Empirical study of correlated survival times for recurrent events with proportional hazards margins and the effect of correlation and censoring.

Background: In longitudinal studies where subjects experience recurrent incidents over a period of time, such as respiratory infections, fever or diarrhea, statistical methods are required to take into account the within-subject correlation. Methods: For repeated events data with censored failure, the independent increment (AG), marginal (WLW) and conditional (PWP) models are three multiple failure models that generalize Cox"s proportional hazard model. In this paper, we revise the efficiency, accuracy and robustness of all three models under simulated scenarios with varying degrees of within-subject correlation, censoring levels, maximum number of possible recurrences and sample size. We also study the methods performance on a real dataset from a cohort study with bronchial obstruction. Results: We find substantial differences between methods and there is not an optimal method. AG and PWP seem to be preferable to WLW for low correlation levels but the situation reverts for high correlations. Conclusions: All methods are stable in front of censoring, worsen with increasing recurrence levels and share a bias problem which, among other consequences, makes asymptotic normal confidence intervals not fully reliable, although they are well developed theoretically.

Spine trabecular bone score subsequent to bone mineral density improves fracture discrimination in women.

Bone mineral density (BMD) measured by dual-energy X-ray absorptiometry (DXA) is used to diagnose osteoporosis and assess fracture risk. However, DXA cannot evaluate trabecular microarchitecture. This study used a novel software program (TBS iNsight; Med-Imaps, Geneva, Switzerland) to estimate bone texture (trabecular bone score [TBS]) from standard spine DXA images. We hypothesized that TBS assessment would differentiate women with low trauma fracture from those without. In this study, TBS was performed blinded to fracture status on existing research DXA lumbar spine (LS) images from 429 women. Mean participant age was 71.3 yr, and 158 had prior fractures. The correlation between LS BMD and TBS was low (r = 0.28), suggesting these parameters reflect different bone properties. Age- and body mass index-adjusted odds ratios (ORs) ranged from 1.36 to 1.63 for LS or hip BMD in discriminating women with low trauma nonvertebral and vertebral fractures. TBS demonstrated ORs from 2.46 to 2.49 for these respective fractures; these remained significant after lowest BMD T-score adjustment (OR = 2.38 and 2.44). Seventy-three percent of all fractures occurred in women without osteoporosis (BMD T-score > -2.5); 72% of these women had a TBS score below the median, thereby appropriately classified them as being at increased risk. In conclusion, TBS assessment enhances DXA by evaluating trabecular pattern and identifying individuals with vertebral or low trauma fracture. TBS identifies 66-70% of women with fracture who were not classified with osteoporosis by BMD alone.

Proteomic and transcriptomic profiling of Staphylococcus aureus surface LPXTG-proteins: correlation with agr genotypes and adherence phenotypes.

Staphylococcus aureus infections involve numerous adhesins and toxins, which expression depends on complex regulatory networks. Adhesins include a family of surface proteins covalently attached to the peptidoglycan via a conserved LPXTG motif. Here we determined the protein and mRNA expression of LPXTG-proteins of S. aureus Newman in time-course experiments, and their relation to fibrinogen adherence in vitro. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa), and fibrinogen-binding protein A (ClfA), as well as during growth in iron-rich or iron-poor media. Surface proteins were recovered by trypsin-shaving of live bacteria. Released peptides were analyzed by liquid chromatography coupled to tandem mass-spectrometry. To unambiguously identify peptides unique to LPXTG-proteins, the analytical conditions were refined using a reference library of S. aureus LPXTG-proteins heterogeneously expressed in surrogate Lactococcus lactis. Transcriptomes were determined by microarrays. Sixteen of the 18 LPXTG-proteins present in S. aureus Newman were detected by proteomics. Nine LPXTG-proteins showed a bell-shape agr-like expression that was abrogated in agr-negative mutants including Spa, fibronectin-binding protein A (FnBPA), ClfA, iron-binding IsdA, and IsdB, immunomodulator SasH, functionally uncharacterized SasD, biofilm-related SasG and methicillin resistance-related FmtB. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr- mutant, whereas all other LPXTG-proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in fibrinogen-adherence tests during late growth (24 h), whereas it remained poorly detected by proteomics. On the other hand, iron-regulated IsdA-B-C increased their protein expression by >10-times in iron-poor conditions. Thus, proteomic, transcriptomic, and adherence-phenotype demonstrated differential profiles in S. aureus. Moreover, trypsin peptide signatures suggested differential protein domain exposures in various environments, which might be relevant for anti-adhesin vaccines. A comprehensive understanding of the S. aureus physiology should integrate all three approaches.

