Combinatorics on Words. New Aspects on Avoidability, Defect Effect, Equations and Palindromes

In this thesis we examine four well-known and traditional concepts of combinatorics on words. However the contexts in which these topics are treated are not the traditional ones. More precisely, the question of avoidability is asked, for example, in terms of k-abelian squares. Two words are said to be k-abelian equivalent if they have the same number of occurrences of each factor up to length k. Consequently, k-abelian equivalence can be seen as a sharpening of abelian equivalence. This fairly new concept is discussed broader than the other topics of this thesis. The second main subject concerns the defect property. The defect theorem is a well-known result for words. We will analyze the property, for example, among the sets of 2-dimensional words, i.e., polyominoes composed of labelled unit squares. From the defect effect we move to equations. We will use a special way to define a product operation for words and then solve a few basic equations over constructed partial semigroup. We will also consider the satisfiability question and the compactness property with respect to this kind of equations. The final topic of the thesis deals with palindromes. Some finite words, including all binary words, are uniquely determined up to word isomorphism by the position and length of some of its palindromic factors. The famous Thue-Morse word has the property that for each positive integer n, there exists a factor which cannot be generated by fewer than n palindromes. We prove that in general, every non ultimately periodic word contains a factor which cannot be generated by fewer than 3 palindromes, and we obtain a classification of those binary words each of whose factors are generated by at most 3 palindromes. Surprisingly these words are related to another much studied set of words, Sturmian words.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

Service offering classification for logistics services

This thesis studies the development of service offering model that creates added-value for customers in the field of logistics services. The study focusses on offering classification and structures of model. The purpose of model is to provide value-added solutions for customers and enable superior service experience. The aim of thesis is to define what customers expect from logistics solution provider and what value customers appreciate so greatly that they could invest in value-added services. Value propositions, costs structures of offerings and appropriate pricing methods are studied. First, literature review of creating solution business model and customer value is conducted. Customer value is found out with customer interviews and qualitative empiric data is used. To exploit expertise knowledge of logistics, innovation workshop tool is utilized. Customers and experts are involved in the design process of model. As a result of thesis, three-level value-added service offering model is created based on empiric and theoretical data. Offerings with value propositions are proposed and the level of model reflects the deepness of customer-provider relationship and the amount of added value. Performance efficiency improvements and cost savings create the most added value for customers. Value-based pricing methods, such as performance-based models are suggested to apply. Results indicate the interest of benefitting networks and partnership in field of logistics services. Networks development is proposed to be investigated further.

