in the syntactic processing of large amounts of texts. Mr. Kubon notes that such a tool would be very useful, especially in the field of corpus linguistics, where creating a large-scale "tree bank" (a collection of syntactic representations of natural language sentences) is a very important step towards the investigation of the properties of a given language. The work involved in syntactically parsing a whole corpus in order to get a representative set of syntactic structures would be almost inconceivable without the help of some kind of robust (semi)automatic parser. The need for the automatic natural language parser to be robust increases with the size of the linguistic data in the corpus or in any other kind of text which is going to be parsed. Practical experience shows that apart from syntactically correct sentences, there are many sentences which contain a "real" grammatical error. These sentences may be corrected in small-scale texts, but not generally in the whole corpus. In order to be able to complete the overall project, it was necessary to address a number of smaller problems. These were; 1. the adaptation of a suitable formalism able to describe the formal grammar of the system; 2. the definition of the structure of the system's dictionary containing all relevant lexico-syntactic information, and the development of a formal grammar able to robustly parse Czech sentences from the test suite; 3. filling the syntactic dictionary with sample data allowing the system to be tested and debugged during its development (about 1000 words); 4. the development of a set of sample sentences containing a reasonable amount of grammatical and ungrammatical phenomena covering some of the most typical syntactic constructions being used in Czech. Number 3, building a formal grammar, was the main task of the project. The grammar is of course far from complete (Mr. Kubon notes that it is debatable whether any formal grammar describing a natural language may ever be complete), but it covers the most frequent syntactic phenomena, allowing for the representation of a syntactic structure of simple clauses and also the structure of certain types of complex sentences. The stress was not so much on building a wide coverage grammar, but on the description and demonstration of a method. This method uses a similar approach as that of grammar-based grammar checking. The problem of reconstructing the "correct" form of the syntactic representation of a sentence is closely related to the problem of localisation and identification of syntactic errors. Without a precise knowledge of the nature and location of syntactic errors it is not possible to build a reliable estimation of a "correct" syntactic tree. The incremental way of building the grammar used in this project is also an important methodological issue. Experience from previous projects showed that building a grammar by creating a huge block of metarules is more complicated than the incremental method, which begins with the metarules covering most common syntactic phenomena first, and adds less important ones later, especially from the point of view of testing and debugging the grammar. The sample of the syntactic dictionary containing lexico-syntactical information (task 4) now has slightly more than 1000 lexical items representing all classes of words. During the creation of the dictionary it turned out that the task of assigning complete and correct lexico-syntactic information to verbs is a very complicated and time-consuming process which would itself be worth a separate project. The final task undertaken in this project was the development of a method allowing effective testing and debugging of the grammar during the process of its development. The problem of the consistency of new and modified rules of the formal grammar with the rules already existing is one of the crucial problems of every project aiming at the development of a large-scale formal grammar of a natural language. This method allows for the detection of any discrepancy or inconsistency of the grammar with respect to a test-bed of sentences containing all syntactic phenomena covered by the grammar. This is not only the first robust parser of Czech, but also one of the first robust parsers of a Slavic language. Since Slavic languages display a wide range of common features, it is reasonable to claim that this system may serve as a pattern for similar systems in other languages. To transfer the system into any other language it is only necessary to revise the grammar and to change the data contained in the dictionary (but not necessarily the structure of primary lexico-syntactic information). The formalism and methods used in this project can be used in other Slavic languages without substantial changes.

Beherrschung stark korrelierter Logistik- und Produktions-Prozesse

Bei der Simulation von Logistik- und Produktionssystem werden Zufallszahlengeneratoren verwendet, um stochastische Einflüsse zu modellieren. Ein wichtiges Qualitätsmerkmal dieser Generatoren ist die Er-zeugung möglichst unabhängiger Zufallszahlen. Werden jedoch reale Prozesse betrachtet, so sind die Daten im Allgemeinen nicht unabhängig. Diese Arbeit befasst sich mit der Analyse von Praxisdaten bezüglich des Auftretens von Abhängigkeiten. Dazu werden Korrelationsstrukturen gesucht. Außerdem wird gezeigt, dass unabhängige Zufallszahlen in der Regel ungeeignet sind, um stochastische Prozesse mit ausgeprägten Abhängigkeiten zu modellieren.

