Hematopoietic Stem Cell Development and Transcriptional Regulation

The continuous production of blood cells, a process termed hematopoiesis, is sustained throughout the lifetime of an individual by a relatively small population of cells known as hematopoietic stem cells (HSCs). HSCs are unique cells characterized by their ability to self-renew and give rise to all types of mature blood cells. Given their high proliferative potential, HSCs need to be tightly regulated on the cellular and molecular levels or could otherwise turn malignant. On the other hand, the tight regulatory control of HSC function also translates into difficulties in culturing and expanding HSCs in vitro. In fact, it is currently not possible to maintain or expand HSCs ex vivo without rapid loss of self-renewal. Increased knowledge of the unique features of important HSC niches and of key transcriptional regulatory programs that govern HSC behavior is thus needed. Additional insight in the mechanisms of stem cell formation could enable us to recapitulate the processes of HSC formation and self-renewal/expansion ex vivo with the ultimate goal of creating an unlimited supply of HSCs from e.g. human embryonic stem cells (hESCs) or induced pluripotent stem cells (iPS) to be used in therapy. We thus asked: How are hematopoietic stem cells formed and in what cellular niches does this happen (Papers I, II)? What are the molecular mechanisms that govern hematopoietic stem cell development and differentiation (Papers III, IV)? Importantly, we could show that placenta is a major fetal hematopoietic niche that harbors a large number of HSCs during midgestation (Paper I)(Gekas et al., 2005). In order to address whether the HSCs found in placenta were formed there we utilized the Runx1-LacZ knock-in and Ncx1 knockout mouse models (Paper II). Importantly, we could show that HSCs emerge de novo in the placental vasculature in the absence of circulation (Rhodes et al., 2008). Furthermore, we could identify defined microenvironmental niches within the placenta with distinct roles in hematopoiesis: the large vessels of the chorioallantoic mesenchyme serve as sites of HSC generation whereas the placental labyrinth is a niche supporting HSC expansion (Rhodes et al., 2008). Overall, these studies illustrate the importance of distinct milieus in the emergence and subsequent maturation of HSCs. To ensure proper function of HSCs several regulatory mechanisms are in place. The microenvironment in which HSCs reside provides soluble factors and cell-cell interactions. In the cell-nucleus, these cell-extrinsic cues are interpreted in the context of cell-intrinsic developmental programs which are governed by transcription factors. An essential transcription factor for initiation of hematopoiesis is Scl/Tal1 (stem cell leukemia gene/T-cell acute leukemia gene 1). Loss of Scl results in early embryonic death and total lack of all blood cells, yet deactivation of Scl in the adult does not affect HSC function (Mikkola et al., 2003b. In order to define the temporal window of Scl requirement during fetal hematopoietic development, we deactivated Scl in all hematopoietic lineages shortly after hematopoietic specification in the embryo . Interestingly, maturation, expansion and function of fetal HSCs was unaffected, and, as in the adult, red blood cell and platelet differentiation was impaired (Paper III)(Schlaeger et al., 2005). These findings highlight that, once specified, the hematopoietic fate is stable even in the absence of Scl and is maintained through mechanisms that are distinct from those required for the initial fate choice. As the critical downstream targets of Scl remain unknown, we sought to identify and characterize target genes of Scl (Paper IV). We could identify transcription factor Mef2C (myocyte enhancer factor 2 C) as a novel direct target gene of Scl specifically in the megakaryocyte lineage which largely explains the megakaryocyte defect observed in Scl deficient mice. In addition, we observed an Scl-independent requirement of Mef2C in the B-cell compartment, as loss of Mef2C leads to accelerated B-cell aging (Gekas et al. Submitted). Taken together, these studies identify key extracellular microenvironments and intracellular transcriptional regulators that dictate different stages of HSC development, from emergence to lineage choice to aging.