The supermassive binary black hole system OJ287

Abstract This doctoral thesis concerns the active galactic nucleus (AGN) most often referred to with the catalogue number OJ287. The publications in the thesis present new discoveries of the system in the context of a supermassive binary black hole model. In addition, the introduction discusses general characteristics of the OJ287 system and the physical fundamentals behind these characteristics. The place of OJ287 in the hierarchy of known types of AGN is also discussed. The introduction presents a large selection of fundamental physics required to have a basic understanding of active galactic nuclei, binary black holes, relativistic jets and accretion disks. Particularly the general relativistic nature of the orbits of close binaries of supermassive black holes is explored with some detail. Analytic estimates of some of the general relativistic effects in such a binary are presented, as well as numerical methods to calculate the effects more precisely. It is also shown how these results can be applied to the OJ287 system. The binary orbit model forms the basis for models of the recurring optical outbursts in the OJ287 system. In the introduction, two physical outburst models are presented in some detail and compared. The radiation hydrodynamics of the outbursts are discussed and optical light curve predictions are derived. The precursor outbursts studied in Paper III are also presented, and tied into the model of OJ287. To complete the discussion of the observable features of OJ287, the nature of the relativistic jets in the system, and in active galactic nuclei in general, is discussed. Basic physics of relativistic jets are presented, with additional detail added in the form of helical jet models. The results of Papers II, IV and V concerning the jet of OJ287 are presented, and their relation to other facets of the binary black hole model is discussed. As a whole, the introduction serves as a guide, though terse, for the physics and numerical methods required to successfully understand and simulate a close binary of supermassive black holes. For this purpose, the introduction necessarily combines a large number of both fundamental and specific results from broad disciplines like general relativity and radiation hydrodynamics. With the material included in the introduction, the publications of the thesis, which present new results with a much narrower focus, can be readily understood. Of the publications, Paper I presents newly discovered optical data points for OJ287, detected on archival astronomical plates from the Harvard College Observatory. These data points show the 1900 outburst of OJ287 for the first time. In addition, new data points covering the 1913 outburst allowed the determination of the start of the outburst with more precision than was possible before. These outbursts were then successfully numerically modelled with an N-body simulation of the OJ287 binary and accretion disc. In Paper II, mechanisms for the spin-up of the secondary black hole in OJ287 via interaction with the primary accretion disc and the magnetic fields in the system are discussed. Timescales for spin-up and alignment via both processes are estimated. It is found that the secondary black hole likely has a high spin. Paper III reports a new outburst of OJ287 in March 2013. The outburst was found to be rather similar to the ones reported in 1993 and 2004. All these outbursts happened just before the main outburst season, and are called precursor outbursts. In this paper, a mechanism was proposed for the precursor outbursts, where the secondary black hole collides with a gas cloud in the primary accretion disc corona. From this, estimates of brightness and timescales for the precursor were derived, as well as a prediction of the timing of the next precursor outburst. In Paper IV, observations from the 2004–2006 OJ287 observing program are used to investigate the existence of short periodicities in OJ287. The existence of a _50 day quasiperiodic component is confirmed. In addition, statistically significant 250 day and 3.5 day periods are found. Primary black hole accretion of a spiral density wave in the accretion disc is proposed as the source of the 50 day period, with numerical simulations supporting these results. Lorentz contracted jet re-emission is then proposed as the reason for the 3.5 day timescale. Paper V fits optical observations and mm and cm radio observations of OJ287 with a helical jet model. The jet is found to have a spine–sheath structure, with the sheath having a much lower Lorentz gamma factor than the spine. The sheath opening angle and Lorentz factor, as well as the helical wavelength of the jet are reported for the first time. Tiivistelmä Tässä väitöskirjatutkimuksessa on keskitytty tutkimaan aktiivista