Correlation of Locally-Based Performance of Asphalts with Their Physicochemical Parameters, Progress Report 2, HR-298, 1989

This project was undertaken to study the relationships between the performance of locally available asphalts and their physicochemical properties under Iowa conditions with the ultimate objective of development of a locally and performance-based asphalt specification for durable pavements. Physical and physicochemical tests were performed on three sets of asphalt samples including: (a) twelve samples from local asphalt suppliers and their TFOT residues, (b) six core samples of known service records, and (c) a total of 79 asphalts from 10 pavement projects including original, lab aged and recovered asphalts from field mixes, as well as from lab aged mixes. Tests included standard rheological tests, HP-GPC and TMA. Some specific viscoelastic tests (at 5 deg C) were run on b samples and on some a samples. DSC and X-ray diffraction studies were performed on a and b samples. Furthermore, NMR techniques were applied to some a, b and c samples. Efforts were made to identify physicochemical properties which are correlated to physical properties known to affect field performance. The significant physicochemical parameters were used as a basis for an improved performance-based trial specification for Iowa to ensure more durable pavements.

Correlation of physical and chemical attributes of soil with sugarcane yield

The objective of this work was to evaluate the correlation between sugarcane yield and some physical and chemical attributes of soil. For this, a 42‑ha test area in Araras, SP, Brazil, was used. Soil properties were determined from samples collected at the beginning of the 2003/2004 harvest season, using a regular 100x100 m grid. Yield assessment was done with a yield monitor (Simprocana). Correlation analyses were performed between sugarcane yield and the following soil properties: pH, pH CaCl2, N, C, cone index, clay content, soil organic matter, P, K, Ca, Mg, H+AL, cation exchange capacity, and base saturation. Correlation coefficients were respectively ‑0.05, ‑0.29, 0.33, 0.41, ‑0.27, 0.22, 0.44, ‑0.24, trace, ‑0.06, 0.01, 0.32, 0.14, and 0.04. Correlations of chemical and physical attributes of soil with sugarcane yield are weak, and, per se, they are not able to explain sugarcane yield variation, which suggests that other variables, besides soil attributes, should be analysed.

A cophenetic correlation coefficient for Tocher's method

The objective of this work was to propose a way of using the Tocher's method of clustering to obtain a matrix similar to the cophenetic one obtained for hierarchical methods, which would allow the calculation of a cophenetic correlation. To illustrate the obtention of the proposed cophenetic matrix, we used two dissimilarity matrices - one obtained with the generalized squared Mahalanobis distance and the other with the Euclidean distance - between 17 garlic cultivars, based on six morphological characters. Basically, the proposal for obtaining the cophenetic matrix was to use the average distances within and between clusters, after performing the clustering. A function in R language was proposed to compute the cophenetic matrix for Tocher's method. The empirical distribution of this correlation coefficient was briefly studied. For both dissimilarity measures, the values of cophenetic correlation obtained for the Tocher's method were higher than those obtained with the hierarchical methods (Ward's algorithm and average linkage - UPGMA). Comparisons between the clustering made with the agglomerative hierarchical methods and with the Tocher's method can be performed using a criterion in common: the correlation between matrices of original and cophenetic distances.

Predicting rapeseed oil content with near-infrared spectroscopy

The objective of this work was to establish a calibration equation and to estimate the efficiency of near-infrared reflectance (NIR) spectroscopy for evaluating rapeseed oil content in Southern Brazil. Spectral data from 124 half-sib families were correlated with oil contents determined by the chemical method. The accuracy of the equation was verified by coefficient of determination (R²) of 0.92, error of calibration (SEC) of 0.78, and error of performance (SEP) of 1.22. The oil content of ten genotypes, which were not included in the calibration with NIR, was similar to the one obtained by the standard chemical method. NIR spectroscopy is adequate to differentiate oil content of rapeseed genotypes.

Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization

We present a complete Raman spectroscopic study in two structurally well-defined diradical species of different lengths incorporating oligo p-phenylene vinylene bridges between two polychlorinated triphenylmethyl radical units, a disposition that allows sizeable conjugation between the two radicals through and with the bridge. The spectroscopic data are interpreted and supported by quantum chemical calculations. We focus the attention on the Raman frequency changes, interpretable in terms of: (i) bridge length (conjugation length); (ii) bridge conformational structure; and (iii) electronic coupling between the terminal radical units with the bridge and through the bridge, which could delineate through-bond spin polarization, or spin delocalization. These items are addressed by using the"oligomer approach" in conjunction with pressure and temperature dependent Raman spectroscopic data. In summary, we have attempted to translate the well-known strategy to study the electron (charge) structure of π−conjugated molecules by Raman spectroscopy to the case of electron (spin) interactions via the spin delocalization mechanism.

