Time-dependent instantaneous mortality rates from multiple tagging experiments with exact times of release and recovery

Instantaneous natural mortality rates and a nonparametric hunting mortality function are estimated from a multiple-year tagging experiment with arbitrary, time-dependent fishing or hunting mortality. Our theory allows animals to be tagged over a range of times in each year, and to take time to mix into the population. Animals are recovered by hunting or fishing, and death events from natural causes occur but are not observed. We combine a long-standing approach based on yearly totals, described by Brownie et al. (1985, Statistical Inference from Band Recovery Data: A Handbook, Second edition, United States Fish and Wildlife Service, Washington, Resource Publication, 156), with an exact-time-of-recovery approach originated by Hearn, Sandland and Hampton (1987, Journal du Conseil International pour l'Exploration de la Mer, 43, 107-117), who modeled times at liberty without regard to time of tagging. Our model allows for exact times of release and recovery, incomplete reporting of recoveries, and potential tag shedding. We apply our methods to data on the heavily exploited southern bluefin tuna (Thunnus maccoyii).

Absolute quantitation of Marek's disease virus and Herpesvirus of turkeys in chicken lymphocyte, feather tip and dust samples using real-time PCR

The further development of Taqman quantitative real-time PCR (qPCR) assays for the absolute quantitation of Marek's disease virus serotype 1 (MDV1) and Herpesvirus of turkeys (HVT) viruses is described and the sensitivity and reproducibility of each assay reported. Using plasmid DNA copies, the lower limit of detection was determined to be 5 copies for the MDV1 assay and 75 copies for the HVT assay. Both assays were found to be highly reproducible for Ct values and calculated copy numbers with mean intra- and inter-assay coefficients of variation being less than 5% for Ct and 20% for calculated copy number. The genome copy number of MDV1 and HVT viruses was quantified in PBL and feather tips from experimentally infected chickens, and field poultry dust samples. Parallelism was demonstrated between the plasmid-based standard curves, and standard curves derived from infected spleen material containing both viral and host DNA, allowing the latter to be used for absolute quantification. These methods should prove useful for the reliable differentiation and absolute quantitation of MDV1 and HVT viruses in a wide range of samples.

The Link Between Medicaid and the Individuals with Disabilities Education Act (IDEA): Recent History and Current Issues

[From Summary] As a condition of accepting funds under IDEA, public schools must provide special education and related services necessary for children with disabilities to benefit from a public education. Generally, states can finance only a portion of these costs with federal IDEA funds. Medicaid, the federal-state program that finances medical and health services for the poor, can cover IDEA required health-related services for enrolled children as well as related administrative activities (e.g., outreach for Medicaid enrollment purposes, medical care coordination/monitoring). However, the link between IDEA and Medicaid has not been seamless. Despite written federal guidance, schools have a difficult time meeting the myriad complex reimbursement rules applicable to all Medicaid participating providers. According to federal investigations and congressional hearings, Medicaid payments to schools have sometimes been improper. The President’s FY2007 budget proposal would prohibit federal Medicaid reimbursement for IDEA-related school-based administration and transportation costs. This report will be updated.

Mielikuvat transformatiivisen oppimisen välineenä : Tutkimus mielikuvaoppimisesta luontevan esiintymistavan löytämiseksi