galaksiydintä OJ287. Väitöskirjan osana olevat tieteelliset julkaisut esittelevät OJ287-systeemistä saatuja uusia tuloksia kaksoismusta-aukkomallin kontekstissa. Väitöskirjan johdannossa käsitellään OJ287:n yleisiä ominaisuuksia ja niitä fysikaalisia perusilmiöitä, jotka näiden ominaisuuksien taustalla vaikuttavat. Johdanto selvittää myös OJ287-järjestelmän sijoittumisen aktiivisten galaksiytimien hierarkiassa. Johdannossa käydään läpi joitakin perusfysiikan tuloksia, jotka ovat tarpeen aktiivisten galaksiydinten, mustien aukkojen binäärien, relativististen suihkujen ja kertymäkiekkojen ymmärtämiseksi. Kahden toisiaan kiertävän mustan aukon keskinäisen radan suhteellisuusteoreettiset perusteet käydään läpi yksityiskohtaisemmin. Johdannossa esitetään joitakin analyyttisiä tuloksia tällaisessa binäärissä havaittavista suhteellisuusteoreettisista ilmiöistä. Myös numeerisia menetelmiä näiden ilmiöiden tarkempaan laskemiseen esitellään. Tuloksia sovelletaan OJ287-systeemiin, ja verrataan havaintoihin. OJ287:n mustien aukkojen ratamalli muodostaa pohjan systeemin toistuvien optisten purkausten malleille. Johdannossa esitellään yksityiskohtaisemmin kaksi fysikaalista purkausmallia, ja vertaillaan niitä. Purkausten säteilyhydrodynamiikka käydään läpi, ja myös ennusteet purkausten valokäyrille johdetaan. Johdannossa esitellään myös Julkaisussa III johdettu prekursoripurkausten malli, ja osoitetaan sen sopivan yhteen OJ287:n binäärimallin kanssa. Johdanto esittelee myös relativististen suihkujen fysiikkaa sekä OJ287- systeemiin liittyen että aktiivisten galaksiydinten kontekstissa yleisesti. Relativististen suihkujen perusfysiikka esitellään, kuten myös malleja kierteisistä suihkuista. Julkaisujen II, IV ja V OJ287-systeemin suihkuja koskevat tulokset esitellään binäärimallin kontekstissa. Kokonaisuutena johdanto palvelee suppeana oppaana, joka esittelee tarvittavan fysiikan ja tarpeelliset numeeriset menetelmät mustien aukkojen binäärijärjestelmän ymmärtämiseen ja simulointiin. Tätä tarkoitusta varten johdanto yhdistää sekä perustuloksia että joitakin syvällisempiä tuloksia laajoilta fysiikan osa-alueilta kuten suhteellisuusteoriasta ja säteilyhydrodynamiikasta. Johdannon sisältämän materiaalin avulla väitöskirjan julkaisut, ja niiden esittämät tulokset, ovat hyvin ymmärrettävissä. Väitöskirjan julkaisuista ensimmäinen esittelee uusia OJ287-systeemistä saatuja havaintopisteitä, jotka on paikallistettu Harvardin yliopiston observatorion arkiston valokuvauslevyiltä. OJ287:n vuonna 1900 tapahtunut purkaus nähdään ensimmäistä kertaa näissä havaintopisteissä. Uudet havaintopisteet mahdollistivat myös vuoden 1913 purkauksen alun ajoittamisen tarkemmin kuin aiemmin oli mahdollista. Havaitut purkaukset mallinnettiin onnistuneesti simuloimalla OJ287-järjestelmän mustien aukkojen paria ja kertymäkiekkoa. Julkaisussa II käsitellään mekanismeja OJ287:n sekundäärisen mustan aukon spinin kasvamiseen vuorovaikutuksessa primäärin kertymäkiekon ja systeemin magneettikenttien kanssa. Julkaisussa arvioidaan maksimispinin saavuttamisen ja spinin suunnan vakiintumisen aikaskaalat kummallakin mekanismilla. Tutkimuksessa havaitaan sekundäärin spinin olevan todennäköisesti suuri. Julkaisu III esittelee OJ287-systeemissä maaliskuussa 2013 tapahtuneen purkauksen. Purkauksen havaittiin muistuttavan vuosina 1993 ja 2004 tapahtuneita purkauksia, joita kutsutaan yhteisnimityksellä prekursoripurkaus (precursor outburst). Julkaisussa esitellään purkauksen synnylle mekanismi, jossa OJ287-systeemin sekundäärinen musta aukko osuu primäärisen mustan aukon kertymäkiekon koronassa olevaan kaasupilveen. Mekanismin avulla johdetaan arviot prekursoripurkausten kirkkaudelle ja aikaskaalalle. Julkaisussa johdetaan myös ennuste seuraavan prekursoripurkauksen ajankohdalle. Julkaisussa IV käytetään vuosina 2004–2006 kerättyjä havaintoja OJ287- systeemistä lyhyiden jaksollisuuksien etsintään. Julkaisussa varmennetaan systeemissä esiintyvä n. 50 päivän kvasiperiodisuus. Lisäksi tilastollisesti merkittävät 250 päivän ja 3,5 päivän jaksollisuudet havaitaan. Julkaisussa esitetään malli, jossa primäärisen mustan aukon kertymäkiekossa oleva spiraalitiheysaalto aiheuttaa 50 päivän jaksollisuuden. Mallista tehty numeerinen simulaatio tukee tulosta. Systeemin relativistisen suihkun emittoima aikadilatoitunut säteily esitetään aiheuttajaksi 3,5 päivän jaksollisuusaikaskaalalle. Julkaisussa V sovitetaan kierresuihkumalli OJ287-systeemistä tehtyihin optisiin havaintoihin ja millimetri- sekä senttimetriaallonpituuden radiohavaintoihin. Suihkun rakenteen havaitaan olevan kaksijakoinen ja koostuvan ytimestä ja kuoresta. Suihkun kuorella on merkittävästi pienempi Lorentzin gamma-tekijä kuin suihkun ytimellä. Kuoren avautumiskulma ja Lorentztekijä sekä suihkun kierteen aallonpituus raportoidaan julkaisussa ensimmäistä kertaa.

