Epitypification and phylogeny of Colletotrichum acutatum J.H. Simmonds

Simmonds introduced Colletotrichum acutatum in 1965, validated in 1968, with a broad concept, as demonstrated by the selection of several type specimens from a range of hosts. This has created some confusion in the species concept and identification of C. acutatum. There are no viable ex-type cultures of C. acutatum and furthermore there are no existing cultures of C. acutatum on Carica papaya from the type locality in south-east Queensland. The application of molecular phylogenetic studies to isolates of C. acutatum is only meaningful if the taxonomy is stable and species are properly named. In order to clarify the species concept of C. acutatum, an isolate of Colletotrichum acutatum from Carica papaya from Yandina in Southeast Queensland (Australia) is designated as an epitype. A detailed morphological description is provided. Phylogenies based on a combined ITS and beta-tubulin gene analysis indicate that C. acutatum bears close phylogenetic affinities to C. gloeosporioides and C. capsici. Results also indicate that C. acutatum is monophyletic and there is a close relationship between the epitype and other Australian C. acutatum isolates from Carica papaya. Molecular data, however did not provide further evidence to properly elucidate the taxonomie affinities of C. acutatum especially the holotype and epitype. Our studies indicate that given the complexity of the genus Colletotrichum, there is a need to check previously described type specimens and redesign neotypes where necessary in order to clarify taxonomie uncertainties.

Immunomodulatory effects of probiotic bacteria in healthy adults

Probiooteilla kantakohtaisia vaikutuksia ihmisen immuunijärjestelmään terveillä aikuisilla Probiooteilla on kantakohtaisia tulehduksen välittäjäaineita vähentäviä vaikutuksia ja probioottien yhdistelmien vaikutukset eroavat yksittäisten kantojen vaikutuksista selviää TtM Riina Kekkosen tuoreesta väitöstutkimuksesta. TtM Riina Kekkonen on selvittänyt väitöskirjassaan eri probioottikantojen vaikutuksia immuunivasteeseen valkosolumallissa sekä terveillä aikuisilla lumekontrolloiduissa kliinisissä tutkimuksissa. Aikaisemmin probioottien vaikutuksia on tutkittu lähinnä allergian ja erilaisten vatsavaivojen ehkäisyssä ja hoidossa. Probiootteja sisältäviä tuotteita käyttävät kuluttajat ovat kuitenkin useimmiten terveitä aikuisia, ja probioottien vaikutus terveiden aikuisten immuunijärjestelmään on ollut puutteellisesti selvitettyä. Valkosolumallissa probioottikantojen havaittiin poikkeavan toisistaan niiden kyvyssä aktivoida immuunivasteen välittäjäaineiden, sytokiinien, tuotantoa. Anti-inflammatorisia, eli tulehdusta lievittäviä vaikutuksia nähtiin lähinnä Bifidobacterium ja Propionibacterium sukuihin kuuluvilla kannoilla. Streptococcus ja Leuconostoc sukuihin kuuluvat kannat puolestaan aktivoivat Th1 tyyppistä, soluvälitteistä immuunivastetta. Eri probioottien kombinaatiot eivät saaneet aikaan voimakkaampaa aktivaatiota yksittäisiin kantoihin verrattuna, joka viittaa probioottien keskinäiseen kilpailuun niiden ollessa kontaktissa ihmisen solujen kanssa. Probioottikantojen valinta kliinisiin tutkimuksiin tehtiin niiden anti-inflammatoristen ominaisuuksien perusteella. Parhaita anti-inflammatorisia kantoja olivat B. lactis ssp. animalis Bb12 ja P. freudenreichii ssp. shermanii JS, joiden lisäksi tutkimuksiin valittiin myös L. rhamnosus GG (LGG) hyvin tutkittuna referenssikantana. Solutöiden tulokset eivät olleet täysin verrannollisia kliinisen työn tuloksiin, koska LGG näytti omaavan parhaat anti-inflammatoriset ominaisuudet kliinisissä tutkimuksissa vaikka solutyössä sen aikaansaamat vasteet olivat melko vaimeita. Kolmen viikon kliinisessä tutkimuksessa terveillä aikuisilla LGG alensi mm. tulehdusta kuvaavan C-reaktiivisen proteiinin ja inflammatoristen sytokiinien määrää. Pidemmässä kolmen kuukauden pituisessa kliinisessä tutkimuksessa LGG:llä ei ollut vaikutusta terveiden aikuisten infektiosairastavuuteen, mutta LGG lyhensi vatsavaivojen kestoa. Probioottien vaikutukset immuunijärjestelmään näyttävät olevan kantakohtaisia ja erityisesti Lactobacillus rhamnosus GG:llä havaittiin anti-inflammatorisia vaikutuksia. Valkosolumallia ei tulisi käyttää ainoana probioottikantojen skriinausmenetelmänä niiden immunologisia vaikutuksia selvitettäessä, koska solutöiden tulokset eivät olleet täysin verrannollisia kliinisten tutkimusten tuloksiin. Sen sijaan veren perifeeristen lymfosyyttien eristäminen ja niiden aktivoitumisen selvittäminen lyhytaikaisessa kliinisessä tutkimuksessa voisi toimia suhteellisen helppona skiinausmenetelmänä.