The research focus of this study is imagery-based learning aimed at discovering an authentic way of public speaking in the context of transformative learning. The experiences of the participants in this learning process were also a subject of study. This learning process consisted of both guided and independent imagery-based training techniques. Critical reflection plays an important role in transformative learning. Actions, and interpretations and assumptions guiding them, are recognised and subjected to critical reflection. The goal of the learning process is an authentic and wide meaning perspective. Imagery-based training benefits from the gap between the new and the old experience of public speaking, and this is utilised as an activating factor for learning. The study is qualitative, looking at the imagery learning process and its outcomes from the subjective viewpoint of the participants personal experience. The imagery training acted as an intervention in the process of learning authentic public performance. The number of participants in this study was ten, five men and five women from four different working backgrounds. There were 80 individual training sessions, each attended by one person. The author conducted the imagery-based training. For each participant the learning process took roughly nine months. The research data consisted in the answers to questions in writing, diary entries, interviews and researcher notes. The data gathered by these methods was compiled into a personal report for each participant. The learners perceived authentic public speaking performance at the end of the learning process as wider, more flexible and more genuine than at the start of the training. Authenticity was defined through an internal process of becoming aware instead of some external characteristics. The learners understood the process of imagery learning as training for public performance and as an opportunity to become familiar with one s own personal way of acting and with one s own attitudes. They also perceived it as a tool that enabled the observation of personal experiences from different points of view. The learners reflected on ways of acting related to public speaking as well as on contributing factors to performance anxiety during the imagery learning process. Towards the end of the learning process, even critical reflection took place. The learners were categorized into three groups according to differences in their learning processes: the participants, the actors and the critical reflectors. This grouping reflected the relative amount of transformation in their learning processes. The participants became aware of their actions and assumptions. They took part in guided training sessions only. Worries in private life also had some consequences to their training in imagery learning. Apart from than becoming more conscious, the learning process did not yield much difference to the public speaking experiences of the participants. The actors attended both guided imagery training sessions and did individual training on their own. They became aware of their assumptions and their ways of acting. The encounter of the new and the old way of acting stimulated their learning. The actors advanced towards their own goals or even achieved them. The critical reflectors recognised their own assumptions and ways of acting and started to reflect critically on their own attitudes, as well as external attitudes and interpretations. Their assumptions, interpretations and experiences of public performance started to change in a positive direction. The learning process of the critical reflectors was functioning as a transformative process. This learning process revealed old assumptions hindering learning and old ways of acting resulting from these assumptions, thus opening up an opportunity for critical reflection and transformation. Avainsanat Nyckelord imagery learning, imagery-based training, transformative learning, reflection, critical reflection, public speaking anxiety, authentic public performance

Identification of the Meckel syndrome gene (MKS1) exposes a novel ciliopathy

Meckel syndrome (MKS, MIM 249000) is an autosomal recessive developmental disorder causing death in utero or shortly after birth. The hallmarks of the disease are cystic kidney dysplasia and fibrotic changes of the liver, occipital encephalocele with or without hydrocephalus and polydactyly. Other anomalies frequently seen in the patients are incomplete development of the male genitalia, club feet and cleft lip or palate. The clinical picture has been well characterized in the literature while the molecular pathology underlying the disease has remained unclear until now. In this study we identified the first MKS gene by utilizing the disease haplotypes in Finnish MKS families linked to the MKS1 locus on chromosome 17q23 (MKS1) locus. Subsequently, the genetic heterogeneity of MKS was established in the Finnish families. Mutations in at least four different genes can cause MKS. These genes have been mapped to the chromosomes 17q23 (MKS1), 11q13 (MKS2), 8q22 (MKS3) and 9q33 (MKS4). Two of these genes have been identified so far: The MKS1 gene (this work) and the MKS3 gene. The identified MKS1 gene was initially a novel human gene which is conserved among species. We found three different MKS mutations, one of them being the Finnish founder mutation. The information available from MKS1 orthologs in other species convinced us that the MKS1 gene is required for normal ciliogenesis. Defects of the cilial system in other human diseases and model organisms actually cause phenotypic features similar to those seen in MKS patients. The MKS3 (TMEM67) gene encodes a transmembrane protein and the gene maps to the syntenic Wpk locus in the rat, which is a model with polycystic kidney disease, agenesis of the corpus callosum and hydrocephalus. The available information from these two genes suggest that MKS1 would encode a structural component of the centriole required for normal ciliary functions, and MKS3 would be a transmembrane component most likely required for normal ciliary sensory signaling. The MKS4 locus was localized to chromosme 9q32-33 in this study by using an inbred Finnish family with two affected and two healthy children. This fourth locus contains TRIM32 gene, which is associated to another well characterized human ciliopathy, Bardet Biedl syndrome (BBS). Future studies should identify the MKS4 gene on chromosome 9q and confirm if there are more than two genes causing MKS Finnish families. The research on critical signaling pathways in organogenesis have shown that both Wnt and Hedgehog pathways are dependent on functional cilia. The MKS gene products will serve as excellent model molecules for more detailed studies of the functional role of cilia in organogenesis in more detail.

