Partial correlation : Network analysis

The final year project came to us as an opportunity to get involved in a topic which has appeared to be attractive during the learning process of majoring in economics: statistics and its application to the analysis of economic data, i.e. econometrics.Moreover, the combination of econometrics and computer science is a very hot topic nowadays, given the Information Technologies boom in the last decades and the consequent exponential increase in the amount of data collected and stored day by day. Data analysts able to deal with Big Data and to find useful results from it are verydemanded in these days and, according to our understanding, the work they do, although sometimes controversial in terms of ethics, is a clear source of value added both for private corporations and the public sector. For these reasons, the essence of this project is the study of a statistical instrument valid for the analysis of large datasets which is directly related to computer science: Partial Correlation Networks.The structure of the project has been determined by our objectives through the development of it. At first, the characteristics of the studied instrument are explained, from the basic ideas up to the features of the model behind it, with the final goal of presenting SPACE model as a tool for estimating interconnections in between elements in large data sets. Afterwards, an illustrated simulation is performed in order to show the power and efficiency of the model presented. And at last, the model is put into practice by analyzing a relatively large data set of real world data, with the objective of assessing whether the proposed statistical instrument is valid and useful when applied to a real multivariate time series. In short, our main goals are to present the model and evaluate if Partial Correlation Network Analysis is an effective, useful instrument and allows finding valuable results from Big Data.As a result, the findings all along this project suggest the Partial Correlation Estimation by Joint Sparse Regression Models approach presented by Peng et al. (2009) to work well under the assumption of sparsity of data. Moreover, partial correlation networks are shown to be a very valid tool to represent cross-sectional interconnections in between elements in large data sets.The scope of this project is however limited, as there are some sections in which deeper analysis would have been appropriate. Considering intertemporal connections in between elements, the choice of the tuning parameter lambda, or a deeper analysis of the results in the real data application are examples of aspects in which this project could be completed.To sum up, the analyzed statistical tool has been proved to be a very useful instrument to find relationships that connect the elements present in a large data set. And after all, partial correlation networks allow the owner of this set to observe and analyze the existing linkages that could have been omitted otherwise.

Superjumborullien rullauksen hallinta

UPM-Kymmene Oyj:n Jämsänkosken PK6:n ongelmana ovat olleet ajoittaiset pohjakatkot suurilla rullilla. Diplomityön tavoitteena oli parantaa superjumborullien rullauksen hallintaa Jagenbergin rakentamalla VariTop keskiörullaimella. Kirjallisuusosassa selvitettiin rullanmuodostumista ja erilaisia rullausteorioita. Samalla käytiin läpi paperin rullautuvuuteen vaikuttavia tekijöitä, rullausperäisten vikojen muodostumisen syitä sekä pehmeän rullaussylinterin etuja verrattuna kovaan sylinteriin. Kokeellisessa osassa suoritettiin koeajoja tuotannon pituusleikkurilla. Näistä kokeista saatujen tulosten perusteella leikkurin ajoreseptit päivitettiin vastaamaanoptimaalisinta rullarakennetta. Pehmeän rullaussylinterin etuja verrattuna kovaan rullaussylinteriin selvitettiin koeajoissa Voithin koeleikkurilla Saksan Krefeldissä. Tuloksista selvisi, että samalla ajoreseptillä rullattaessa pehmeä sylinteri antoi valmiille rullalle suuremman kovuuden. Myös paperissa olevien profiilivirheiden vaikutukset lievenivät käytettäessä pehmeää rullaussylinteriä. Istukoiden luistamisesta johtuvaa hylsyjen sisäpinnan jauhautumista on ilmennyt suurilla jumborullilla. Tämä johtuu todennäköisimmin kasvaneesta rasituksesta hylsyn sisäpinnalla, mikä on seurausta rullien kasvusta. Ratkaisuina tälle ongelmalle on mahdollinen istukan pidentäminen sekä välyksen pienentäminen istukan ja hylsyn välissä. Myös hylsyjen toimintaa testattiin rullauksessa jahuomattiin niiden täyttävän toimittajien antamat laatuarvot. Lepo- ja liikekitkalla tiedetään olevan suuri merkitys rullausperäisten vikojenmuodostumiseen. Eri lajeista lähetettiin paperinäytteitä UPM-Kymmene Oyj:n Lappeenrannan tutkimuskeskukseen kitkojen määrittämiseksi. Tulosten perusteella havaittiin luettelolajilla lepo- ja liikekitkassa merkittävä ero. Standardi SC lajilla ero oli selvästi pienempi kuin luettelolajilla. Tämä saattaa olla yksi syy luettelolajeilla ilmeneviin pohjaongelmiin.

Partial protection and intrathecal invasion of CD8(+) T cells in acute canine distemper virus infection.