Structural equation modeling of the medical outcome study: Short Form 36 (SF-36)

The factorial validity of the SF-36 was evaluated using confirmatory factor analysis (CFA) methods, structural equation modeling (SEM), and multigroup structural equation modeling (MSEM). First, the measurement and structural model of the hypothesized SF-36 was explicated. Second, the model was tested for the validity of a second-order factorial structure, upon evidence of model misfit, determined the best-fitting model, and tested the validity of the best-fitting model on a second random sample from the same population. Third, the best-fitting model was tested for invariance of the factorial structure across race, age, and educational subgroups using MSEM.^ The findings support the second-order factorial structure of the SF-36 as proposed by Ware and Sherbourne (1992). However, the results suggest that: (a) Mental Health and Physical Health covary; (b) general mental health cross-loads onto Physical Health; (c) general health perception loads onto Mental Health instead of Physical Health; (d) many of the error terms are correlated; and (e) the physical function scale is not reliable across these two samples. This hierarchical factor pattern was replicated across both samples of health care workers, suggesting that the post hoc model fitting was not data specific. Subgroup analysis suggests that the physical function scale is not reliable across the "age" or "education" subgroups and that the general mental health scale path from Mental Health is not reliable across the "white/nonwhite" or "education" subgroups.^ The importance of this study is in the use of SEM and MSEM in evaluating sample data from the use of the SF-36. These methods are uniquely suited to the analysis of latent variable structures and are widely used in other fields. The use of latent variable models for self reported outcome measures has become widespread, and should now be applied to medical outcomes research. Invariance testing is superior to mean scores or summary scores when evaluating differences between groups. From a practical, as well as, psychometric perspective, it seems imperative that construct validity research related to the SF-36 establish whether this same hierarchical structure and invariance holds for other populations.^ This project is presented as three articles to be submitted for publication. ^

Correlation between serum total globulins and gamma globulins and their use to diagnose failure of passive transfer in foals.

Various assays have been used as an aid to diagnose failure of passive transfer (FPT) of immunoglobulins in neonatal foals, but often lack sensitivity as screening tests, or are time consuming to perform and impractical as confirmatory tests. The aim of the present study was to evaluate whether measurement of serum total globulins (TG; i.e. total protein minus albumin) can be used to estimate the electrophoretic gamma globulin (EGG) fraction in hospitalised neonatal foals with suspected FPT. Sample data from 56 foals were evaluated retrospectively. The coefficient of rank correlation was 0.84. The area under the curve of ROC analysis was 0.887, 0.922 and 0.930 for EGG concentrations <2 g/L, < 4 g/L and <8 g/L, respectively. Cut-offs for TG achieved ≥90% sensitivity for detecting EGG <2 g/L, < 4 g/L and <8 g/L, with negative predictive values of >97% and >94%, using prevalence of 15% and 30%, respectively. These results suggest that measurement of TG can be used as a guide to predicting EGG, provided that appropriate cut-off values are selected, and this technique could be a useful initial screening test for FPT in foals.