Studies on immune activation in rheumatoid arthritis and reactive arthritis

Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovitis, progressive joint destruction, and disability. Reactive arthritis (ReA) is a sterile joint inflammation following a distant mucosal infection. The clinical course of these diseases is variable and cannot be predicted with reasonable accuracy by clinical and laboratory markers. The predictive value of circulating soluble interleukin-2 receptor (sIL-2R), a marker of lymphocyte activation, measured by Immulite® automated immunoassay analyzer, was evaluated in two cohorts of RA patients. In 175 patients with active early RA randomized to treatment with either on disease-modifying antirheumatic drug (DMARD) or a combination of 3 DMARDs and prednisolone, low baseline sIL-2R level predicted remission after 6 months in patients treated with a single DMARD. In 24 patients with active RA refractory to DMARDs, low baseline sIL-2R level predicted rapid clinical response to treatment with infliximab, an anti-tumour necrosis factor antibody. Furthermore, in a cohort of 26 patients with acute ReA, high baseline sIL-2R level predicted remission after 6 months. Levels of circulating soluble E-selectin (sE-selectin), a marker of endothelial activation, were measured annually by enzyme-linked immunosorbent assay (ELISA) in a cohort of 85 patients with early RA. During a five-year follow-up, sE-selectin levels were associated with activity and outcome of RA. The levels of neutrophil and monocyte CD11b/CD18 expression measured by flow cytometry, and circulating levels of sE-selectin measured by ELISA, and procalcitonin by immunoluminometric assay, were compared in 28 patients with acute ReA and 16 patients with early RA. The levels of the markers were comparable in ReA, RA, and healthy control subjects. In conlusion, sIL-2R may provide a new predictive marker in early RA treated with a single DMARD and refractory RA treated with infliximab. In addition, sIL-2R level predicts remission in acute ReA.

Molecular and Cellular Mechanisms Behind Juvenile Neuronal Ceroid Lipofuscinosis (JNCL, Batten disease)

Neurodegenerative disorders are chronic, progressive, and often fatal disorders of the nervous system caused by dysfunction, and ultimately, death of neuronal cells. The underlying mechanisms of neurodegeneration are poorly understood, and monogenic disorders can be utilised as disease models to elucidate the pathogenesis. Juvenile neuronal ceroid-lipofuscinosis (JNCL, Batten disease) is a recessively inherited lysosomal storage disorder with progressive neurodegeneration and accumulation of autofluorescent storage material in most tissues. It is caused by mutations in the CLN3 gene; however, the exact function of the corresponding CLN3 protein, as well as the molecular mechanisms of JNCL pathogenesis have remained elusive. JNCL disease exclusively affects the central nervous system leaving other organs unaffected, and therefore it is of a particular importance to conduct studies in brain tissue and neuronal cells. The aim of this thesis project was to elucidate the molecular and cell biological mechanisms underlying JNCL. This was the first study to describe the endogenous Cln3 protein, and it was shown that Cln3 localised to neuronal cells in the mouse brain. At a subcellular level, endogenous Cln3 was localised to the presynaptic terminals and to the synaptosome compartment, but not to the synaptic vesicles. Studies with the CLN3-deficient cells demonstrated an impaired endocytic membrane trafficking, and established an interconnection between CLN3, microtubulus-binding Hook1 and Rab proteins. This novel data was not only important in characterising the roles of CLN3 in cells, but also provided significant information delineating the versatile role of the Rab proteins. To identify affected cellular pathways in JNCL, global gene expression profiling of the knock-out mouse Cln3-/- neurons was performed and systematically analysed; this revealed a slight dysfunction of the mitochondria, cytoskeletal abnormality in the microtubule plus-end, and an impaired recovery from depolarizing stimulus when specific N-type Ca2+ channels were inhibited, thus leading to a prolonged time of higher intracellular calcium. All these defective pathways are interrelated, and may together be sufficient to initiate the neurodegenerative process. Results of this thesis also suggest that in neuronal cells, CLN3 most likely functions at endocytic vesicles at the presynaptic terminal, potentially involved in the regulation of the calcium-mediated synaptic transmission.