World War I Osterschlacht (Easter Battle).

Handwritten caption: 105. Deutsche Artill. am Marsch nach Izbugyab (Osterschlacht) 3. April 1915 (German artillery marching to Izbugyab. (Easter Battle) )

Milton Weill papers, 1918-1950.

Contains correspondence, memoranda, speeches, etc. to various departments on the National Jewish Welfare Board, the Anti-Defamation League, and the Jewish War Veterans of the U.S. relating to Jewish personnel in the U.S. Armed Forces during World War II and concerned with public relations, anti-Semitism and discrimination, the chaplaincy, etc.; includes also published articles and radio addresses for the same period and extensive correspondence with Rabbi Milton Steinberg from 1946 to 1950, as well as material by and about Rabbi Steinberg. The collection also contains personal family correspondence while Weill was serving overseas during World War I, memorabilia and a scrapbook relating to these military experiences, and undated typescript copies of dramatic sketches.

Reconstruction of the ocular surface using biomaterial templates

This chapter discusses the effect on vision of a large group of pathological conditions, known as ocular surface disorders (OSDs), and presents the therapeutic strategies to reconstruct the abnormal ocular surface. If left untreated, most of the OSDs will lead to partial or total loss of eyesight, especially when limbal stem cell deficiency is involved. An overview of various treatment strategies is presented, with the emphasis on the development of the ex vivo expansion of corneal limbal epithelial cells (presumed to be progenitor or stem cells) and the creation of transplantable epithelial constructs. The use of naturally derived biomaterials (collagen, fibrin, amnion, etc.) or synthetic polymers (polylactides, thermoresponsive polymers, etc.) as substrata in these constructs is critically analyzed. Emphasis is placed on the templates from silk proteins, which are being developed by the authors.

Fertility in Namibia : Changes in fertility levels in North-Central Namibia 1960-2001, including an assessment of the impact of HIV