Ruumis ja rauta : esseitä esineiden sosiaalisuudesta

"Body and Iron: Essays on the Socialness of Objects" focuses on the bodily-material interaction of human subjects and technical objects. It poses a question, how is it possible that objects have an impact on their human users and examines the preconditions of active efficacy of objects. In this theoretical task the work relies on various discussions drawing from realistic ontology, phenomenology of body, neurophysiology of Antonio Damasio and psychoanalysis to establish both objects and bodies as material entities related in a causal interaction with each other. Out of material interaction emerge a symbolic field, psyche and culture that produce representations of interactions with material world they remain dependent on and conditioned by. Interaction with objects informs the human body via its somatosensory systems: interoseptive and proprioseptive (or kinesthetic) systems provide information to central nervous system of the internal state of the body and muscle tensions and motor activity of the limbs. Capability to control the movements of one's body by the internal "feel" of being a body turns out to be a precondition to the ability to control artificial extensions of the body. Motor activity of the body is involved in every perception of environment as the feel of one's own body is constitutive of any perception of external objects. Perception of an object cause changes in the internal milieu of the body and these changes in the organism form a bodily representation of an external object. Via these "muscle images" the subject can develop a feel for an instrument. Bodily feel for an object is pre-conceptual, practical knowledge that resists articulation but allows sensing the world through the object. This is what I would call sensual knowledge. Technical objects intervene between body and environment, transforming the relation of perception and motor activity. Once connected to a vehicle, human subject has to calibrate visual information of his or her position and movement in space to the bodily actions controlling the machine. It is the machine that mediates the relation of human actions to the relation of her body to its environment. Learning to use the machine necessarily means adjusting his or her bodily actions to the responses of the machine in relation to environmental changes it causes. Responsiveness of the machine to human touch "teaches" its subject by providing feedback of the "correctitude" of his or her bodily actions. Correct actions form a body technique of handling the object. This is the way of socialness of objects. While responding to human actions they generate their subjects. Learning to handle a machine means accepting the position of the user in the program of action materialized in the construction of the object. Objects mediate, channel and transform the relation of the body to its environment and via environment to the body itself according to their material and technical construction. Objects are sensory media: they channel signals and information from the environment thus constituting a representation of environment, a virtual or artificial reality. They also feed the body directly with their powers equipping their user with means of regulating somatic and psychic states of her self. For these reasons humans look for the company of objects. Keywords: material objects, material culture, sociology of technology, sociology of body, mobility, driving

Psykoterapian vaikutusten arvioiminen : Keskustelunanalyttinen tutkimus arviointihaastattelun käytänteistä

In the field of psychiatry semi-structured interview is one of the central tools in assessing the psychiatric state of a patient. In semi-structured interview the interviewer participates in the interaction both by the prepared interview questions and by his or her own, unstructured turns. It has been stated that in the context of psychiatric assessment interviewers' unstructured turns help to get focused information but simultaneously may weaken the reliability of the data. This study examines the practices by which semi-structured psychiatric interviews are conducted. The method for the study is conversation analysis, which is both a theory of interaction and a methodology for its empirical, detailed analysis. Using data from 80 video-recorded psychiatric interviews with 16 patients and five interviewers it describes in detail both the structured and unstructured interviewing practices. In the analysis also psychotherapeutic concepts are used to describe phenomena that are characteristic for therapeutic discourse. The data was received from the Helsinki Psychotherapy Study (HPS). HPS is a randomized clinical trial comparing the effectiveness of four forms of psychotherapy in the treatment of depressive and anxiety disorders. A total of 326 patients were randomly assigned to one of three treatment groups: solution-focused therapy, short-term psychodynamic psychotherapy, and long-term psychodynamic psychotherapy. The patients assigned to the long-term psychodynamic psychotherapy group and 41 patients self-selected for psychoanalysis were included in a quasi-experimental design. The primary outcome measures were depressive and anxiety symptoms, while secondary measures included work ability, need for treatment, personality functions, social functioning, and life style. Cost-effectiveness was determined. The data were collected from interviews, questionnaires, psychological tests, and public health registers. The follow-up interviews were conducted five times during a 5-year follow-up. The study shows that interviewers pose elaborated questions that are formulated in a friendly and sensitive way and that make relevant patients' long and story-like responses. When receiving patients' answers interviewers use a wide variety of different interviewing practices by which they direct patients' talk or offer an understanding of the meaning of patients' response. The results of the study are two-fold. Firstly, the study shows that understanding the meaning of mental experiences requires interaction between interviewer and patient. It is stated that therefore semi-structured interview is both relevant and necessary method for collecting data in psychotherapy outcome study. Secondly, the study suggests that conversation analysis, enriched with psychotherapeutic concepts, offers methodological possibilities for psychotherapy process research, especially for process-outcome paradigm.