Initial non-inflammatory demyelination in canine distemper virus infection (CDV) develops against a background of severe immunosuppression and is therefore, thought to be virus-induced. However, recently we found a marked invasion of T cells throughout the central nervous system (CNS) in dogs with acute distemper despite drastic damage to the immune system. In the present study, this apparent paradox was further investigated by immunophenotyping of lymphocytes, following experimental CDV challenge in vaccinated and non-vaccinated dogs. In contrast to CDV infected, unprotected dogs, vaccinated dogs did not become immunosuppressed and exhibited a strong antiviral immune response following challenge with virulent CDV. In unprotected dogs rapid and drastic lymphopenia was initially due to depletion of T cells. In peripheral blood, CD4(+) T cells were more sensitive and depleted earlier and for a longer time than CD8(+) cells which recovered soon. In the cerebrospinal fluid (CSF) we could observe an increase in the T cell to B cell and CD8(+) to CD4(+) ratios. Thus, partial protection of the CD8(+) cell population could explain why part of the immune function in acute distemper is preserved. As found earlier, T cells invaded the CNS parenchyma in these dogs but also in the protected challenged dogs, which did not develop any CNS disease at all. Since markers of T cell activation were upregulated in both groups of animals, this phenomenon could in part be related to non-specific penetration of activated T cells through the blood brain barrier. However, in diseased animals much larger numbers of T cells were found in the CNS than in the protected dogs, suggesting that massive invasion of T cells in the brain requires CDV expression in the CNS.

Reconstruction of 3D Planar Objects with Partial Occlusion

Kolmiulotteisten kappaleiden rekonstruktio on yksi konenäön haastavimmista ongelmista, koska kappaleiden kolmiulotteisia etäisyyksiä ei voida selvittää yhdestä kaksiulotteisesta kuvasta. Ongelma voidaan ratkaista stereonäön avulla, jossa näkymän kolmiulotteinen rakenne päätellään usean kuvan perusteella. Tämä lähestymistapa mahdollistaa kuitenkin vain rekonstruktion niille kappaleiden osille, jotka näkyvät vähintään kahdessa kuvassa. Piilossa olevien osien rekonstruktio ei ole mahdollista pelkästään stereonäön avulla. Tässä työssä on kehitetty uusi menetelmä osittain piilossa olevien kolmiulotteisten tasomaisten kappaleiden rekonstruktioon. Menetelmän avulla voidaan selvittää hyvällä tarkkuudella tasomaisista pinnoista koostuvan kappaleen muoto ja paikka käyttäen kahta kuvaa kappaleesta. Menetelmä perustuu epipolaarigeometriaan, jonka avulla selvitetään molemmissa kuvissa näkyvät kappaleiden osat. Osittain piilossa olevien piirteiden rekonstruointi suoritetaan käyttämäen stereonäköä sekä tietoa kappaleen rakenteesta. Esitettyä ratkaisua voitaisiin käyttää esimerkiksi kolmiulotteisten kappaleiden visualisointiin, robotin navigointiin tai esineentunnistukseen.

Partial cricotracheal resection for paediatric subglottic stenosis: update of the Lausanne experience with 129 cases.

OBJECTIVES: Partial cricotracheal resection (PCTR) is widely accepted for treating severe paediatric laryngotracheal stenosis (LTS). However, it remains limited to a few experienced centres. Here we report an update of the Lausanne experience in paediatric PCTR performed or supervised by a senior surgeon (Philippe Monnier). METHODS: An ongoing database of 129 paediatric patients who underwent PCTR for benign LTS between March 1978 and July 2012 at our hospital was retrospectively reviewed. Demographic characteristics and information on preoperative status, stenosis and surgery were collected. Primary outcomes were measured as overall and operation-specific decannulation rates (ODR and OSDR, respectively), and secondary outcomes as morbidity, mortality and postoperative functional results. RESULTS: A total of 129 paediatric patients [79 males and 50 females; mean age, 4.1 years (1 month-16 years, median age of 2 years old)] underwent PCTR during the study period. ODR and OSDR were 90 and 81%, respectively. The decannulation rates were significantly superior for single-stage PCTR compared with double-stage PCTR in both ODR and OSDR. Eight patients died postoperatively for reasons unrelated to surgery. Partial anastomotic dehiscence was seen in 13 patients, 9 of whom were successfully treated by revision surgery. Respiratory, voice and swallowing functions were near normal or only minimally impaired in 86, 65 and 81% of patients, respectively. CONCLUSIONS: PCTR is effective and feasible with good ODR and OSDR for highgrade / severe LTS. Glottic involvement and the presence of comorbidities were negative predictive factors of decannulation. Early detection and reintervention of postoperative incipient dehiscence contribute to avoiding the progress to late restenosis; however, voice improvement remains a challenge.

