Kinetic equations for difussion in the presence of entropic barriers

We use the mesoscopic nonequilibrium thermodynamics theory to derive the general kinetic equation of a system in the presence of potential barriers. The result is applied to a description of the evolution of systems whose dynamics is influenced by entropic barriers. We analyze in detail the case of diffusion in a domain of irregular geometry in which the presence of the boundaries induces an entropy barrier when approaching the exact dynamics by a coarsening of the description. The corresponding kinetic equation, named the Fick-Jacobs equation, is obtained, and its validity is generalized through the formulation of a scaling law for the diffusion coefficient which depends on the shape of the boundaries. The method we propose can be useful to analyze the dynamics of systems at the nanoscale where the presence of entropy barriers is a common feature.

Efficiency in inventories of ants in a forest reservein Central Amazonia

The objective of this work was to evaluate an inventory method efficiency for ants. We used subsamples collected in 24 transects of 100 m, distributed in 6 plots of 600 ha each in primary forest, as part of a long-term project. Ten litter subsamples were extracted per transect using Winkler extractors. Ants were identified to genus level, and Crematogaster, Gnamptogenys and Pachycondyla genera to species/morphospecies level. To evaluate the consequences of reduced sampling on the retention of ecological information, we estimated the lowest number of subsamples needed to detect the effects of environmental variables. Multidimensional scaling (MDS) was used to generate dissimilarity matrices, and Mantel correlations between each reduced-sampling effort and maximum effort were used as an index of how much information was maintained and could still be used in multivariate analyses. Lower p-values was observed on the effect of soil pH in the community of genera, and on the effect of the litter volume for the community of Crematogaster. The trend was still detectable in the analysis based on reduced-sampling. The number of subsamples can be reduced, and the cost-efficiency of the protocol can be improved with little loss of information.

Leaf development and growth of selected sugarcane clones in a subtropical environment

The objective of this work was to compare phyllochron and leaf area on individual stalks of selected sugarcane (Saccharum officinarum) clones grown in a subtropical environment. A two-year field experiment was carried out in Santa Maria, RS, Brazil, during the 2007/2008 and 2008/2009 growing seasons. Three sugarcane clones were used: IAC 822045 (early), SP 711406 (median) and CB 4176 (late), in a complete randomized block design, with four replications. Expanded leaf and total leaf (tips) number were determined, and expanded leaf area was measured. The phyllochron (ºC day leaf-1) based on expanded and tip leaf number was estimated, using 10ºC as base temperature. Allometric relationships between individual area and number of expanded leaves were fitted. Phyllochron was analysed as a four-factor experiment: clone, growing season, phyllochron phase, and phyllochron type. The early clone had the greatest potential for growing in a subtropical climate because of higher leaf output and leaf area.

Self-similar community structure in a network of human interactions

We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar. This suggests that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.

Nonequilibrium phase transition in a model for the propagation of innovations among economic agents

We characterize the different morphological phases that occur in a simple one-dimensional model of propagation of innovations among economic agents [X. Guardiola et al., Phys. Rev E 66, 026121 (2002)]. We show that the model can be regarded as a nonequilibrium surface growth model. This allows us to demonstrate the presence of a continuous roughening transition between a flat (system size independent fluctuations) and a rough phase (system size dependent fluctuations). Finite-size scaling studies at the transition strongly suggest that the dynamic critical transition does not belong to directed percolation and, in fact, critical exponents do not seem to fit in any of the known universality classes of nonequilibrium phase transitions. Finally, we present an explanation for the occurrence of the roughening transition and argue that avalanche driven dynamics is responsible for the novel critical behavior.

Contribution of neural networks to Alzheimer disease's progression.

The neuropathology of Alzheimer disease is characterized by senile plaques, neurofibrillary tangles and cell death. These hallmarks develop according to the differential vulnerability of brain networks, senile plaques accumulating preferentially in the associative cortical areas and neurofibrillary tangles in the entorhinal cortex and the hippocampus. We suggest that the main aetiological hypotheses such as the beta-amyloid cascade hypothesis or its variant, the synaptic beta-amyloid hypothesis, will have to consider neural networks not just as targets of degenerative processes but also as contributors of the disease's progression and of its phenotype. Three domains of research are highlighted in this review. First, the cerebral reserve and the redundancy of the network's elements are related to brain vulnerability. Indeed, an enriched environment appears to increase the cerebral reserve as well as the threshold of disease's onset. Second, disease's progression and memory performance cannot be explained by synaptic or neuronal loss only, but also by the presence of compensatory mechanisms, such as synaptic scaling, at the microcircuit level. Third, some phenotypes of Alzheimer disease, such as hallucinations, appear to be related to progressive dysfunction of neural networks as a result, for instance, of a decreased signal to noise ratio, involving a diminished activity of the cholinergic system. Overall, converging results from studies of biological as well as artificial neural networks lead to the conclusion that changes in neural networks contribute strongly to Alzheimer disease's progression.