Sampled longest common prefix array

When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main building blocks in many compressed suffix tree proposals. In this paper, we describe a new compressed LCP representation: the sampled LCP array. We show that when used with a compressed suffix array (CSA), the sampled LCP array often offers better time/space trade-offs than the existing alternatives. We also show how to construct the compressed representations of the LCP array directly from a CSA

Fast in-memory XPath search using compressed indexes

A large fraction of an XML document typically consists of text data. The XPath query language allows text search via the equal, contains, and starts-with predicates. Such predicates can be efficiently implemented using a compressed self-index of the document's text nodes. Most queries, however, contain some parts querying the text of the document, plus some parts querying the tree structure. It is therefore a challenge to choose an appropriate evaluation order for a given query, which optimally leverages the execution speeds of the text and tree indexes. Here the SXSI system is introduced. It stores the tree structure of an XML document using a bit array of opening and closing brackets plus a sequence of labels, and stores the text nodes of the document using a global compressed self-index. On top of these indexes sits an XPath query engine that is based on tree automata. The engine uses fast counting queries of the text index in order to dynamically determine whether to evaluate top-down or bottom-up with respect to the tree structure. The resulting system has several advantages over existing systems: (1) on pure tree queries (without text search) such as the XPathMark queries, the SXSI system performs on par or better than the fastest known systems MonetDB and Qizx, (2) on queries that use text search, SXSI outperforms the existing systems by 1-3 orders of magnitude (depending on the size of the result set), and (3) with respect to memory consumption, SXSI outperforms all other systems for counting-only queries.

Measurements of the top-quark mass using charged particle tracking

We present three measurements of the top-quark mass in the lepton plus jets channel with approximately 1.9 fb-1 of integrated luminosity collected with the CDF II detector using quantities with minimal dependence on the jet energy scale. One measurement exploits the transverse decay length of b-tagged jets to determine a top-quark mass of 166.9+9.5-8.5 (stat) +/- 2.9 (syst) GeV/c2, and another the transverse momentum of electrons and muons from W-boson decays to determine a top-quark mass of 173.5+8.8-8.9 (stat) +/- 3.8 (syst) GeV/c2. These quantities are combined in a third, simultaneous mass measurement to determine a top-quark mass of 170.7 +/- 6.3 (stat) +/- 2.6 (syst) GeV/c2.

Phonetic tone signals quantity and word structure

Many languages exploit suprasegmental devices in signaling word meaning. Tone languages exploit fundamental frequency whereas quantity languages rely on segmental durations to distinguish otherwise similar words. Traditionally, duration and tone have been taken as mutually exclusive. However, some evidence suggests that, in addition to durational cues, phonological quantity is associated with and co-signaled by changes in fundamental frequency in quantity languages such as Finnish, Estonian, and Serbo-Croat. The results from the present experiment show that the structure of disyllabic word stems in Finnish are indeed signaled tonally and that the phonological length of the stressed syllable is further tonally distinguished within the disyllabic sequence. The results further indicate that the observed association of tone and duration in perception is systematically exploited in speech production in Finnish.