Reconstruction of Fresnel Holograms using partial wave front information

n this work we analyze the behavior of complex information in Fresnel domain taking into account the limited capability to display complex transmittance values of current liquid crystal devices, when used as holographic displays. In order to do this analysis we compute the reconstruction of Fresnel holograms at several distances using the different parts of the complex distribution (real and imaginary parts, amplitude and phase) as well as using the full complex information adjusted with a method that combines two configurations of the devices in an adding architecture. The RMS error between the amplitude of these reconstructions and the original amplitude is used to evaluate the quality of the information displayed. The results of the error analysis show different behavior for the reconstructions using the different parts of the complex distribution and using the combined method of two devices. Better reconstructions are obtained when using two devices whose configurations densely cover the complex plane when they are added. Simulated and experimental results are also presented.

Mild guanidinoacetate increase under partial guanidinoacetate methyltransferase deficiency strongly affects brain cell development.

Among cerebral creatine deficiency syndromes, guanidinoacetate methyltransferase (GAMT) deficiency can present the most severe symptoms, and is characterized by neurocognitive dysfunction due to creatine deficiency and accumulation of guanidinoacetate in the brain. So far, every patient was found with negligible GAMT activity. However, GAMT deficiency is thought under-diagnosed, in particular due to unforeseen mutations allowing sufficient residual activity avoiding creatine deficiency, but enough guanidinoacetate accumulation to be toxic. With poorly known GAA-specific neuropathological mechanisms, we developed an RNAi-induced partial GAMT deficiency in organotypic rat brain cell cultures. As expected, the 85% decrease of GAMT protein was insufficient to cause creatine deficiency, but generated guanidinoacetate accumulation causing axonal hypersprouting and decrease in natural apoptosis, followed by induction of non-apoptotic cell death. Specific guanidinoacetate-induced effects were completely prevented by creatine co-treatment. We show that guanidinoacetate accumulation without creatine deficiency is sufficient to affect CNS development, and suggest that additional partial GAMT deficiencies, which may not show the classical brain creatine deficiency, may be discovered through guanidinoacetate measurement.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Reaction time asymmetries between expansion and contraction

Different asymmetries between expansion and contraction (radial motions) have been reported in the literature. Often these patterns have been regarded as implying different channels for each type of radial direction (outward versus inwards) operating at a higher level of visual motion processing. In two experiments (detection and discrimination tasks) we report reaction time asymmetries between expansion and contraction. Power functions were fitted to the data. While an exponent of 0.5 accounted for the expansion data better, a value of unity yielded the best fit for the contraction data. Instead of interpreting these differences as corresponding to different higher order motion detectors, we regard these findings as reflecting the fact that expansion and contraction tap two distinct psychophysical input channels underlying the processing of fast and slow velocities respectively.

On the Adoption of Partial Least Squares in Psychological Research: Caveat Emptor

The partial least squares technique (PLS) has been touted as a viable alternative to latent variable structural equation modeling (SEM) for evaluating theoretical models in the differential psychology domain. We bring some balance to the discussion by reviewing the broader methodological literature to highlight: (1) the misleading characterization of PLS as an SEM method; (2) limitations of PLS for global model testing; (3) problems in testing the significance of path coefficients; (4) extremely high false positive rates when using empirical confidence intervals in conjunction with a new "sign change correction" for path coefficients; (5) misconceptions surrounding the supposedly superior ability of PLS to handle small sample sizes and non-normality; and (6) conceptual and statistical problems with formative measurement and the application of PLS to such models. Additionally, we also reanalyze the dataset provided by Willaby et al. (2015; doi:10.1016/j.paid.2014.09.008) to highlight the limitations of PLS. Our broader review and analysis of the available evidence makes it clear that PLS is not useful for statistical estimation and testing.

Caloric restriction induces energy-sparing alterations in skeletal muscle contraction, fiber composition and local thyroid hormone metabolism that persist during catch-up fat upon refeeding.

Weight regain after caloric restriction results in accelerated fat storage in adipose tissue. This catch-up fat phenomenon is postulated to result partly from suppressed skeletal muscle thermogenesis, but the underlying mechanisms are elusive. We investigated whether the reduced rate of skeletal muscle contraction-relaxation cycle that occurs after caloric restriction persists during weight recovery and could contribute to catch-up fat. Using a rat model of semistarvation-refeeding, in which fat recovery is driven by suppressed thermogenesis, we show that contraction and relaxation of leg muscles are slower after both semistarvation and refeeding. These effects are associated with (i) higher expression of muscle deiodinase type 3 (DIO3), which inactivates tri-iodothyronine (T3), and lower expression of T3-activating enzyme, deiodinase type 2 (DIO2), (ii) slower net formation of T3 from its T4 precursor in muscles, and (iii) accumulation of slow fibers at the expense of fast fibers. These semistarvation-induced changes persisted during recovery and correlated with impaired expression of transcription factors involved in slow-twitch muscle development. We conclude that diminished muscle thermogenesis following caloric restriction results from reduced muscle T3 levels, alteration in muscle-specific transcription factors, and fast-to-slow fiber shift causing slower contractility. These energy-sparing effects persist during weight recovery and contribute to catch-up fat.