Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease. Conclusions: The MDH1 gene is not the cause of RP28-linked arRP. Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration.

Revisiting Coptotermes (Isoptera: Rhinotermitidae): a global taxonomic road map for species validity and distribution of an economically important subterranean termite genus

Coptotermes Wasmann (Isoptera: Rhinotermitidae) is one of the most economically important subterranean termite genera and some species are successful invaders. However, despite its important pest status, the taxonomic validity of many named Coptotermes species remains unclear. In this study, we reviewed all named species within the genus and investigated evidence supporting the validity of each named species. Species were systematically scrutinized according to the region of their original description: Southeast Asia, India, China, Africa, the Neotropics, and Australia. We estimate that of the currently 69 named species described by accepted nomenclatural rules, only 21 taxa have solid evidence for validity, 44 names have uncertain status, and the remaining species names should be synonymized or were made unavailable. Species with high degrees of invasiveness may be known under additional junior synonyms due to independent parochial descriptions. Molecular data for a vast majority of species are scarce and significant effort is needed to complete the taxonomic and phylogenetic revision of the genus. Because of the wide distribution of Coptotermes, we advocate for an integrative taxonomic effort to establish the distribution of each putative species, provide specimens and corresponding molecular data, check original descriptions and type specimens (if available), and provide evidence for a more robust phylogenetic position of each species. This study embodies both consensus and contention of those studying Coptotermes and thus pinpoints the current uncertainty of many species. This project is intended to be a roadmap for identifying those Coptotermes species names that need to be more thoroughly investigated, as an incentive to complete a necessary revision process.

Stability of scheduled multi-access communication over quasi-static flat fading channels with random coding and independent decoding

The stability of scheduled multiaccess communication with random coding and independent decoding of messages is investigated. The number of messages that may be scheduled for simultaneous transmission is limited to a given maximum value, and the channels from transmitters to receiver are quasistatic, flat, and have independent fades. Requests for message transmissions are assumed to arrive according to an i.i.d. arrival process. Then, we show the following: (1) in the limit of large message alphabet size, the stability region has an interference limited information-theoretic capacity interpretation, (2) state-independent scheduling policies achieve this asymptotic stability region, and (3) in the asymptotic limit corresponding to immediate access, the stability region for non-idling scheduling policies is shown to be identical irrespective of received signal powers.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease.

Primer-independent initiation of RNA synthesis by SeMV recombinant RNA-dependent RNA polymerase

Sesbania mosaic virus (SeMV),a single-strand positive-sense RNA plant virus, belongs to the genus Sobemoviruses. Mechanism of replication in Sobemoviruses is poorly understood. In the present study, SeMV RNA-dependent RNA polymerase (RdRp) was overexpressed and purified as a thioredoxin-tagged protein. The recombinant SeMV RdRp could synthesize RNA from genomic or subgenomic RNA templates, even in the absence ofthe protein primer, VPg. Analysis of the product indicated that it was double-stranded and that the mode of initiation was de novo. Mutational analysis of the 3' UTR of subgenomic RNA revealed that a stem-loop structure at the 3' end was important. Further, analysis of this stem-loop showed that the SeMV RdRp was capable of recognizing stem-loop structures of various lengths and forms. These results demonstrate that the SeMV RdRp is capable of primer-independent RNAsynthesis in vitro. (C) 2010 Elsevier Inc. All rights reserved.

Hiippakunta diakoniatyön tekijänä ja tukijana : Diakoniatyön kehitys Mikkelin hiippakunnassa 1945-1991