Measurement of $d\sigma/dy$ of Drell-Yan $e^+e^-$ pairs in the $Z$ Mass Region from $p\bar{p}$ Collisions at $\sqrt{s}=1.96$ TeV

We report on a CDF measurement of the total cross section and rapidity distribution, $d\sigma/dy$, for $q\bar{q}\to \gamma^{*}/Z\to e^{+}e^{-}$ events in the $Z$ boson mass region ($66M_{ee}

Search for Higgs bosons predicted in two-Higgs-doublet models via decays to tau lepton pairs in 1.96 TeV proton-antiproton collisions

We present the results of a search for Higgs bosons predicted in two-Higgs-doublet models, in the case where the Higgs bosons decay to tau lepton pairs, using 1.8 inverse fb of integrated luminosity of proton-antiproton collisions recorded by the CDF II experiment at the Fermilab Tevatron. Studying the observed mass distribution in events where one or both tau leptons decay leptonically, no evidence for a Higgs boson signal is observed. The result is used to infer exclusion limits in the two-dimensional parameter space of tan beta versus m(A).

Production of psi(2S) Mesons in ppbar Collisions at 1.96 TeV

We have measured the differential cross section for the inclusive production of psi(2S) mesons decaying to mu^{+} mu^{-1} that were produced in prompt or B-decay processes from ppbar collisions at 1.96 TeV. These measurements have been made using a data set from an integrated luminosity of 1.1 fb^{-1} collected by the CDF II detector at Fermilab. For events with transverse momentum p_{T} (psi(2S)) > 2 GeV/c and rapidity |y(psi(2S))| psi(2S)X) Br(psi(2S) -> mu^{+} mu^{-}) to be 3.29 +- 0.04(stat.) +- 0.32(syst.) nb.

Observation of exclusive charmonium production and gamma+gamma to mu+mu- in p+pbar collisions at sqrt{s} = 1.96 TeV

We have observed the reactions p+pbar --> p+X+pbar, with X being a centrally produced J/psi, psi(2S) or chi_c0, and gamma+gamma --> mu+mu-, in proton- antiproton collisions at sqrt{s} = 1.96 TeV using the Run II Collider Detector at Fermilab. The event signature requires two oppositely charged muons, each with pseudorapidity |eta| mu+mu-. Events with a J/psi and an associated photon candidate are consistent with exclusive chi_c0 production through double pomeron exchange. The exclusive vector meson production is as expected for elastic photo- production, gamma+p --> J/psi(psi(2S)) + p, which is observed here for the first time in hadron-hadron collisions. The cross sections ds/dy(y=0) for p + pbar --> p + X + pbar with X = J/psi, psi(2S) orchi_c0 are 3.92+/-0.62 nb, 0.53+/-0.14 nb, and 75+/-14 nb respectively. The cross section for the continuum, with |eta(mu+/-)|

Intonation of Finnish Verbs

A production experiment investigated the tonal shape of Finnish finite verbs in transitive sentences without narrow focus. Traditional descriptions of Finnish stating that non- focused finite verbs do not receive accents were only partly supported. Verbs were found to have a consistently smaller pitch range than words in other word classes, but their pitch contours were neither flat nor explainable by pure interpolation.

Acquisition of focus by normal hearing and Cochlear implanted children

Two experiments investigated the perception of compound vs. phrasal stress and narrow focus in normally hearing children and children with Cochlear Implants (CI). Additionally, we investigated whether musical experience would predict children’s performance in these tasks. The results showed no difference between CI and normal-hearing (NH) children in either experiment. However, whereas we found no clear effect of age in the children’s stress detection, there was a clear age related trajectory in the ability to recognise (narrow) focus. Moreover, this trend was similar to what has been found previously for English children. Importantly, prior music experience was significantly linked to CI children’s perception of focus.