In-line Monitoring of Precipitation Process using Raman Spectroscopy and ATR-FTIR

Polymorfian jatkuva seuranta saostuksessa on hyödyllistä suunnittelun ja kidetuotteen ominaisuuksien sekä kiteytystä seuraavan jatkoprosessoinnin kannalta. Tässä diplomityössä on tutkittu L-glutamiinihapon kahden (- ja ß) polymorfimuodon liukoisuuden riippuvuutta pH:sta ja lämpötilasta.Tulokseksi saatiin, että kummankin polymorfin liukoisuus kasvoi sekä pH:ta ettälämpötilaa kasvatettaessa. ¿¿muodon liukoisuus oli korkeampi kuin ß-muodon liukoisuus valituilla pH-arvoilla eri lämpötiloissa. Lisäksi seurattiin puolipanostoimisen saostuksen aikana 1-litraisella laboratoriokiteyttimellä muodostuvan kiteisen polymorfiseoksen koostumusta hyödyntäen in-line Raman-spektroskopiaa. Myös liuoksen pH-muutosta seurattiin sekä liuoksen koostumusta ATR FTIR-spektroskopian (Attenuated Total Reflection Fourier Transform Infrared Spectrometer) avulla. Tutkittavina muuttujina olivat mm. sekoitusintensiteetti, sekoitintyyppi, reaktanttien (natriumglutamaatti ja rikkihappo) konsentraatiot sekä syötetyn rikkihapon syöttökohta kiteyttimessä. Työhön sisältyi 36 koetta ja osa kokeista toistettiin tulosten oikeellisuuden tarkistamiseksi. Inline-mittaustulosten verifioimiseksi kidenäytteet analysoitiin myös käyttämällä konfokaali Raman-mikroskooppia. Kidemorfologiaa tutkittiin SEM-kuvien (Scanning Eletronic Microscope) avulla. Työ osoitti, että Raman-spektroskopia on joustava ja luotettava menetelmä saostusprosessin jatkuvaan seurantaan L-glutamiinihapolla. Alhaiset lähtöainepitoisuudet tuottivat pääasiassa ¿¿muotoa, kun taas alhainen sekoitusteho edisti ß-muodon muodostumista. Syöttökohta vaikutti merkittävästi polymorfiaan. Kun rikkihapon syöttökohta oli epäideaalisesti sekoitetulla vyöhykkeellä, nousi ylikylläisyystaso korkeaksi ja päätuote oli tällöin ß-muotoa. 6-lapainen vinolapaturbiini (nousukulma 45o) ja 6-lapainen levyturbiini eivät merkittävästi poikenneet toisistaan muodostuvien polymorfien osalta.

Colloid cysts of the third ventricle: correlation of MR and CT findings with histology and chemical analysis.

Eight patients with colloid cysts of the third ventricle were examined with CT and MR. In six, surgical resection was performed and the material was subjected to histologic evaluation; the concentrations of trace elements were determined by particle-induced X-ray emission. Stereotaxic aspiration was performed in two. The investigation showed that colloid cysts are often iso- or hypodense relative to brain on CT (5/8), but sometimes have a center of increased density. Increased density did not correlate with increased concentration of calcium or other metals but did not correlate with high cholesterol content. Colloid cysts appear more heterogeneous on MR (6/8) than on CT (3/8), despite a homogeneous appearance at histology. High signal on short TR/TE sequences is correlated with a high cholesterol content. A marked shortening of the T2 relaxation time is often noticed in the central part of the cyst. Analysis of trace elements showed that this phenomenon is not related to the presence of metals with paramagnetic effects. Our analysis of the contents of colloid cysts does not support the theory that differing metallic concentrations are responsible for differences in MR signal intensity or CT density. We did find that increased CT density and high MR signal correlated with high cholesterol content.

Raman spectroscopy and microspectroscopy of reactive dyes on cotton fibres: analysis and detection limits