ABSTRACT The diocese as the agent and advocate of diaconial work. The development of diaconial work in the Mikkeli diocese 1945–1991. The roots of Finnish diacony are in the individual devotional life of Pietism. An acting faith had to be evident in acts of love. Following German institutional diacony, diaconial institutions were established in Finland until congregational diacony emerged alongside these institutions in the 1890s. Pastor Otto Aarnisalo acted as a pathfinder in this. He aimed to unite diacony with the Church and the life of the congregation. Diacony had been based on the idea of volunteering to separate it from statutory social work. In 1944 the church law was amended, which made diacony the concern of every member of the congregation. In the years immediately following the Second World War, discussion took place in the Church of Finland about the direction that diacony should take. In the consequential debate, caritative services overcame social diacony. The diocese administration moved to Mikkeli in 1945, when the majority of the Vyborg diocese became part of the USSR in the armistice negotiations. The Mikkeli diocese acted in its diaconial work with the same objectives as the diaconial solutions of the whole church. The acting principle of the diocese diacony became a form of helping which emphasised assistance of the individual. Especially from the 1960s onwards, the country's industrialisation and the reduction of agricultural trade had an effect on the Mikkeli diocese. The diocese administration, specifically Bishop Martti Simojoki and his successor Osmo Alaja, aimed to open up connections to the political left and people working in industry. At least indirectly this helped the diaconial work in industrial localities. In the Mikkeli diocese, a diaconial committee was established in 1971, and its work was overseen by the diocesan chapter of the bishop's office. This enabled the work of the diocese to be organised for the different areas of diacony. Previously, the diaconial work of the Finnish church had primarily been in nursing. The Health Insurance Law of 1972 brought a change to this when the responsibility for health services was transferred to the municipalities. Diacony began to move towards a psychological and spiritual emphasis. Beginning in the 1970s, the diocese started holding diaconial themed days at prescribed intervals. Although these did not result in great realignments, they did help clarify the direction that diacony would take. Large international collections were also carried out, especially in the 1980s. At the same time, socio-ethical activity vitalised and diversified Christian services. The idea that every member of the congregation should practice diacony was a strong factor in the Mikkeli diocese as well. The diocese's vision for diacony was holistic; Christian service was the responsibility of every member of the congregation. During the period of study (1945–1991), the theology of diacony was rather tenuous. Bishop Kalevi Toiviainen, however, brought forth the viewpoint of church doctrine and officially sanctioned theology. Diacony was part of the complete faith of the Church.

Kokoomus ja kommunismin uhka. Puolueen antikommunismi vuoden 1929 eduskuntavaalitaistossa.

Tämän Pro gradu -tutkielman tarkoituksena on selventää Kansallisen Kokoomuspuolueen kommunisminvastaisuutta 1920-luvulla, tarkemmin ottaen vuoden 1929 eduskuntavaalikamppailussa. Tutkimuskysymykseni liittyvät puolueen identiteetin ja kommunisminvastaisuuden yhteyteen: miten kokoomuspuolueen suhtautuminen kommunismiin kytkeytyi, yhtäältä, oman porvarillisen poliittis-kansallisen identiteetin puolustamiseen, ja toisaalta, vuonna 1929 vallitseviin poliittisiin oloihin, jolloin muun muassa parlamentaarinen järjestelmä herätti laajaa epäluottamusta, kokoomus ajautui sisäiseen kriisiin ja kommunistien kumoustavoite korostui suomalaisessa julkisuudessa? Etsimällä vastauksia näihin kysymyksiin pyrin selittämään mistä osakokonaisuuksista antikommunismi koostui, miten uhkaa muokattiin ja perusteltiin. Mielestäni tärkeää ja mielenkiintoista on miettiä, kuinka kommunisminvastaisuus ilmeni ikään kuin vastauksena muihin yhteiskunnallis-poliittisiin ongelmiin ja turhautumiin. Tutkimukseni teoreettinen viitekehys perustuu toiseuden ja viholliskuvien tutkimukseen, koska toiseuden merkitys identiteetin kehittymiselle on kiistaton. Tähän liittyvän kirjallisuuden lisäksi olen käyttänyt lähteinäni tutkimuskirjallisuutta, sanomalehtiä ja julkaisemattomia arkistolähteitä. Tutkimukseni aatehistoriallisen luonteen vuoksi ensisijainen alkuperäislähteeni on julkaistu materiaali – vaalijulkaisut ja kokoomuslehdistö – jonka avulla olen pyrkinyt analysoimaan puolueen suhtautumista kommunismiin ja sen vaikutusta puolueen identiteetille. Metodini on historiallis-kvalitatiivinen, joka tarkoittaa sitä, että pyrin samaan aikaan huomioimaan sekä puolueen julkisuuskuvan että sen toiminnan kulisseissa. Tämä edellyttää huomion kohdistamista sekä julkaistuun että julkaisemattomaan lähdeaineistoon. Julkaistuun materiaaliin kohdistuneen analyysin pohjalta on mahdollista päätellä, että kokoomus halusi luoda itsestään kuvan jyrkästi kommunisminvastaisena puolueena. Toiseus-analyysin perusteella voidaan sanoa, että kommunismi oli puolueen selvä toinen. Julkisuuskuva ei kuitenkaan välttämättä vastannut puolueen todellisia käsityksiä kommunismista ja sen pohjalle muodostetusta viholliskuvasta. Antikommunismi ja viholliskuvan vahvistaminen palvelivat myös muita päämääriä, joista merkittävimmät liittyivät katkenneen kokoomuksen yhtenäisyyden pönkittämiseen ja huomion kääntämiseen pois muista vuonna 1929 esiin työntyneistä ongelmista. Kommunismin muodostamaa uhkaa Suomen kansalliselle olemassaololle pyrittiin perustelemaan monelta eri kantilta. Kommunismin nähtiin rapauttavan kristillisen moraalin ja siveellisyyden, lisäävän yhteiskunnallisia levottomuuksia, heikentävän parlamentarismia sekä vaarantavan Suomen sotilaallisen turvallisuuden ja pyhäksi koetun etuvartiotehtävän. Antikommunismi yhdistyi läheisesti myös ideologisen venäläisvastaisuuden ääri-ilmiöön, ryssävihaan. Näihin eri ilmiöihin liittyvä "antikommunistinen diskurssi" oli siis yksi niistä perustoista, jonka päällä kokoomuksen poliittis-kansallinen identiteetti kehittyi 1920-luvun mittaan. Kevätkesän 1929 tuomien, lähes ylitsepääsemättömien vaikeuksien myötä antikommunistisen diskurssin merkitys kasvoi entisestään ja loi pohjan puolueen suhtautumiselle lapualaisvuosiin.