The aim of this study was to estimate the development of fertility in North-Central Namibia, former Ovamboland, from 1960 to 2001. Special attention was given to the onset of fertility decline and to the impact of the HIV epidemic on fertility. An additional aim was to introduce parish registers as a source of data for fertility research in Africa. Data used consisted of parish registers from Evangelical Lutheran congregations, the 1991 and 2001 Population and Housing Censuses, the 1992 and 2000 Namibia Demographic and Health Surveys, and the HIV sentinel surveillances of 1992-2004. Both period and cohort fertility were analysed. The P/F ratio method was used when analysing census data. The impact of HIV infection on fertility was estimated indirectly by comparing the fertility histories of women who died at an age of less than 50 years with the fertility of other women. The impact of the HIV epidemic on fertility was assessed both among infected women and in the general population. Fertility in the study population began to decline in 1980. The decline was rapid during the 1980s, levelled off in the early 1990s at the end of war of independence and then continued to decline until the end of the study period. According to parish registers, total fertility was 6.4 in the 1960s and 6.5 in the 1970s, and declined to 5.1 in the 1980s and 4.2 in the 1990s. Adjustment of these total fertility rates to correspond to levels of fertility based on data from the 1991 and 2001 censuses resulted in total fertility declining from 7.6 in 1960-79 to 6.0 in 1980-89, and to 4.9 in 1990-99. The decline was associated with increased age at first marriage, declining marital fertility and increasing premarital fertility. Fertility among adolescents increased, whereas the fertility of women in all other age groups declined. During the 1980s, the war of independence contributed to declining fertility through spousal separation and delayed marriages. Contraception has been employed in the study region since the 1980s, but in the early 1990s, use of contraceptives was still so limited that fertility was higher in North-Central Namibia than in other regions of the country. In the 1990s, fertility decline was largely a result of the increased prevalence of contraception. HIV prevalence among pregnant women increased from 4% in 1992 to 25% in 2001. In 2001, total fertility among HIV-infected women (3.7) was lower than that among other women (4.8), resulting in total fertility of 4.4 among the general population in 2001. The HIV epidemic explained more than a quarter of the decline in total fertility at population level during most of the 1990s. The HIV epidemic also reduced the number of children born by reducing the number of potential mothers. In the future, HIV will have an extensive influence on both the size and age structure of the Namibian population. Although HIV influences demographic development through both fertility and mortality, the effect through changes in fertility will be smaller than the effect through mortality. In the study region, as in some other regions of southern Africa, a new type of demographic transition is under way, one in which population growth stagnates or even reverses because of the combined effects of declining fertility and increasing mortality, both of which are consequences of the HIV pandemic.

SiD Letter of Intent

Letter of intent describing SiD (Silicon Detector) for consideration by the International Linear Collider IDAG panel. This detector concept is founded on the use of silicon detectors for vertexing, tracking, and electromagnetic calorimetry. The detector has been cost-optimized as a general-purpose detector for a 500 GeV electron-positron linear collider.

SiD Letter of Intent

Letter of intent describing SiD (Silicon Detector) for consideration by the International Linear Collider IDAG panel. This detector concept is founded on the use of silicon detectors for vertexing, tracking, and electromagnetic calorimetry. The detector has been cost-optimized as a general-purpose detector for a 500 GeV electron-positron linear collider.

First measurement of the ratio of branching fractions B(Λb0→Λc+μ-ν̅ μ)/B(Λb0→Λc+π-)

This article presents the first measurement of the ratio of branching fractions B(Λb0→Λc+μ-ν̅ μ)/B(Λb0→Λc+π-). Measurements in two control samples using the same technique B(B̅ 0→D+μ-ν̅ μ)/B(B̅ 0→D+π-) and B(B̅ 0→D*(2010)+μ-ν̅ μ)/B(B̅ 0→D*(2010)+π-) are also reported. The analysis uses data from an integrated luminosity of approximately 172  pb-1 of pp̅ collisions at √s=1.96  TeV, collected with the CDF II detector at the Fermilab Tevatron. The relative branching fractions are measured to be B(Λb0→Λc+μ-ν̅ μ)/B(Λb0→Λc+π-)=16.6±3.0(stat)±1.0(syst)+2.6/-3.4(PDG)±0.3(EBR), B(B̅ 0→D+μ-ν̅ μ)/B(B̅ 0→D+π-)= 9.9±1.0(stat)±0.6(syst)±0.4(PDG)±0.5(EBR), and B(B̅ 0→D*(2010)+μ-ν̅ μ)/B(B̅ 0→D*(2010)+π-)=16.5±2.3(stat)± 0.6(syst)±0.5(PDG)±0.8(EBR). The uncertainties are from statistics (stat), internal systematics (syst), world averages of measurements published by the Particle Data Group or subsidiary measurements in this analysis (PDG), and unmeasured branching fractions estimated from theory (EBR), respectively. This article also presents measurements of the branching fractions of four new Λb0 semileptonic decays: Λb0→Λc(2595)+μ-ν̅ μ, Λb0→Λc(2625)+μ-ν̅ μ, Λb0→Σc(2455)0π+μ-ν̅ μ, and Λb0→Σc(2455)++π-μ-ν̅ μ, relative to the branching fraction of the Λb0→Λc+μ-ν̅ μ decay. Finally, the transverse-momentum distribution of Λb0 baryons produced in pp̅ collisions is measured and found to be significantly different from that of B̅ 0 mesons, which results in a modification in the production cross-section ratio σΛb0/σB̅ 0 with respect to the CDF I measurement.