Lost in Translation : Translation Mechanisms in Production of Cocksfoot Mottle Virus Proteins

The present study focuses on the translational strategies of Cocksfoot mottle virus (CfMV, genus Sobemovirus), which infects monocotyledonous plants. CfMV RNA lacks the 5'cap and the 3'poly(A) tail that ensure efficient translation of cellular messenger RNAs (mRNAs). Instead, CfMV RNA is covalently linked to a viral protein VPg (viral protein, genome-linked). This indicates that the viral untranslated regions (UTRs) must functionally compensate for the lack of the cap and poly(A) tail. We examined the efficacy of translation initiation in CfMV by comparing it to well-studied viral translational enhancers. Although insertion of the CfMV 5'UTR (CfMVe) into plant expression vectors improved gene expression in barley more than the other translational enhancers examined, studies at the RNA level showed that CfMVe alone or in combination with the CfMV 3'UTR did not provide the RNAs translational advantage. Mutation analysis revealed that translation initiation from CfMVe involved scanning. Interestingly, CfMVe also promoted translation initiation from an intercistronic position of dicistronic mRNAs in vitro. Furthermore, internal initiation occurred with similar efficacy in translation lysates that had reduced concentrations of eukaryotic initiation factor (eIF) 4E, suggesting that initiation was independent of the eIF4E. In contrast, reduced translation in the eIF4G-depleted lysates indicated that translation from internally positioned CfMVe was eIF4G-dependent. After successful translation initiation, leaky scanning brings the ribosomes to the second open reading frame (ORF). The CfMV polyprotein is produced from this and the following overlapping ORF via programmed -1 ribosomal frameshift (-1 PRF). Two signals in the mRNA at the beginning of the overlap program approximately every fifth ribosome to slip one nucleotide backwards and continue translation in the new -1 frame. This leads to the production of C-terminally extended polyprotein, which encodes the viral RNA-dependent RNA polymerase (RdRp). The -1 PRF event in CfMV was very efficient, even though it was programmed by a simple stem-loop structure instead of a pseudoknot, which is usually required for high -1 PRF frequencies. Interestingly, regions surrounding the -1 PRF signals improved the -1 PRF frequencies. Viral protein P27 inhibited the -1 PRF event in vivo, putatively by binding to the -1 PRF site. This suggested that P27 could regulate the occurrence of -1 PRF. Initiation of viral replication requires that viral proteins are released from the polyprotein. This is catalyzed by viral serine protease, which is also encoded from the polyprotein. N-terminal amino acid sequencing of CfMV VPg revealed that the junction of the protease and VPg was cleaved between glutamate (E) and asparagine (N) residues. This suggested that the processing sites used in CfMV differ from the glutamate and serine (S) or threonine (T) sites utilized in other sobemoviruses. However, further analysis revealed that the E/S and E/T sites may be used to cleave out some of the CfMV proteins.

Mittauslaitteiston suunnittelu piidiodien vuotovirtamittauksiin matalissa lämpötiloissa

Tässä työssä on suunniteltu mittauslaitteisto ja toteutettu diodien vuotovirtamittaukset matalissa lämpötiloissa. Suunnittelun pääpaino oli tuottaa mittauslaitteisto, joka kestäisi mittausolosuhteitten matalan lämpötilan (80 K) ja toisaalta myös lämpötilavaihtelut huoneen lämpötilasta mataliin lämpötiloihin. Lisäksi mittauslaitteiston oli kestettävä myös tutkimusprojektin myöhemmissä vaiheissa mukaan tulevaa protonisäteilytystä, mikä asetti omat valintaperusteensa materiaaleille. Mittauslaitteiston kohinaa pyrittiin vaimentamaan kontaktipintojen kultapinnoitteilla ja kiinnittämällä huomiota virtajohtimien eristyksiin. Työssä mitattiin erilailla prosessoitujen piidiodien vuotovirtoja eri lämpötiloissa. Mitatut diodit olivat sekä etukäteen säteilytettyjä että säteilyttämättömiä ja työn yhtenä päämääränä oli verrata säteilytyksen vaikutuksia vuotovirran lämpötilakorrelaatioon. Diodien piimateriaaleja oli valmistettu magneettisella Czochralski-menetelmällä sekä Float Zone-menetelmällä, lisäksi osaa diodeista oli muokattu erilaisilla lämpökäsittelyillä parempien säteilynkesto-ominaisuuksien aikaansaamiseksi. Mittauksissa diodin lämpötila laskettiin jäähdytyslaitteistolla systeemin minimilämpötilaan ja diodin ominaiskäyrä mitattiin välillä 0-450 V. Lämpötilaa nostettiin asteittain ja ominaiskäyrät mitattiin määrätyissä lämpötiloissa, minkä jälkeen tuloksia verrattiin teoreettisiin arvioihin vuotovirran lämpötilakäyttäytymisestä. Tulosten perusteella voidaan todeta teoreettisten arvojen vastaavan kokeellisia, mittauslaitteiston erottelukyvyn kynnykselle asti (10-11A), mutta tämän jälkeen mahdollinen lämpötilan laskun aiheuttama virranlasku hukkuu mittalaitteiston kohinan sekaan. Säteilytettyjen diodien kohdalla lämpötilan laskeminen madalsi vuotovirtaa 6 dekadia huoneenlämmöstä 190 K lämpötilaan, kunnes mittauskynnys ylittyi. Säteilyttämättömillä diodeilla vuotovirta oli jo huoneenlämpötilassa erittäin pientä ja lämpötilan laskiessa minimiarvoonsa vuotovirta pieneni n. 2 dekadia, kunnes mittalaitteiston mittatarkkuus tuli vastaan.

