Emerging single-cell technologies in immunology.

During evolution, the immune system has diversified to protect the host from the extremely wide array of possible pathogens. Until recently, immune responses were dissected by use of global approaches and bulk tools, averaging responses across samples and potentially missing particular contributions of individual cells. This is a strongly limiting factor, considering that initial immune responses are likely to be triggered by a restricted number of cells at the vanguard of host defenses. The development of novel, single-cell technologies is a major innovation offering great promise for basic and translational immunology with the potential to overcome some of the limitations of traditional research tools, such as polychromatic flow cytometry or microscopy-based methods. At the transcriptional level, much progress has been made in the fields of microfluidics and single-cell RNA sequencing. At the protein level, mass cytometry already allows the analysis of twice as many parameters as flow cytometry. In this review, we explore the basis and outcome of immune-cell diversity, how genetically identical cells become functionally different, and the consequences for the exploration of host-immune defense responses. We will highlight the advantages, trade-offs, and potential pitfalls of emerging, single-cell-based technologies and how they provide unprecedented detail of immune responses.

Populaation monimuotoisuuden mittaaminen liukulukukoodatuissa evoluutioalgoritmeissa

Diplomityössä esitetään menetelmä populaation monimuotoisuuden mittaamiseen liukulukukoodatuissa evoluutioalgoritmeissa, ja tarkastellaan kokeellisesti sen toimintaa. Evoluutioalgoritmit ovat populaatiopohjaisia menetelmiä, joilla pyritään ratkaisemaan optimointiongelmia. Evoluutioalgoritmeissa populaation monimuotoisuuden hallinta on välttämätöntä, jotta suoritettu haku olisi riittävän luotettavaa ja toisaalta riittävän nopeaa. Monimuotoisuuden mittaaminen on erityisen tarpeellista tutkittaessa evoluutioalgoritmien dynaamista käyttäytymistä. Työssä tarkastellaan haku- ja tavoitefunktioavaruuden monimuotoisuuden mittaamista. Toistaiseksi ei ole ollut olemassa täysin tyydyttäviä monimuotoisuuden mittareita, ja työn tavoitteena on kehittää yleiskäyttöinen menetelmä liukulukukoodattujen evoluutioalgoritmien suhteellisen ja absoluuttisen monimuotoisuuden mittaamiseen hakuavaruudessa. Kehitettyjen mittareiden toimintaa ja käyttökelpoisuutta tarkastellaan kokeellisesti ratkaisemalla optimointiongelmia differentiaalievoluutioalgoritmilla. Toteutettujen mittareiden toiminta perustuu keskihajontojen laskemiseen populaatiosta. Keskihajonnoille suoritetaan skaalaus, joko alkupopulaation tai nykyisen populaation suhteen, riippuen lasketaanko absoluuttista vai suhteellista monimuotoisuutta. Kokeellisessa tarkastelussa havaittiin kehitetyt mittarit toimiviksi ja käyttökelpoisiksi. Tavoitefunktion venyttäminen koordinaattiakseleiden suunnassa ei vaikuta mittarin toimintaan. Myöskään tavoitefunktion kiertäminen koordinaatistossa ei vaikuta mittareiden tuloksiin. Esitetyn menetelmän aikakompleksisuus riippuu lineaarisesti populaation koosta, ja mittarin toiminta on siten nopeaa suuriakin populaatioita käytettäessä. Suhteellinen monimuotoisuus antaa vertailukelpoisia tuloksia riippumatta parametrien lukumäärästä tai populaation koosta.

Kernel-PCA data integration with enhanced interpretability

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge.