First Observation of B̅ s0→Ds±K∓ and Measurement of the Ratio of Branching Fractions B(B̅ s0→Ds±K∓)/B(B̅ s0→Ds+π-)

A combined mass and particle identification fit is used to make the first observation of the decay B̅ s0→Ds±K∓ and measure the branching fraction of B̅ s0→Ds±K∓ relative to B̅ s0→Ds+π-. This analysis uses 1.2  fb-1 integrated luminosity of pp̅ collisions at √s=1.96  TeV collected with the CDF II detector at the Fermilab Tevatron collider. We observe a B̅ s0→Ds±K∓ signal with a statistical significance of 8.1σ and measure B(B̅ s0→Ds±K∓)/B(B̅ s0→Ds+π-)=0.097±0.018(stat)±0.009(syst).

Direct Measurement of the W Production Charge Asymmetry in pp̅ Collisions at √s=1.96 TeV

We present the first direct measurement of the $W$ production charge asymmetry as a function of the $W$ boson rapidity $\yW$ in $\ppbar$ collisions at $\sqrt{s} = 1.96$ $\TeV$. We use a sample of $\wenu$ events in data from 1 $\ifb$ of integrated luminosity collected using the CDF II detector. In the region $|\yW|

Precision Measurement of the X(3872) Mass in J/ψπ+π- Decays

We present an analysis of the mass of the X(3872) reconstructed via its decay to J/psi pi+ pi- using 2.4 fb^-1 of integrated luminosity from ppbar collisions at sqrt(s) = 1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. The possible existence of two nearby mass states is investigated. Within the limits of our experimental resolution the data are consistent with a single state, and having no evidence for two states we set upper limits on the mass difference between two hypothetical states for different assumed ratios of contributions to the observed peak. For equal contributions, the 95% confidence level upper limit on the mass difference is 3.6 MeV/c^2. Under the single-state model the X(3872) mass is measured to be 3871.61 +- 0.16 (stat) +- 0.19 (syst) MeV/c^2, which is the most precise determination to date.

First Observation of B̅ s0→Ds±K∓ and Measurement of the Ratio of Branching Fractions B(B̅ s0→Ds±K∓)/B(B̅ s0→Ds+π-)

A combined mass and particle identification fit is used to make the first observation of the decay Bs --> Ds K and measure the branching fraction of Bs --> Ds K relative to Bs --> Ds pi. This analysis uses 1.2 fb^-1 integrated luminosity of pbar-p collisions at sqrt(s) = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron collider. We observe a Bs --> Ds K signal with a statistical significance of 8.1 sigma and measure Br(Bs --> Ds K)/Br(Bs --> Ds pi) = 0.097 +- 0.018(stat) +- 0.009(sys).

Essays on the Modeling and Prediction of Volatility and Higher Moments of Stock Returns (summary section only)

One of the most fundamental and widely accepted ideas in finance is that investors are compensated through higher returns for taking on non-diversifiable risk. Hence the quantification, modeling and prediction of risk have been, and still are one of the most prolific research areas in financial economics. It was recognized early on that there are predictable patterns in the variance of speculative prices. Later research has shown that there may also be systematic variation in the skewness and kurtosis of financial returns. Lacking in the literature so far, is an out-of-sample forecast evaluation of the potential benefits of these new more complicated models with time-varying higher moments. Such an evaluation is the topic of this dissertation. Essay 1 investigates the forecast performance of the GARCH (1,1) model when estimated with 9 different error distributions on Standard and Poor’s 500 Index Future returns. By utilizing the theory of realized variance to construct an appropriate ex post measure of variance from intra-day data it is shown that allowing for a leptokurtic error distribution leads to significant improvements in variance forecasts compared to using the normal distribution. This result holds for daily, weekly as well as monthly forecast horizons. It is also found that allowing for skewness and time variation in the higher moments of the distribution does not further improve forecasts. In Essay 2, by using 20 years of daily Standard and Poor 500 index returns, it is found that density forecasts are much improved by allowing for constant excess kurtosis but not improved by allowing for skewness. By allowing the kurtosis and skewness to be time varying the density forecasts are not further improved but on the contrary made slightly worse. In Essay 3 a new model incorporating conditional variance, skewness and kurtosis based on the Normal Inverse Gaussian (NIG) distribution is proposed. The new model and two previously used NIG models are evaluated by their Value at Risk (VaR) forecasts on a long series of daily Standard and Poor’s 500 returns. The results show that only the new model produces satisfactory VaR forecasts for both 1% and 5% VaR Taken together the results of the thesis show that kurtosis appears not to exhibit predictable time variation, whereas there is found some predictability in the skewness. However, the dynamic properties of the skewness are not completely captured by any of the models.