Maternal Role & High-Risk Pregnancy Experience with Antepartum Hospitalization

Purpose. The focus of maternal role development, historically, has been on the tasks and processes during pregnancy as they relate to postpartum role transition. The purpose of this study was to investigate how women hospitalized with high-risk pregnancy cognitively construct pregnancy and impending motherhood. ^ Design. The study employed a triangulation design using a convergence model with a dominant focused ethnographic approach. ^ Setting. The antepartum units of two tertiary care centers in a large metropolitan city in southeast Texas. ^ Sample. Data saturation was determined with thirteen (13) primigravid women who had been hospitalized more than 72 hours with preterm labor (PTL) or preterm premature rupture of membranes (PPROM) who subsequently delivered seventeen (17) infants which included 4 sets of twins. ^ Methods. Open-ended, semi-structured interviews and field work were used to explore the development of maternal role in this population. After collecting descriptive data, long individual interviews were conducted and the Prenatal Self Evaluation Questionnaire (PSEQ), an instrument to measure prenatal adaptation to pregnancy, was administered. The interview focused on exploring the woman's experiences of pregnancy and impending motherhood while hospitalized. Interview data and field notes were coded and analyzed using qualitative thematic analytic techniques. The PSEQ was scored and the findings of the qualitative data and PSEQ data were compared. ^ Findings. Thematic analysis of the qualitative data provided an understanding of the cognitive process that occurs as the pregnant woman builds a relationship with the fetus. Thematic analysis resulted in a conceptual model with two complementary components that occur throughout the pregnancy: Establishing a Relationship and Dynamic Equilibrium. Establishing a Relationship includes subthemes of: Courting, Building a Connection, and Engagement. Dynamic equilibrium is the balance between expectations and reality and exists regardless of pregnancy complications. The negotiation of this potential imbalance is triggered by uncertainty, loss of autonomy and control, and isolation and is exacerbated by the high-risk pregnancy and subsequent hospitalization. These triggers can serve as obstacles to maternal role development, but may be mediated by external support from friends and family or health care providers. Support from others may come in the form of anticipatory guidance, presence, or activities that promote self-agency. PSEQ scores were similar to previous reports, but due to the small sample, scores were used primarily for comparison to qualitative data. The qualitative findings were congruent with the PSEQ findings in all of the subscales except in the concern for the well-being of the baby. Interview reports included comments demonstrating significant concern for the well-being of the infant, yet the related subscale did not demonstrate such concern. ^ Conclusions. An understanding of the cognitive process involved in establishing a relationship with the developing fetus related to impending motherhood and the importance of dynamic equilibrium can allow healthcare providers and those who interact with pregnant women to support development of the maternal role and anticipate those barriers that may impede that process. Findings from this study identify those triggers and mediators that influence development of the maternal role and suggest potential intervening strategies for those involved in the care of childbearing families. ^

A STUDY ON THE EPIDEMIOLOGY OF POSITIVE PHYSICAL HEALTH (NHANES I)

HANES 1 detailed sample data were used to operationalize a definition of health in the absence of disease and to describe and compare the characteristics of the normal (healthy) group versus an abnormal (unhealthy) group.^ Parallel screening gave a 3.8 percent prevalence proportion of physical health, with a female:male ratio of 2:1 and younger ages in the healthy group. Statistically significant Mantel-Haenszel gender-age-adjusted odds ratios (MHOR) were estimated among abnormal non-migrants (1.53), skilled workers/unemployed (1.76), annual family incomes of less than $10,000 (1.56), having ever smoked (1.58), and started smoking before 18 years of age (1.58). Significant MHOR were also found for abnormals for health promoting measures: non-iodized salt use (1.94), needed dental care (1.91); and for fair to poor perceived health (4.28), perceiving health problems (2.52), and low energy level (1.68). Significant protective effects for much to moderate recreational exercise (MHOR 0.42) and very active to moderate non-recreational activity (MHOR 0.49) were also obtained. Covariance analysis additive models detected statistically significant higher mean values for abnormals than normals for serum magnesium, hemoglobin, hematocrit, urinary creatinine, and systolic and diastolic blood pressures, and lower values for abnormals than normals for serum iron. No difference was detected for serum cholesterol. Significant non-additive joint effects were found for body mass index.^ The results suggest positive physical health can be measured with cross-sectional survey data. Gender differentials, and associations between ecologic, socioeconomic, hazardous risk factors, health promoting activities and physical health are in general agreement with published findings on studies of morbidity. Longitudinal prospective studies are suggested to establish the direction of the associations and to enhance present knowledge of health and its promoting factors. ^