Paperitehtaan avaintehtävissä tarvittava talousosaaminen

Tutkielman päätavoitteena oli määritellä, mitä on paperitehtaan avaintehtävissä tarvittava, tulos- ja kustannustietoista toimintaa edistävä talousosaaminen. Kirjallisuusanalyysin perusteella muodostettiin malli talousosaamisen rakentumisesta. Mallia testattiin haastattelemalla erään paperitehtaan avaintehtävissä toimivia henkilöitä. Tulosten perusteella muodostettiin lopullinen käsitys paperitehtaassa tarvittavasta talousosaamisesta ja sen kehittämiseksi soveltuvista menetelmistä. Tutkimus osoitti, että talousosaaminen rakentuu sekä työntekijän sisäisten ominaisuuksien että hänen tiedollisen ja taidollisen talousosaamisen yhdistelmästä. Tietotaitotaso näyttäisi jakautuvan useaan eri kerrokseen sen mukaan, miten laajalti tiedot ja taidot ovat organisaatiossa sovellettavissa. Tärkeimmiksi sisäisiksi ominaisuuksiksi muodostuivat vuorovaikutusosaaminen, vastuuntuntoisuus ja ongelmanratkaisukyky. Talousosaamisen vahvistamisessa avainasemaan nousivat vuorovaikutukselliset, erityisesti viestintään liittyvät keinot ja osaamisen hyödyntämistä tukevan työympäristön luominen.

Clinical Development Strategies and Outcomes in First-in-Human Trials of Monoclonal Antibodies.

PURPOSE: We conducted a comprehensive review of the design, implementation, and outcome of first-in-human (FIH) trials of monoclonal antibodies (mAbs) to clearly determine early clinical development strategies for this class of compounds. METHODS: We performed a PubMed search using appropriate terms to identify reports of FIH trials of mAbs published in peer-reviewed journals between January 2000 and April 2013. RESULTS: A total of 82 publications describing FIH trials were selected for analysis. Only 27 articles (33%) reported the criteria used for selecting the starting dose (SD). Dose escalation was performed using rule-based methods in 66 trials (80%). The median number of planned dose levels was five (range, two to 13). The median of the ratio between the highest planned dose and the SD was 27 (range, two to 3,333). Although in 56 studies (68%) at least one grade 3 or 4 toxicity event was reported, no dose-limiting toxicity was observed in 47 trials (57%). The highest planned dose was reached in all trials, but the maximum-tolerated dose (MTD) was defined in only 13 studies (16%). The median of the ratio between MTD and SD was eight (range, four to 1,000). The recommended phase II dose was indicated in 34 studies (41%), but in 25 (73%) of these trials, this dose was chosen without considering toxicity as the main selection criterion. CONCLUSION: This literature review highlights the broad design heterogeneity of FIH trials testing mAbs. Because of the limited observed toxicity, the MTD was infrequently reached, and therefore, the recommended phase II dose for subsequent clinical trials was only tentatively defined.

Adsorption energy and spin state of first-row transition metals adsorbed on MgO(100)

Slab and cluster model spin-polarized calculations have been carried out to study various properties of isolated first-row transition metal atoms adsorbed on the anionic sites of the regular MgO(100) surface. The calculated adsorption energies follow the trend of the metal cohesive energies, indicating that the changes in the metal-support and metal-metal interactions along the series are dominated by atomic properties. In all cases, except for Ni at the generalized gradient approximation level, the number of unpaired electron is maintained as in the isolated metal atom. The energy required to change the atomic state from high to low spin has been computed using the PW91 and B3LYP density-functional-theory-based methods. PW91 fails to predict the proper ground state of V and Ni, but the results for the isolated and adsorbed atom are consistent within the method. B3LYP properly predicts the ground state of all first-row transition atom the high- to low-spin transition considered is comparable to experiment. In all cases, the interaction with the surface results in a reduced high- to low-spin transition energy.

Exploring the relative DNA contribution of first and second object's users on mock touch DNA mixtures

Contact stains recovered at break-in crime scenes are frequently characterized by mixtures of DNA from several persons. Broad knowledge on the relative contribution of DNA left behind by different users overtime is of paramount importance. Such information might help crime investigators to robustly evaluate the possibility of detecting a specific (or known) individual's DNA profile based on the type and history of an object. To address this issue, a contact stain simulation-based protocol was designed. Fourteen volunteers either acting as first or second object's users were recruited. The first user was required to regularly handle/wear 9 different items during an 8-10-day period, whilst the second user for 5, 30 and 120 min, in three independent simulation sessions producing a total of 231 stains. Subsequently, the relative DNA profile contribution of each individual pair was investigated. Preliminary results showed a progressive increase of the percentage contribution of the second user compared to the first. Interestingly, the second user generally became the major DNA contributor when most objects were handled/worn for 120 min, Furthermore, the observation of unexpected additional alleles will then prompt the investigation of indirect DNA transfer events.