A contribution to the phytogeography of Brazilian campos: an analysis based on Poaceae

Twenty areas from eight Brazilian states were compared according to a list of 224 species of Poaceae. In order to determinate affinity patterns between the areas, a binary matrix was submitted to cluster and ordination analysis. The patterns found were then faced to climate and geographic position. The scores corresponding to the areas obtained from the cluster analysis showed a strong correlation to temperature. The scores corresponding to the species suggest a gradient that associates distribution patterns to the photosynthetic pathway (C3 or C4). The current results suggest that the traditional classification of the Southern American grasslands might require some modification in order to be broadly applicable in the Brazilian context.

Floristic composition and similarity analysis of an Atlantic rain forest fragment in Cananéia, São Paulo State, Brazil

The aim of this study is to investigate the floristic composition of an Atlantic rain forest fragment located in Cananéia, São Paulo, Brazil, and to contribute to the knowledge on Atlantic forest through the comparative analysis of this and other floristic surveys both on the southern and southeastern Brazil, in different soil and relief types. We surveyed 215 species in 132 genera and 51 families. Classification and ordination analysis were applied to a binary matrix in order to analyze the similarity among 24 surveys, including the present one, of Atlantic forest from the south and southeast coast of Brazil. Higher floristic similarity was observed among this area and the ones where there was marine influence and more rugged relief. The surveys in areas with greater marine influence (sandy soil) were separated from those in other conditions, possibly indicating a species replacement gradient from the steep slopes towards the lowland and were probably related to different edaphic conditions. A latitudinal gradient was found among the surveys apparently confirming a continuous species replacement along the Atlantic forest, related to a restricted distribution of the species. This suggests that it is essential to preserve areas from the whole Atlantic coast. Atlantic forest distribution is quite complex and its composition cannot be adequately represented by small localized areas.

Noninvasive classification of liver disease in asymptomatic and oligosymptomatic male alcoholics

The predominant type of liver alteration in asymptomatic or oligosymptomatic chronic male alcoholics (N = 169) admitted to a psychiatric hospital for detoxification was classified by two independent methods: liver palpation and multiple quadratic discriminant analysis (QDA), the latter applied to two parameters reported by the patient (duration of alcoholism and daily amount ingested) and to the data obtained from eight biochemical blood determinations (total bilirubin, alkaline phosphatase, glycemia, potassium, aspartate aminotransferase, albumin, globulin, and sodium). All 11 soft and sensitive, and 13 firm and sensitive livers formed fully concordant groups as determined by QDA. Among the 22 soft and not sensitive livers, 95% were concordant by QDA grouping. Concordance rates were low (55%) in the 73 firm and not sensitive livers, and intermediate (76%) in the 50 not palpable livers. Prediction of the liver palpation characteristics by QDA was 95% correct for the firm and not sensitive livers and moderate for the other groups. On a preliminary basis, the variables considered to be most informative by QDA were the two anamnestic data and bilirubin levels, followed by alkaline phosphatase, glycemia and potassium, and then by aspartate aminotransferase and albumin. We conclude that, when biopsies would be too costly or potentially injurious to the patients to varying extents, clinical data could be considered valid to guide patient care, at least in the three groups (soft, not sensitive; soft, sensitive; firm, sensitive livers) in which the two noninvasive procedures were highly concordant in the present study.