A collaborative study on Raman spectroscopy and microspectrophotometry (MSP) was carried out by members of the ENFSI (European Network of Forensic Science Institutes) European Fibres Group (EFG) on different dyed cotton fabrics. The detection limits of the two methods were tested on two cotton sets with a dye concentration ranging from 0.5 to 0.005% (w/w). This survey shows that it is possible to detect the presence of dye in fibres with concentrations below that detectable by the traditional methods of light microscopy and microspectrophotometry (MSP). The MSP detection limit for the dyes used in this study was found to be a concentration of 0.5% (w/w). At this concentration, the fibres appear colourless with light microscopy. Raman spectroscopy clearly shows a higher potential to detect concentrations of dyes as low as 0.05% for the yellow dye RY145 and 0.005% for the blue dye RB221. This detection limit was found to depend both on the chemical composition of the dye itself and on the analytical conditions, particularly the laser wavelength. Furthermore, analysis of binary mixtures of dyes showed that while the minor dye was detected at 1.5% (w/w) (30% of the total dye concentration) using microspectrophotometry, it was detected at a level as low as 0.05% (w/w) (10% of the total dye concentration) using Raman spectroscopy. This work also highlights the importance of a flexible Raman instrument equipped with several lasers at different wavelengths for the analysis of dyed fibres. The operator and the set up of the analytical conditions are also of prime importance in order to obtain high quality spectra. Changing the laser wavelength is important to detect different dyes in a mixture.

Determination of the size of quantum dots by fluorescence spectroscopy.

There has been a lack of quick, simple and reliable methods for determination of nanoparticle size. An investigation of the size of hydrophobic (CdSe) and hydrophilic (CdSe/ZnS) quantum dots was performed by using the maximum position of the corresponding fluorescence spectrum. It has been found that fluorescence spectroscopy is a simple and reliable methodology to estimate the size of both quantum dot types. For a given solution, the homogeneity of the size of quantum dots is correlated to the relationship between the fluorescence maximum position (FMP) and the quantum dot size. This methodology can be extended to the other fluorescent nanoparticles. The employment of evolving factor analysis and multivariate curve resolution-alternating least squares for decomposition of the series of quantum dots fluorescence spectra recorded by a specific measuring procedure reveals the number of quantum dot fractions having different diameters. The size of the quantum dots in a particular group is defined by the FMP of the corresponding component in the decomposed spectrum. These results show that a combination of the fluorescence and appropriate statistical method for decomposition of the emission spectra of nanoparticles may be a quick and trusted method for the screening of the inhomogeneity of their solution.

Monitoring of crystallization processes by using infrared spectroscopy and multivariate methods