Wavelets in real-time paper web analysis

Online paper web analysis relies on traversing scanners that criss-cross on top of a rapidly moving paper web. The sensors embedded in the scanners measure many important quality variables of paper, such as basis weight, caliper and porosity. Most of these quantities are varying a lot and the measurements are noisy at many different scales. The zigzagging nature of scanning makes it difficult to separate machine direction (MD) and cross direction (CD) variability from one another. For improving the 2D resolution of the quality variables above, the paper quality control team at the Department of Mathematics and Physics at LUT has implemented efficient Kalman filtering based methods that currently use 2D Fourier series. Fourier series are global and therefore resolve local spatial detail on the paper web rather poorly. The target of the current thesis is to study alternative wavelet based representations as candidates to replace the Fourier basis for a higher resolution spatial reconstruction of these quality variables. The accuracy of wavelet compressed 2D web fields will be compared with corresponding truncated Fourier series based fields.

Anthropomorphic model observer performance in three-dimensional detection task for low-contrast computed tomography.

X-ray medical imaging is increasingly becoming three-dimensional (3-D). The dose to the population and its management are of special concern in computed tomography (CT). Task-based methods with model observers to assess the dose-image quality trade-off are promising tools, but they still need to be validated for real volumetric images. The purpose of the present work is to evaluate anthropomorphic model observers in 3-D detection tasks for low-contrast CT images. We scanned a low-contrast phantom containing four types of signals at three dose levels and used two reconstruction algorithms. We implemented a multislice model observer based on the channelized Hotelling observer (msCHO) with anthropomorphic channels and investigated different internal noise methods. We found a good correlation for all tested model observers. These results suggest that the msCHO can be used as a relevant task-based method to evaluate low-contrast detection for CT and optimize scan protocols to lower dose in an efficient way.

Characterisation of anatomical properties of the human basal ganglia using magnetic resonance imaging

The detailed in-vivo characterization of subcortical brain structures is essential not only to understand the basic organizational principles of the healthy brain but also for the study of the involvement of the basal ganglia in brain disorders. The particular tissue properties of basal ganglia - most importantly their high iron content, strongly affect the contrast of magnetic resonance imaging (MRI) images, hampering the accurate automated assessment of these regions. This technical challenge explains the substantial controversy in the literature about the magnitude, directionality and neurobiological interpretation of basal ganglia structural changes estimated from MRI and computational anatomy techniques. My scientific project addresses the pertinent need for accurate automated delineation of basal ganglia using two complementary strategies: ? Empirical testing of the utility of novel imaging protocols to provide superior contrast in the basal ganglia and to quantify brain tissue properties; ? Improvement of the algorithms for the reliable automated detection of basal ganglia and thalamus Previous research demonstrated that MRI protocols based on magnetization transfer (MT) saturation maps provide optimal grey-white matter contrast in subcortical structures compared with the widely used Tl-weighted (Tlw) images (Helms et al., 2009). Under the assumption of a direct impact of brain tissue properties on MR contrast my first study addressed the question of the mechanisms underlying the regional specificities effect of the basal ganglia. I used established whole-brain voxel-based methods to test for grey matter volume differences between MT and Tlw imaging protocols with an emphasis on subcortical structures. I applied a regression model to explain the observed grey matter differences from the regionally specific impact of brain tissue properties on the MR contrast. The results of my first project prompted further methodological developments to create adequate priors for the basal ganglia and thalamus allowing optimal automated delineation of these structures in a probabilistic tissue classification framework. I established a standardized workflow for manual labelling of the basal ganglia, thalamus and cerebellar dentate to create new tissue probability maps from quantitative MR maps featuring optimal grey-white matter contrast in subcortical areas. The validation step of the new tissue priors included a comparison of the classification performance with the existing probability maps. In my third project I continued investigating the factors impacting automated brain tissue classification that result in interpretational shortcomings when using Tlw MRI data in the framework of computational anatomy. While the intensity in Tlw images is predominantly