JPEG standard uniform quantization error modeling with applications to sequential and progressive operation modes

In this paper we propose a method for computing JPEG quantization matrices for a given mean square error or PSNR. Then, we employ our method to compute JPEG standard progressive operation mode definition scripts using a quantization approach. Therefore, it is no longer necessary to use a trial and error procedure to obtain a desired PSNR and/or definition script, reducing cost. Firstly, we establish a relationship between a Laplacian source and its uniform quantization error. We apply this model to the coefficients obtained in the discrete cosine transform stage of the JPEG standard. Then, an image may be compressed using the JPEG standard under a global MSE (or PSNR) constraint and a set of local constraints determined by the JPEG standard and visual criteria. Secondly, we study the JPEG standard progressive operation mode from a quantization based approach. A relationship between the measured image quality at a given stage of the coding process and a quantization matrix is found. Thus, the definition script construction problem can be reduced to a quantization problem. Simulations show that our method generates better quantization matrices than the classical method based on scaling the JPEG default quantization matrix. The estimation of PSNR has usually an error smaller than 1 dB. This figure decreases for high PSNR values. Definition scripts may be generated avoiding an excessive number of stages and removing small stages that do not contribute during the decoding process with a noticeable image quality improvement.

Investigating the relationship between pollination strategies and the size-advantage model in zoophilous plants using the reproductive biology of Arum cylindraceum and other European Arum species as case studies

The size-advantage model (SAM) explains the temporal variation of energetic investment on reproductive structures (i.e. male and female gametes and reproductive organs) in long-lived hermaphroditic plants and animals. It proposes that an increase in the resources available to an organism induces a higher relative investment on the most energetically costly sexual structures. In plants, pollination interactions are known to play an important role in the evolution of floral features. Because the SAM directly concerns flower characters, pollinators are expected to have a strong influence on the application of the model. This hypothesis, however, has never been tested. Here, we investigate whether the identity and diversity of pollinators can be used as a proxy to predict the application of the SAM in exclusive zoophilous plants. We present a new approach to unravel the dynamics of the model and test it on several widespread Arum (Araceae) species. By identifying the species composition, abundance and spatial variation of arthropods trapped in inflorescences, we show that some species (i.e. A. cylindraceum and A. italicum) display a generalist reproductive strategy, relying on the exploitation of a low number of dipterans, in contrast to the pattern seen in the specialist A. maculatum (pollinated specifically by two fly species only). Based on the model presented here, the application of the SAM is predicted for the first two and not expected in the latter species, those predictions being further confirmed by allometric measures. We here demonstrate that while an increase in the female zone occurs in larger inflorescences of generalist species, this does not happen in species demonstrating specific pollinators. This is the first time that this theory is both proposed and empirically tested in zoophilous plants. Its overall biological importance is discussed through its application in other non-Arum systems.