A Computationally Efficient Generalized Poisson Solution for Independent Double-Gate Transistors

Previous techniques used for solving the 1-D Poisson equation ( PE) rigorously for long-channel asymmetric and independent double-gate (IDG) transistors result in potential models that involve multiple intercoupled implicit equations. As these equations need to be solved self-consistently, such potential models are clearly inefficient for compact modeling. This paper reports a different rigorous technique for solving the same PE by which one can obtain the potential profile of a generalized IDG transistor that involves a single implicit equation. The proposed Poisson solution is shown to be computationally more efficient for circuit simulation than the previous solutions.

Avoimesti sitoutuneena : Lähetystyö kristillisessä kasvatuksessa ja vapaaehtoistyössä

In this study the junction of Christian mission, Christian education and voluntary work are examined in the Christian student voluntary association Opiskelijain Lähetysliitto (OL), which is the Finnish successor to the Student Volunteer Movement. The main subjects are the structure and content of the mission education as one aspect of Lutheran education and the reasons for expressing the mission interest through voluntary work. The research questions are as follows: What kind of organization has the OL been? What has mission education been like in the OL? Why have the former chairpersons participated in the OL? How have purposiveness and intentionality arisen among the former chairpersons? The study is empirical despite having a historical and retrospective view, since the OL is explored during the period 1972 2000. The data consists of the OL s annual reports, membership applications (N=629) and interviews of all 25 former chairmen. Data is analysed by qualitative and quantitative content analysis in a partly inductive and partly deductive manner. The pedagogical framework arises from situational learning theory (Lave - Wenger 1991), which was complemented with the criteria for meaningful learning (Jonassen 1995), the octagon model of volunteer motivation (Yeung 2004) and the definitions of intentionality and purposiveness in the theory of teachers pedagogical thinking (Kansanen et al. 2000). The analysis of the archive data showed that the activities of the OL are reminiscent of those of the missions of the Finnish Evangelical Lutheran Church congregations. The biggest difference was that all OL participants were young adults, the age group that is the greatest challenge to the Church. The OL is therefore an interesting context in which to explore mission education and mission interest. The key result of the study was the forming of a model of mission educa-tion. The model has three educational components: values, goals and methods. The gist of the model is formed by the goals. The main goal is the arousing and strengthening of mission interest which has emotional, cognitive and practical aspects. The subgoals create the horizontal vertical and inward outward dimensions of the model, which are the metalevels of mission education. The subgoals reveal that societal and religious education may embody a missionary dimension when they are understood as missionary training. Further, a distinction between mission education and missionary training was observed. The former emphasizes the main goal of the model and the latter underlines the subgoals. Based on the vertical dimension of the model the study suggests that the definition of religious competence needs to be complemented with missional competence. Reasons for participating in the OL were found to be diverse as noted in other studies on volunteering and motivating factors, and were typical to young people such as the importance of social relations. The study created new motivational themes that occurred in the middle of the continuity newness and the distance proximity dimensions, which were not found in Yeung s research. Mission interest as voluntary work appeared as oriented towards one s own spirituality or towards the social community. On the other hand, mission interest was manifested as intentional education in order to either improve the community or to promote the Christian mission. In the latter case the mission was seen as a purpose in life and as a future profession. Keywords: mission, Christian education, voluntary work, mission education, mission interest, stu-dent movement