Novel Proteins Involved in Dynamics of The Photosynthetic Apparatus

During the past few years, a considerable number of research articles have been published relating to the structure and function of the major photosynthetic protein complexes, photosystem (PS) I, PSII, cytochrome (Cyt) b6f, and adenosine triphosphate (ATP) synthase. Sequencing of the Arabidopsis thaliana (Arabidopsis) genome together with several high-quality proteomics studies has, however, revealed that the thylakoid membrane network of plant chloroplasts still contains a number of functionally unknown proteins. These proteins may have a role as auxiliary proteins guiding the assembly, maintenance, and turnover of the thylakoid protein complexes, or they may be as yet unknown subunits of the photosynthetic complexes. Novel subunits are most likely to be found in the NAD(P)H dehydrogenase (NDH) complex, the structure and function of which have remained obscure in the absence of detailed crystallographic data, thus making this thylakoid protein complex a particularly interesting target of investigation. In this thesis, several novel thylakoid-associated proteins were identified by proteomics-based methods. The major goal of characterization of the stroma thylakoid associated polysome-nascent chain complexes was to determine the proteins that guide the dynamic life cycle of PSII. In addition, a large protein complex of ≥ 1,000 kDa, residing in the stroma thylakoid, was characterized in greater depth and it was found to be a supercomplex composed of the PSI and NDH complexes. A set of newly identified proteins from Arabidopsis thylakoids was subjected to detailed characterization using the reverse genetics approach and extensive biochemical and biophysical analysis. The role of the novel proteins, either as auxiliary proteins or subunits of the photosynthetic protein complexes, was revealed. Two novel thylakoid lumen proteins, TLP18.3 and AtCYP38, function as auxiliary proteins assisting specific steps of the assembly/repair of PSII. The role of the 10-kDa thylakoid lumen protein PsbR is related to the optimization of oxygen evolution of PSII by assisting the assembly of the PsbP protein. Two integral thylakoid membrane proteins, NDH45 and NDH48, are novel subunits of the chloroplast NDH complex. Finally, the thylakoid lumen immunophilin AtCYP20-2 is suggested to interact with the NDH complex, instead of PSII as was hypothesized earlier.

Vaneritehtaan kustannustehokkuuden arvioimiseen käytettävän simulaatiojärjestelmän kehittäminen

Tämän työn tarkoituksena oli luoda kokonaisvaltainen tuotannollinen simulaatiomalli vaneritehtaasta sekä tutkia kustannuslaskennan mahdollisuuksia mallin yhteydessä. Perusolettamuksena on, että jos tuotannollinen malli toimii esikuvansa mukaisesti, myös sillä laskettuun kustannustietoon voidaan luottaa. Johdantona on tarkasteltu työn perustana olevia teorialähteitä. Ensimmäisenä asiana on esitetty vanerin valmistusprosessia ja siinä käytettyjä linja- ja laitetyyppejä. Toisena asiana on esitetty simulaatiotutkimuksen periaatteita, lainalaisuuksia ja mahdollisuuksia. Lisäksi on tarkasteltu kustannuslaskentaa, sen eri periaatteita ja muotoja sekä tuotannon- ja varastonohjausta. Aineistona ja menetelminä työssä on esitetty simulaatiomallin luomiseen tarvittavan pohjatiedon kerääminen sekä soveltaminen. Sitten on kuvattu tehdasmallin muodostavat eri tuotantolinjoja kuvaavat komponentit ja mallin käyttöliittymä. Lopuksi on kuvattu teoreettisen tehdasmallin soveltaminen todellisen vaneritehtaan mukaiseksi. Sovelletulla mallilla on ajettu kolme erilaista vuorokausituotantoa ja niistä saatua kustannustietoa on vertailtu optimitilannetta kuvaavaan taulukkoon.

Polímeros com capacidade de reconhecimento molecular no controlo da libertação de fármacos. Parte 1: síntese e caracterização

Molecularly imprinted polymers (MIPs) consist of synthetic macromolecular matrix, obtained through molecular imprinting-based methods that show ability to selectively recognize important biological molecules and its application in the drug delivery field is under development. In the present review the main aspects related to the synthesis and characterization of MIPs are studied. The fundamental variables participating in the synthesis process, such as template molecule, functional monomers, cross-linking agents, solvents and imprinting approaches are discussed. Moreover, the main available methods for MIPs chemical and morphological characterization are presented and the importance of the obtained information is discussed.