Performance analysis of software run-time behaviour using 3D-visualisation

Monimutkaisen tietokonejärjestelmän suorituskykyoptimointi edellyttää järjestelmän ajonaikaisen käyttäytymisen ymmärtämistä. Ohjelmiston koon ja monimutkaisuuden kasvun myötä suorituskykyoptimointi tulee yhä tärkeämmäksi osaksi tuotekehitysprosessia. Tehokkaampien prosessorien käytön myötä myös energiankulutus ja lämmöntuotto ovat nousseet yhä suuremmiksi ongelmiksi, erityisesti pienissä, kannettavissa laitteissa. Lämpö- ja energiaongelmien rajoittamiseksi on kehitetty suorituskyvyn skaalausmenetelmiä, jotka edelleen lisäävät järjestelmän kompleksisuutta ja suorituskykyoptimoinnin tarvetta. Tässä työssä kehitettiin visualisointi- ja analysointityökalu ajonaikaisen käyttäytymisen ymmärtämisen helpottamiseksi. Lisäksi kehitettiin suorituskyvyn mitta, joka mahdollistaa erilaisten skaalausmenetelmien vertailun ja arvioimisen suoritusympäristöstä riippumatta, perustuen joko suoritustallenteen tai teoreettiseen analyysiin. Työkalu esittää ajonaikaisesti kerätyn tallenteen helposti ymmärrettävällä tavalla. Se näyttää mm. prosessit, prosessorikuorman, skaalausmenetelmien toiminnan sekä energiankulutuksen kolmiulotteista grafiikkaa käyttäen. Työkalu tuottaa myös käyttäjän valitsemasta osasta suorituskuvaa numeerista tietoa, joka sisältää useita oleellisia suorituskykyarvoja ja tilastotietoa. Työkalun sovellettavuutta tarkasteltiin todellisesta laitteesta saatua suoritustallennetta sekä suorituskyvyn skaalauksen simulointia analysoimalla. Skaalausmekanismin parametrien vaikutus simuloidun laitteen suorituskykyyn analysoitiin.

An international validation study of the EORTC brain cancer module (EORTC QLQ-BN20) for assessing health-related quality of life and symptoms in brain cancer patients.

Aims: The psychometric properties of the EORTC QLQ-BN20, a brain cancer-specific HRQOL questionnaire, have been previously determined in an English-speaking sample of patients. This study examined the validity and reliability of the questionnaire in a multi-national, multi-lingual study. Methods: QLQ-BN20 data were selected from two completed phase III EORTC/NCIC clinical trials in brain cancer (N=891), including 12 languages. Experimental treatments were surgery followed by radiotherapy (RT) and adjuvant PCV chemotherapy or surgery followed by concomitant RT plus temozolomide (TMZ) chemotherapy and adjuvant TMZ chemotherapy. Standard treatment consisted of surgery and postoperative RT alone. The psychometrics of the QLQ-BN20 were examined by means of multi-trait scaling analyses, reliability estimation, known groups validity testing, and responsiveness analysis. Results: All QLQ-BN20 items correlated more strongly with their own scale (r>0.70) than with other QLQ-BN20 scales. Internal consistency reliability coefficients were high (all alpha0.70). Known-groups comparisons yielded positive results, with the QLQ-BN20 distinguishing between patients with differing levels of performance status and mental functioning. Responsiveness of the questionnaire to changes over time was acceptable. Conclusion: The QLQ-BN20 demonstrates adequate psychometric properties and can be recommended for use in conjunction with the QLQ-C30 in assessing the HRQOL of brain cancer patients in international studies.

Modeling of Pressurizer Using APROS and TRACE Thermal Hydraulic Codes

Diplomityön tavoitteena on paineistimen yksityiskohtainen mallintaminen APROS- ja TRACE- termohydrauliikkaohjelmistoja käyttäen. Rakennetut paineistinmallit testattiin vertaamalla laskentatuloksia paineistimen täyttymistä, tyhjentymistä ja ruiskutusta käsittelevistä erilliskokeista saatuun mittausdataan. Tutkimuksen päätavoitteena on APROSin paineistinmallin validoiminen käyttäen vertailuaineistona PACTEL ATWS-koesarjan sopivia paineistinkokeita sekä MIT Pressurizer- ja Neptunus- erilliskokeita. Lisäksi rakennettiin malli Loviisan ydinvoimalaitoksen paineistimesta, jota käytettiin turbiinitrippitransientin simulointiin tarkoituksena selvittää mahdolliset voimalaitoksen ja koelaitteistojen mittakaavaerosta johtuvat vaikutukset APROSin paineistinlaskentaan. Kokeiden simuloinnissa testattiin erilaisia noodituksia ja mallinnusvaihtoehtoja, kuten entalpian ensimmäisen ja toisen kertaluvun diskretisointia, ja APROSin sekä TRACEn antamia tuloksia vertailtiin kattavasti toisiinsa. APROSin paineistinmallin lämmönsiirtokorrelaatioissa havaittiin merkittävä puute ja laskentatuloksiin saatiin huomattava parannus ottamalla käyttöön uusi seinämälauhtumismalli. Työssä tehdyt TRACE-simulaatiot ovat osa United States Nuclear Regulatory Commissionin kansainvälistä CAMP-koodinkehitys-ja validointiohjelmaa.