Language independent automated segmentation of speech using Bach scale filter-banks

This correspondence describes a method for automated segmentation of speech. The method proposed in this paper uses a specially designed filter-bank called Bach filter-bank which makes use of 'music' related perception criteria. The speech signal is treated as continuously time varying signal as against a short time stationary model. A comparative study has been made of the performances using Mel, Bark and Bach scale filter banks. The preliminary results show up to 80 % matches within 20 ms of the manually segmented data, without any information of the content of the text and without any language dependence. The Bach filters are seen to marginally outperform the other filters.

Keskeytyksiä elämässä : Naisten toimijuudet aborttikertomuksissa

The present study focuses on the question of agency in the narratives of women who have experienced an abortion. The study scrutinizes agency by analyzing narratives and their context, that is, how narratives are entwined with cultural discourses and societal practices. The study thus addresses also the wider framework within which experiences and actions can be constructed in abortion narratives in the contemporary Finnish society. The women who wrote their stories or were interviewed were of different ages and had different social and religious backgrounds. Many variations of agency were found when abortion experiences were analyzed through the women s embodied and historically specific accounts. Independent and rational choices are entwined with emotions and choices made together with other people. Intimate relationships with family and friends have an important role in the choices regarding abortion. These relationships do not, however, simply belong in the private sphere but reflect the wider socio-cultural meanings of social bonds and family ties. Women s agency with regard to abortion is also constructed in encounters with the medical profession and within the wider framework of abortion legislation. The Finnish legislation grants women an abortion within certain parameters but not solely on the basis of a woman s wish to have an abortion. The data consists primarily of written narratives and interviews. All together 39 women shared their experiences with the researcher. The analysis focuses on decision-making regarding abortion, depictions of freedom and responsibility, emotions around abortion and expressions of values and religious views. The links between the women's experiences and the wider socio-cultural norms and institutions are analyzed through materials consisting of public debate on abortion in the media, ethical statements as well as literature and legislation on abortion. The analysis sheds light on the tensions apparent in the women's narratives between the legal status of abortion and more traditional views on abortion. The study demonstrates that the freedom linked to abortion is not solely to do with the right to have an abortion but also how abortion can be experienced, understood and where one can talk about the experience afterwards. The analysis reveals that Christian values shape women's experiences but that there are also new religious ways to deal with the ethical considerations brought about by abortion. Annually over 10 000 Finnish women experience an abortion, which is a situation involving ethical considerations. The study provides a nuanced account of the ways in which one can think and act when going through an abortion.

Length-independent voltage fluctuations in small conductors

The mean-squared voltage fluctuation of a disordered conductor of lengthL smaller than the phase coherence lengthL ϕ, is independent of the distance between the probes. We obtain this result using the voltage additivity and the known results for the conductance fluctuation. Our results complement the recent theoretical and experimental findings.

Shell-model calculation of defect energies in alkali halides employing crystal-independent interionic potential parameters

Shell model calculation of defect energies in alkali halides have been carried out using the ion-dependent, crystal-independent potential parameters of Sangster and Atwood (1978). Results indicate that appreciable differences exist between barrier heights for migration of cations and anions. While barrier heights for cations are generally lower than for anions in alkali halides of NaCl structure, the opposite is true in alkali halides of CsCl structure.

Characterization of unitary processes with independent and stationary increments

This is a continuation of the earlier work (Publ. Res. Inst. Math. Sci. 45 (2009) 745-785) to characterize unitary stationary independent increment Gaussian processes. The earlier assumption of uniform continuity is replaced by weak continuity and with technical assumptions on the domain of the generator, unitary equivalence of the process to the solution of an appropriate Hudson-Parthasarathy equation is proved.