Alumiinipainevalujen purseen- ja jäysteenpoiston kehitysmahdollisuudet

Valupurseiden ja jäysteiden poistaminen on osa alumiinipainevalujen tuotantoprosessia. Työssä on tutkittu käytössä olevien ja uusien menetelmien mahdollisuuksia taloudellisempaan tuotantoon. Purseiden ja jäysteiden poistamiseen käytettävien menetelmien lisäksi tutkimuskohteita ja ideoita on haettu muista metallien työstömenetelmistä. Valupurseiden ja jäysteiden määritelmiä, muodostumista ja luokittelua on esitelty laajasti. Menetelmien tutkimus on painottunut valupurseiden poistamiseen ja valun jälkeistä leikkaamista on tutkittu erityisesti sisäpuolisten muotojen työstämiseen käytettyjen pistintyökalujen kautta. Muotin ulostyöntötapin purseen poistaminen on ollut tärkeä asia menetelmien tutkimuksissa. Valupurseiden, leikkaus- ja koneistusjäysteiden poistamiseksi lastuavista työstömenetelmistä tutkittuja ovat koneistaminen koneistuskeskuksella, aventaminen, hiertopuhallus, suihkuhiertäminen, vesisuihkuleikkaus, ultraäänityöstö, harjaus, painehiertäminen, hiominen kohdistetuilla ja kohdistamattomilla menetelmillä. Myös terminen jäysteenpoistomenetelmä (TEM), kemiallinen työstö (ECM) ja laserleikkaus on otettu esiin tutkimuksessa. Työn tuloksena on näkemys tutkittujen menetelmien jatkokehitystarpeesta ja mahdollisuudesta soveltaa niitä sarjatuotantoon.

Boundary identification in the domain of a parabolic partial differential equation

Bakgrunden och inspirationen till föreliggande studie är tidigare forskning i tillämpningar på randidentifiering i metallindustrin. Effektiv randidentifiering möjliggör mindre säkerhetsmarginaler och längre serviceintervall för apparaturen i industriella högtemperaturprocesser, utan ökad risk för materielhaverier. I idealfallet vore en metod för randidentifiering baserad på uppföljning av någon indirekt variabel som kan mätas rutinmässigt eller till en ringa kostnad. En dylik variabel för smältugnar är temperaturen i olika positioner i väggen. Denna kan utnyttjas som insignal till en randidentifieringsmetod för att övervaka ugnens väggtjocklek. Vi ger en bakgrund och motivering till valet av den geometriskt endimensionella dynamiska modellen för randidentifiering, som diskuteras i arbetets senare del, framom en flerdimensionell geometrisk beskrivning. I de aktuella industriella tillämpningarna är dynamiken samt fördelarna med en enkel modellstruktur viktigare än exakt geometrisk beskrivning. Lösningsmetoder för den s.k. sidledes värmeledningsekvationen har många saker gemensamt med randidentifiering. Därför studerar vi egenskaper hos lösningarna till denna ekvation, inverkan av mätfel och något som brukar kallas förorening av mätbrus, regularisering och allmännare följder av icke-välställdheten hos sidledes värmeledningsekvationen. Vi studerar en uppsättning av tre olika metoder för randidentifiering, av vilka de två första är utvecklade från en strikt matematisk och den tredje från en mera tillämpad utgångspunkt. Metoderna har olika egenskaper med specifika fördelar och nackdelar. De rent matematiskt baserade metoderna karakteriseras av god noggrannhet och låg numerisk kostnad, dock till priset av låg flexibilitet i formuleringen av den modellbeskrivande partiella differentialekvationen. Den tredje, mera tillämpade, metoden kännetecknas av en sämre noggrannhet förorsakad av en högre grad av icke-välställdhet hos den mera flexibla modellen. För denna gjordes även en ansats till feluppskattning, som senare kunde observeras överensstämma med praktiska beräkningar med metoden. Studien kan anses vara en god startpunkt och matematisk bas för utveckling av industriella tillämpningar av randidentifiering, speciellt mot hantering av olinjära och diskontinuerliga materialegenskaper och plötsliga förändringar orsakade av “nedfallande” väggmaterial. Med de behandlade metoderna förefaller det möjligt att uppnå en robust, snabb och tillräckligt noggrann metod av begränsad komplexitet för randidentifiering.