Robustness of Drosophila early embryo and wing imaginal disc development

Within a developing organism, cells require information on where they are in order to differentiate into the correct cell-type. Pattern formation is the process by which cells acquire and process positional cues and thus determine their fate. This can be achieved by the production and release of a diffusible signaling molecule, called a morphogen, which forms a concentration gradient: exposure to different morphogen levels leads to the activation of specific signaling pathways. Thus, in response to the morphogen gradient, cells start to express different sets of genes, forming domains characterized by a unique combination of differentially expressed genes. As a result, a pattern of cell fates and specification emerges.Though morphogens have been known for decades, it is not yet clear how these gradients form and are interpreted in order to yield highly robust patterns of gene expression. During my PhD thesis, I investigated the properties of Bicoid (Bcd) and Decapentaplegic (Dpp), two morphogens involved in the patterning of the anterior-posterior axis of Drosophila embryo and wing primordium, respectively. In particular, I have been interested in understanding how the pattern proportions are maintained across embryos of different sizes or within a growing tissue. This property is commonly referred to as scaling and is essential for yielding functional organs or organisms. In order to tackle these questions, I analysed fluorescence images showing the pattern of gene expression domains in the early embryo and wing imaginal disc. After characterizing the extent of these domains in a quantitative and systematic manner, I introduced and applied a new scaling measure in order to assess how well proportions are maintained. I found that scaling emerged as a universal property both in early embryos (at least far away from the Bcd source) and in wing imaginal discs (across different developmental stages). Since we were also interested in understanding the mechanisms underlying scaling and how it is transmitted from the morphogen to the target genes down in the signaling cascade, I also quantified scaling in mutant flies where this property could be disrupted. While scaling is largely conserved in embryos with altered bcd dosage, my modeling suggests that Bcd trapping by the nuclei as well as pre-steady state decoding of the morphogen gradient are essential to ensure precise and scaled patterning of the Bcd signaling cascade. In the wing imaginal disc, it appears that as the disc grows, the Dpp response expands and scales with the tissue size. Interestingly, scaling is not perfect at all positions in the field. The scaling of the target gene domains is best where they have a function; Spalt, for example, scales best at the position in the anterior compartment where it helps to form one of the anterior veins of the wing. Analysis of mutants for pentagone, a transcriptional target of Dpp that encodes a secreted feedback regulator of the pathway, indicates that Pentagone plays a key role in scaling the Dpp gradient activity.

Levylämmönsiirtimen mitoitus ja optimointi erityisesti lämpöpumpuissa

Työn tavoitteena on laatia käsikirjamainen läpileikkaus levylämmönsiirtimen rakenteesta ja käytöstä lämpöpumppulaitteistoissa. Kylmäprosessin tarkastelun lisäksi on eri lähteistä haettu yhtälöitä lämmönsiirron ja painehäviönlaskentaan. Lähdeaineistona on käytetty lämmönsiirron oppikirjoja, joiden lisäksi on käyty läpi suuri joukko tieteellisen tutkimuksen julkaisemia tutkimusraportteja levylämmönsiirtimen mitoituksesta erilaisissa käyttökohteissa. Oppikirjoissa ei ole esitetty varsinaisesti levylämmönsiirtimen laskentamenetelmiä, vaan niissä esitetään lämmönsiirron perusyhtälöt. Varsinainen lämmönsiirtolevyprofiilin laskentaan perustuva lähdeaineisto on löytynyt lämmönsiirtoon erikoistuneista julkaisuista. Lämmönsiirto tapahtuu aina kuumemmasta kylmempään tilaan. Lämmönsiirto eri virtausaineiden välillä toteutetaan lämmönsiirtimien avulla. Lämmönsiirrintyyppejä on olemassa lukuisia, joista yksi yleisesti käytetty tyyppi on levylämmönsiirrin. Tässä konstruktiossa on mahdutettu paljon lämmönsiirtopintaa ulkomitoiltaan pieneen tilaan. Tämä siirrintyyppi on eduksi silloin, kun virtaavat aineet ovat puhtaita ja niillä ei ole likaavaa vaikutusta lämmönsiirtopinnoille. Lämpöpumpulla tarkoitetaan laitetta, jolla voidaan käyttää hyödyksi lämmönlähteen matalaa lämpötilatasoa nostamalla lämpötilatasoa kompressorin puristustyön avulla korkeampaan lämpötilatasoon. Lämpöpumppulaitteiston toiminta perustuu kylmäprosessin toimintaan. Kylmäprosessin läpikäynti auttaa lukijaa hahmottamaan, millainen prosessi on kysymyksessä ja mitä komponentteja liittyy kylmäprosessiin. Tässä diplomityössä esitetyt yhtälöt antavat suuntaa, millä tavalla levylämmönsiirtimien ominaisuuksia voidaan laskea ja mitkä tekijät vaikuttavat siirtimien mitoittamiseen. Tarkemmat vaihdinkohtaiset laskentakorrelaatiot muotoutuvat vasta sitten, kun valmis tuote on testattu laboratorio-olosuhteissa ja siitä on saatu lämpötila-, virtaus- ja painesuhteet selville. Tämän jälkeen voidaan mittaustuloksiin perustuen rakentaa matemaattinen malli, jolla laskennallisesti määritelläänvaihtimien ominaisuudet. Lisäksi on esitetty yleisiä tapoja, joilla voidaan määritellä lämmönsiirtimien lämpöpintoja.