Differential evolution based classification with pool of distances and aggregation operators

The objective of this thesis is to develop and generalize further the differential evolution based data classification method. For many years, evolutionary algorithms have been successfully applied to many classification tasks. Evolution algorithms are population based, stochastic search algorithms that mimic natural selection and genetics. Differential evolution is an evolutionary algorithm that has gained popularity because of its simplicity and good observed performance. In this thesis a differential evolution classifier with pool of distances is proposed, demonstrated and initially evaluated. The differential evolution classifier is a nearest prototype vector based classifier that applies a global optimization algorithm, differential evolution, to determine the optimal values for all free parameters of the classifier model during the training phase of the classifier. The differential evolution classifier applies the individually optimized distance measure for each new data set to be classified is generalized to cover a pool of distances. Instead of optimizing a single distance measure for the given data set, the selection of the optimal distance measure from a predefined pool of alternative measures is attempted systematically and automatically. Furthermore, instead of only selecting the optimal distance measure from a set of alternatives, an attempt is made to optimize the values of the possible control parameters related with the selected distance measure. Specifically, a pool of alternative distance measures is first created and then the differential evolution algorithm is applied to select the optimal distance measure that yields the highest classification accuracy with the current data. After determining the optimal distance measures for the given data set together with their optimal parameters, all determined distance measures are aggregated to form a single total distance measure. The total distance measure is applied to the final classification decisions. The actual classification process is still based on the nearest prototype vector principle; a sample belongs to the class represented by the nearest prototype vector when measured with the optimized total distance measure. During the training process the differential evolution algorithm determines the optimal class vectors, selects optimal distance metrics, and determines the optimal values for the free parameters of each selected distance measure. The results obtained with the above method confirm that the choice of distance measure is one of the most crucial factors for obtaining higher classification accuracy. The results also demonstrate that it is possible to build a classifier that is able to select the optimal distance measure for the given data set automatically and systematically. After finding optimal distance measures together with optimal parameters from the particular distance measure results are then aggregated to form a total distance, which will be used to form the deviation between the class vectors and samples and thus classify the samples. This thesis also discusses two types of aggregation operators, namely, ordered weighted averaging (OWA) based multi-distances and generalized ordered weighted averaging (GOWA). These aggregation operators were applied in this work to the aggregation of the normalized distance values. The results demonstrate that a proper combination of aggregation operator and weight generation scheme play an important role in obtaining good classification accuracy. The main outcomes of the work are the six new generalized versions of previous method called differential evolution classifier. All these DE classifier demonstrated good results in the classification tasks.

Clinical classification of tetanus patients

The authors propose a clinical classification to monitor the evolution of tetanus patients, ranging from grade I to IV according to severity. It was applied on admission and repeated on alternate days up to the 10th day to patients aged > or = 12 years admitted to the State University Hospital, Recife, Brazil. Patients were also classified upon admission according to three prognostic indicators to determine if the proposed classification is in agreement with the traditionally used indicators. Upon admission, the distribution of the 64 patients among the different levels of the proposed classification was similar for the groups of better and worse prognosis according to the three indicators (P > 0.05), most of the patients belonging to grades I and II of the proposed classification. In the later reclassifications, severe forms of tetanus (grades III and IV) were more frequent in the categories of worse prognosis and these differences were statistically significant. There was a reduction in the proportion of mild forms (grades I and II) of tetanus with time for the categories of worse prognostic indicators (chi-square for trend: P = 0.00006, 0.03, and 0.00000) whereas no such trend was observed for the categories of better prognosis (grades I and II). This serially used classification reflected the prognosis of the traditional indicators and permitted the comparison of the dynamics of the disease in different groups. Thus, it becomes a useful tool for monitoring patients by determining clinical category changes with time, and for assessing responses to different therapeutic measures.