Väitöstutkimuksessa on tarkasteltuinfrapunaspektroskopian ja monimuuttujaisten aineistonkäsittelymenetelmien soveltamista kiteytysprosessin monitoroinnissa ja kidemäisen tuotteen analysoinnissa. Parhaillaan kiteytysprosessitutkimuksessa maailmanlaajuisesti tutkitaan intensiivisesti erilaisten mittausmenetelmien soveltamista kiteytysprosessin ilmiöidenjatkuvaan mittaamiseen niin nestefaasista kuin syntyvistä kiteistäkin. Lisäksi tuotteen karakterisointi on välttämätöntä tuotteen laadun varmistamiseksi. Erityisesti lääkeaineiden valmistuksessa kiinnostusta tämäntyyppiseen tutkimukseen edistää Yhdysvaltain elintarvike- ja lääkeaineviraston (FDA) prosessianalyyttisiintekniikoihin (PAT) liittyvä ohjeistus, jossa määritellään laajasti vaatimukset lääkeaineiden valmistuksessa ja tuotteen karakterisoinnissa tarvittaville mittauksille turvallisten valmistusprosessien takaamiseksi. Jäähdytyskiteytyson erityisesti lääketeollisuudessa paljon käytetty erotusmenetelmä kiinteän raakatuotteen puhdistuksessa. Menetelmässä puhdistettava kiinteä raaka-aine liuotetaan sopivaan liuottimeen suhteellisen korkeassa lämpötilassa. Puhdistettavan aineen liukoisuus käytettävään liuottimeen laskee lämpötilan laskiessa, joten systeemiä jäähdytettäessä liuenneen aineen konsentraatio prosessissa ylittää liukoisuuskonsentraation. Tällaiseen ylikylläiseen systeemiin pyrkii muodostumaan uusia kiteitä tai olemassa olevat kiteet kasvavat. Ylikylläisyys on yksi tärkeimmistä kidetuotteen laatuun vaikuttavista tekijöistä. Jäähdytyskiteytyksessä syntyvän tuotteen ominaisuuksiin voidaan vaikuttaa mm. liuottimen valinnalla, jäähdytyprofiililla ja sekoituksella. Lisäksi kiteytysprosessin käynnistymisvaihe eli ensimmäisten kiteiden muodostumishetki vaikuttaa tuotteen ominaisuuksiin. Kidemäisen tuotteen laatu määritellään kiteiden keskimääräisen koon, koko- ja muotojakaumansekä puhtauden perusteella. Lääketeollisuudessa on usein vaatimuksena, että tuote edustaa tiettyä polymorfimuotoa, mikä tarkoittaa molekyylien kykyä järjestäytyä kidehilassa usealla eri tavalla. Edellä mainitut ominaisuudet vaikuttavat tuotteen jatkokäsiteltävyyteen, kuten mm. suodattuvuuteen, jauhautuvuuteen ja tabletoitavuuteen. Lisäksi polymorfiamuodolla on vaikutusta moniin tuotteen käytettävyysominaisuuksiin, kuten esim. lääkeaineen liukenemisnopeuteen elimistössä. Väitöstyössä on tutkittu sulfatiatsolin jäähdytyskiteytystä käyttäen useita eri liuotinseoksia ja jäähdytysprofiileja sekä tarkasteltu näiden tekijöiden vaikutustatuotteen laatuominaisuuksiin. Infrapunaspektroskopia on laajalti kemian alan tutkimuksissa sovellettava menetelmä. Siinä mitataan tutkittavan näytteenmolekyylien värähtelyjen aiheuttamia spektrimuutoksia IR alueella. Tutkimuksessa prosessinaikaiset mittaukset toteutettiin in-situ reaktoriin sijoitettavalla uppoanturilla käyttäen vaimennettuun kokonaisheijastukseen (ATR) perustuvaa Fourier muunnettua infrapuna (FTIR) spektroskopiaa. Jauhemaiset näytteet mitattiin off-line diffuusioheijastukseen (DRIFT) perustuvalla FTIR spektroskopialla. Monimuuttujamenetelmillä (kemometria) voidaan useita satoja, jopa tuhansia muuttujia käsittävä spektridata jalostaa kvalitatiiviseksi (laadulliseksi) tai kvantitatiiviseksi (määrälliseksi) prosessia kuvaavaksi informaatioksi. Väitöstyössä tarkasteltiin laajasti erilaisten monimuuttujamenetelmien soveltamista mahdollisimman monipuolisen prosessia kuvaavan informaation saamiseksi mitatusta spektriaineistosta. Väitöstyön tuloksena on ehdotettu kalibrointirutiini liuenneen aineen konsentraation ja edelleen ylikylläisyystason mittaamiseksi kiteytysprosessin aikana. Kalibrointirutiinin kehittämiseen kuuluivat aineiston hyvyyden tarkastelumenetelmät, aineiston esikäsittelymenetelmät, varsinainen kalibrointimallinnus sekä mallin validointi. Näin saadaan reaaliaikaista informaatiota kiteytysprosessin ajavasta voimasta, mikä edelleen parantaa kyseisen prosessin tuntemusta ja hallittavuutta. Ylikylläisyystason vaikutuksia syntyvän kidetuotteen laatuun seurattiin usein kiteytyskokein. Työssä on esitetty myös monimuuttujaiseen tilastolliseen prosessinseurantaan perustuva menetelmä, jolla voidaan ennustaa spontaania primääristä ytimenmuodostumishetkeä mitatusta spektriaineistosta sekä mahdollisesti päätellä ydintymisessä syntyvä polymorfimuoto. Ehdotettua menetelmää hyödyntäen voidaan paitsi ennakoida kideytimien muodostumista myös havaita mahdolliset häiriötilanteet kiteytysprosessin alkuhetkillä. Syntyvää polymorfimuotoa ennustamalla voidaan havaita ei-toivotun polymorfin ydintyminen,ja mahdollisesti muuttaa kiteytyksen ohjausta halutun polymorfimuodon saavuttamiseksi. Monimuuttujamenetelmiä sovellettiin myös kiteytyspanosten välisen vaihtelun määrittämiseen mitatusta spektriaineistosta. Tämäntyyppisestä analyysistä saatua informaatiota voidaan hyödyntää kiteytysprosessien suunnittelussa ja optimoinnissa. Väitöstyössä testattiin IR spektroskopian ja erilaisten monimuuttujamenetelmien soveltuvuutta kidetuotteen polymorfikoostumuksen nopeaan määritykseen. Jauhemaisten näytteiden luokittelu eri polymorfeja sisältäviin näytteisiin voitiin tehdä käyttäen tarkoitukseen soveltuvia monimuuttujaisia luokittelumenetelmiä. Tämä tarjoaa nopean menetelmän jauhemaisen näytteen polymorfikoostumuksen karkeaan arviointiin, eli siihen mitä yksittäistä polymorfia kyseinen näyte pääasiassa sisältää. Varsinainen kvantitatiivinen analyysi, eli sen selvittäminen paljonko esim. painoprosentteina näyte sisältää eri polymorfeja, vaatii kaikki polymorfit kattavan fysikaalisen kalibrointisarjan, mikä voi olla puhtaiden polymorfien huonon saatavuuden takia hankalaa.