Relationships of basal metabolic rate, relative testis size and cycle length of spermatogenesis in shrews (Mammalia, Soricidae).

The aim of the present study was to determinate the cycle length of spermatogenesis in three species of shrew, Suncus murinus, Sorex coronatus and Sorex minutus, and to assess the relative influence of variation in basal metabolic rate (BMR) and mating system (level of sperm competition) on the observed rate of spermatogenesis, including data of shrew species studied before (Sorex araneus, Crocidura russula and Neomys fodiens). The dynamics of sperm production were determined by tracing 5-bromodeoxyuridine in the DNA of germ cells. As a continuous scaling of mating systems is not evident, the level of sperm competition was evaluated by the significantly correlated relative testis size (RTS). The cycle durations estimated by linear regression were 14.3 days (RTS 0.3%) in Suncus murinus, 9.0 days (RTS 0.5%) in Sorex coronatus and 8.5 days (RTS 2.8%) in Sorex minutus. In regression and multiple regression analyses including all six studied species of shrew, cycle length was significantly correlated with BMR (r2=0.73) and RTS (r2=0.77). Sperm competition as an ultimate factor obviously leads to a reduction in the time of spermatogenesis in order to increase sperm production. BMR may act in the same way, independently or as a proximate factor, revealed by the covariation, but other factors (related to testes size and thus to mating system) may also be involved.

Coifman-aallokkeet ja skaalaussuotimen muodostus differentiaalievoluut ion avulla

Ortogonaalisen M-kaistaisen moniresoluutioanalyysin matemaattiset perusteet esitetään yksityiskohtaisesti. Coifman-aallokkeiden määritelmä yleistetään dilaatiokertoimelle M ja nollasta poikkeavalle häviävien momenttien keskukselle.Funktion approksimointia näytepisteistä aallokkeiden avulla pohditaan ja erityisesti esitetään approksimaation asymptoottinen virhearvio Coifman-aallokkeille. Skaalaussuotimelle osoitetaan välttämättömät ja riittävät ehdot, jotka johtavat yleistettyihin Coifman-aallokkeisiin. Moniresoluutioanalyysin tiheys todistetaansuoraan Lebesguen integraalin määritelmään perustuen yksikön partitio-ominaisuutta käyttäen. Todistus on riittävä sellaisenaan avaruudessa L2(Wd) käyttämättä Fourier-tason ominaisuuksia tai ehtoja. Mallatin algoritmi johdetaan M-kaistaisille aallokkeille ja moniuloitteisille signaaleille. Algoritmille esitetään myös rekursiivinen muoto. Differentiaalievoluutioalgoritmin avulla ratkaistaan Coifman-aallokkeisiin liittyvien skaalaussuotimien kertoimien arvoja useille skaalausfunktiolle. Approksimaatio- ja kuvanpakkausesimerkkejä esitetään menetelmien havainnollistamiseksi. Differentiaalievoluutioalgoritmin avulla etsitään myös referenssikuville optimoitu skaalaussuodin. Löydetty suodin on regulaarinen ja erittäinsymmetrinen.