Aircraft tracking and classification with vhf passive bistatic radar

Since the times preceding the Second World War the subject of aircraft tracking has been a core interest to both military and non-military aviation. During subsequent years both technology and configuration of the radars allowed the users to deploy it in numerous fields, such as over-the-horizon radar, ballistic missile early warning systems or forward scatter fences. The latter one was arranged in a bistatic configuration. The bistatic radar has continuously re-emerged over the last eighty years for its intriguing capabilities and challenging configuration and formulation. The bistatic radar arrangement is used as the basis of all the analyzes presented in this work. The aircraft tracking method of VHF Doppler-only information, developed in the first part of this study, is solely based on Doppler frequency readings in relation to time instances of their appearance. The corresponding inverse problem is solved by utilising a multistatic radar scenario with two receivers and one transmitter and using their frequency readings as a base for aircraft trajectory estimation. The quality of the resulting trajectory is then compared with ground-truth information based on ADS-B data. The second part of the study deals with the developement of a method for instantaneous Doppler curve extraction from within a VHF time-frequency representation of the transmitted signal, with a three receivers and one transmitter configuration, based on a priori knowledge of the probability density function of the first order derivative of the Doppler shift, and on a system of blocks for identifying, classifying and predicting the Doppler signal. The extraction capabilities of this set-up are tested with a recorded TV signal and simulated synthetic spectrograms. Further analyzes are devoted to more comprehensive testing of the capabilities of the extraction method. Besides testing the method, the classification of aircraft is performed on the extracted Bistatic Radar Cross Section profiles and the correlation between them for different types of aircraft. In order to properly estimate the profiles, the ADS-B aircraft location information is adjusted based on extracted Doppler frequency and then used for Bistatic Radar Cross Section estimation. The classification is based on seven types of aircraft grouped by their size into three classes.

Classification and hearing evolution of patients with sudden sensorineural hearing loss

The aim of this study was to analyze clinical aspects, hearing evolution and efficacy of clinical treatment of patients with sudden sensorineural hearing loss (SSNHL). This was a prospective clinical study of 136 consecutive patients with SSNHL divided into three groups after diagnostic evaluation: patients with defined etiology (DE, N = 13, 10%), concurrent diseases (CD, N = 63, 46.04%) and idiopathic sudden sensorineural hearing loss (ISSHL, N = 60, 43.9%). Initial treatment consisted of prednisone and pentoxifylline. Clinical aspects and hearing evolution for up to 6 months were evaluated. Group CD comprised 73% of patients with metabolic decompensation in the initial evaluation and was significantly older (53.80 years) than groups DE (41.93 years) and ISSHL (39.13 years). Comparison of the mean initial and final hearing loss of the three groups revealed a significant hearing improvement for group CD (P = 0.001) and group ISSHL (P = 0.001). Group DE did not present a significant difference in thresholds. The clinical classification for SSNHL allows the identification of significant differences regarding age, initial and final hearing impairment and likelihood of response to therapy. Elevated age and presence of coexisting disease were associated with a greater initial hearing impact and poorer hearing recovery after 6 months. Patients with defined etiology presented a much more limited response to therapy. The occurrence of decompensated metabolic and cardiovascular diseases and the possibility of first manifestation of auto-immune disease and cerebello-pontine angle tumors justify an adequate protocol for investigation of SSNHL.

Acute kidney injury in AIDS: frequency, RIFLE classification and outcome

The objective of the present study was to evaluate the characteristics of acute kidney injury (AKI) in AIDS patients and the value of RIFLE classification for predicting outcome. The study was conducted on AIDS patients admitted to an infectious diseases hospital inBrazil. The patients with AKI were classified according to the RIFLE classification: R (risk), I (injury), F (failure), L (loss), and E (end-stage renal disease). Univariate and multivariate analyses were used to evaluate the factors associated with AKI. A total of 532 patients with a mean age of 35 ± 8.5 years were included in this study. AKI was observed in 37% of the cases. Patients were classified as "R" (18%), "I" (7.7%) and "F" (11%). Independent risk factors for AKI were thrombocytopenia (OR = 2.9, 95%CI = 1.5-5.6, P < 0.001) and elevation of aspartate aminotransferase (AST) (OR = 3.5, 95%CI = 1.8-6.6, P < 0.001). General mortality was 25.7% and was higher among patients with AKI (40.2 vs17%, P < 0.001). AKI was associated with death and mortality increased according to RIFLE classification - "R" (OR 2.4), "I" (OR 3.0) and "F" (OR 5.1), P < 0.001. AKI is a frequent complication in AIDS patients, which is associated with increased mortality. RIFLE classification is an important indicator of poor outcome for AIDS patients.