Specifying Reuse Interfaces for Task-Oriented Framework Specialization

Reuse of existing carefully designed and tested software improves the quality of new software systems and reduces their development costs. Object-oriented frameworks provide an established means for software reuse on the levels of both architectural design and concrete implementation. Unfortunately, due to frame-works complexity that typically results from their flexibility and overall abstract nature, there are severe problems in using frameworks. Patterns are generally accepted as a convenient way of documenting frameworks and their reuse interfaces. In this thesis it is argued, however, that mere static documentation is not enough to solve the problems related to framework usage. Instead, proper interactive assistance tools are needed in order to enable system-atic framework-based software production. This thesis shows how patterns that document a framework s reuse interface can be represented as dependency graphs, and how dynamic lists of programming tasks can be generated from those graphs to assist the process of using a framework to build an application. This approach to framework specialization combines the ideas of framework cookbooks and task-oriented user interfaces. Tasks provide assistance in (1) cre-ating new code that complies with the framework reuse interface specification, (2) assuring the consistency between existing code and the specification, and (3) adjusting existing code to meet the terms of the specification. Besides illustrating how task-orientation can be applied in the context of using frameworks, this thesis describes a systematic methodology for modeling any framework reuse interface in terms of software patterns based on dependency graphs. The methodology shows how framework-specific reuse interface specifi-cations can be derived from a library of existing reusable pattern hierarchies. Since the methodology focuses on reusing patterns, it also alleviates the recog-nized problem of framework reuse interface specification becoming complicated and unmanageable for frameworks of realistic size. The ideas and methods proposed in this thesis have been tested through imple-menting a framework specialization tool called JavaFrames. JavaFrames uses role-based patterns that specify a reuse interface of a framework to guide frame-work specialization in a task-oriented manner. This thesis reports the results of cases studies in which JavaFrames and the hierarchical framework reuse inter-face modeling methodology were applied to the Struts web application frame-work and the JHotDraw drawing editor framework.

Analysis of Heterogeneous IP Traffic in Wireless Environment

Wireless access is expected to play a crucial role in the future of the Internet. The demands of the wireless environment are not always compatible with the assumptions that were made on the era of the wired links. At the same time, new services that take advantage of the advances in many areas of technology are invented. These services include delivery of mass media like television and radio, Internet phone calls, and video conferencing. The network must be able to deliver these services with acceptable performance and quality to the end user. This thesis presents an experimental study to measure the performance of bulk data TCP transfers, streaming audio flows, and HTTP transfers which compete the limited bandwidth of the GPRS/UMTS-like wireless link. The wireless link characteristics are modeled with a wireless network emulator. We analyze how different competing workload types behave with regular TPC and how the active queue management, the Differentiated services (DiffServ), and a combination of TCP enhancements affect the performance and the quality of service. We test on four link types including an error-free link and the links with different Automatic Repeat reQuest (ARQ) persistency. The analysis consists of comparing the resulting performance in different configurations based on defined metrics. We observed that DiffServ and Random Early Detection (RED) with Explicit Congestion Notification (ECN) are useful, and in some conditions necessary, for quality of service and fairness because a long queuing delay and congestion related packet losses cause problems without DiffServ and RED. However, we observed situations, where there is still room for significant improvements if the link-level is aware of the quality of service. Only very error-prone link diminishes the benefits to nil. The combination of TCP enhancements improves performance. These include initial window of four, Control Block Interdependence (CBI) and Forward RTO recovery (F-RTO). The initial window of four helps a later starting TCP flow to start faster but generates congestion under some conditions. CBI prevents slow-start overshoot and balances slow start in the presence of error drops, and F-RTO reduces unnecessary retransmissions successfully.