Classification of brain tumor extracts by high resolution ¹H MRS using partial least squares discriminant analysis

High resolution proton nuclear magnetic resonance spectroscopy (¹H MRS) can be used to detect biochemical changes in vitro caused by distinct pathologies. It can reveal distinct metabolic profiles of brain tumors although the accurate analysis and classification of different spectra remains a challenge. In this study, the pattern recognition method partial least squares discriminant analysis (PLS-DA) was used to classify 11.7 T ¹H MRS spectra of brain tissue extracts from patients with brain tumors into four classes (high-grade neuroglial, low-grade neuroglial, non-neuroglial, and metastasis) and a group of control brain tissue. PLS-DA revealed 9 metabolites as the most important in group differentiation: γ-aminobutyric acid, acetoacetate, alanine, creatine, glutamate/glutamine, glycine, myo-inositol, N-acetylaspartate, and choline compounds. Leave-one-out cross-validation showed that PLS-DA was efficient in group characterization. The metabolic patterns detected can be explained on the basis of previous multimodal studies of tumor metabolism and are consistent with neoplastic cell abnormalities possibly related to high turnover, resistance to apoptosis, osmotic stress and tumor tendency to use alternative energetic pathways such as glycolysis and ketogenesis.

Manual and semi-automatic quantification of in vivo ¹H-MRS data for the classification of human primary brain tumors

In vivo proton magnetic resonance spectroscopy (¹H-MRS) is a technique capable of assessing biochemical content and pathways in normal and pathological tissue. In the brain, ¹H-MRS complements the information given by magnetic resonance images. The main goal of the present study was to assess the accuracy of ¹H-MRS for the classification of brain tumors in a pilot study comparing results obtained by manual and semi-automatic quantification of metabolites. In vivo single-voxel ¹H-MRS was performed in 24 control subjects and 26 patients with brain neoplasms that included meningiomas, high-grade neuroglial tumors and pilocytic astrocytomas. Seven metabolite groups (lactate, lipids, N-acetyl-aspartate, glutamate and glutamine group, total creatine, total choline, myo-inositol) were evaluated in all spectra by two methods: a manual one consisting of integration of manually defined peak areas, and the advanced method for accurate, robust and efficient spectral fitting (AMARES), a semi-automatic quantification method implemented in the jMRUI software. Statistical methods included discriminant analysis and the leave-one-out cross-validation method. Both manual and semi-automatic analyses detected differences in metabolite content between tumor groups and controls (P < 0.005). The classification accuracy obtained with the manual method was 75% for high-grade neuroglial tumors, 55% for meningiomas and 56% for pilocytic astrocytomas, while for the semi-automatic method it was 78, 70, and 98%, respectively. Both methods classified all control subjects correctly. The study demonstrated that ¹H-MRS accurately differentiated normal from tumoral brain tissue and confirmed the superiority of the semi-automatic quantification method.

Classification of different degrees of adiposity in sedentary rats

In experimental studies, several parameters, such as body weight, body mass index, adiposity index, and dual-energy X-ray absorptiometry, have commonly been used to demonstrate increased adiposity and investigate the mechanisms underlying obesity and sedentary lifestyles. However, these investigations have not classified the degree of adiposity nor defined adiposity categories for rats, such as normal, overweight, and obese. The aim of the study was to characterize the degree of adiposity in rats fed a high-fat diet using cluster analysis and to create adiposity intervals in an experimental model of obesity. Thirty-day-old male Wistar rats were fed a normal (n=41) or a high-fat (n=43) diet for 15 weeks. Obesity was defined based on the adiposity index; and the degree of adiposity was evaluated using cluster analysis. Cluster analysis allowed the rats to be classified into two groups (overweight and obese). The obese group displayed significantly higher total body fat and a higher adiposity index compared with those of the overweight group. No differences in systolic blood pressure or nonesterified fatty acid, glucose, total cholesterol, or triglyceride levels were observed between the obese and overweight groups. The adiposity index of the obese group was positively correlated with final body weight, total body fat, and leptin levels. Despite the classification of sedentary rats into overweight and obese groups, it was not possible to identify differences in the comorbidities between the two groups.