DNA damage recognition in the normal epithelium of human prostate and seminal vesicles

Prostate cancer is one of the most prevalent cancer types in men. The development of prostate tumors is known to require androgen exposure, and several pathways governing cell growth are deregulated in prostate tumorigenesis. Recent genetic studies have revealed that complex gene fusions and copy - number alterations are frequent in prostate cancer, a unique feature among solid tumors. These chromosomal aberrations are though to arise as a consequence of faulty repair of DNA double strand breaks (DSB). Most repair mechanisms have been studied in detail in cancer cell lines, but how DNA damage is detected and repaired in normal differentiated human cells has not been widely addressed. The events leading to the gene fusions in prostate cancer are under rigorous studies, as they not only shed light on the basic pathobiologic mechanisms but may also produce molecular targets for prostate cancer treatment and prevention. Prostate and seminal vesicles are part of the male reproductive system. They share similar structure and function but differ dramatically in their cancer incidence. Approximately fifty primary seminal vesicle carcinomas have been reported worldwide. Surprisingly, only little is known on why seminal vesicles are resistant to neoplastic changes. As both tissues are androgen dependent, it is a mystery that androgen signaling would only lead to tumors in prostate tissue. In this work, we set up novel ex vivo human tissue culture models of prostate and seminal vesicles, and used them to study how DNA damage is recognized in normal epithelium. One of the major DNA - damage inducible pathways, mediated by the ATM kinase, was robustly activated in all main cell types of both tissues. Interestingly, we discovered that secretory epithelial cells had less histone variant H2A.X and after DNA damage lower levels of H2AX were phosphorylated on serine 139 (γH2AX) than in basal or stromal cells. γH2AX has been considered essential for efficient DSB repair, but as there were no significant differences in the γH2AX levels between the two tissues, it seems more likely that the role of γH2AX is less important in postmitotic cells. We also gained insight into the regulation of p53, an important transcription factor that protects genomic integrity via multiple mechanisms, in human tissues. DSBs did not lead to a pronounced activation of p53, but treatments causing transcriptional stress, on the other hand, were able to launch a notable p53 response in both tissue types. In general, ex vivo culturing of human tissues provided unique means to study differentiated cells in their relevant tissue context, and is suited for testing novel therapeutic drugs before clinical trials. In order to study how prostate and seminal vesicle epithelial cells are able to activate DNA damage induced cell cycle checkpoints, we used primary cultures of prostate and seminal vesicle epithelial cells. To our knowledge, we are the first to report isolation of human primary seminal vesicle cells. Surprisingly, human prostate epithelial cells did not activate cell cycle checkpoints after DSBs in part due to low levels of Wee1A, a kinase regulating CDK activity, while primary seminal vesicle epithelial cells possessed proficient cell cycle checkpoints and expressed high levels of Wee1A. Similarly, seminal vesicle cells showed a distinct activation of the p53 - pathway after DSBs that did not occur in prostate epithelial cells. This indicates that p53 protein function is under different control mechanisms in the two cell types, which together with proficient cell cycle checkpoints may be crucial in protecting seminal vesicles from endogenous and exogenous DNA damaging factors and, as a consequence, from carcinogenesis. These data indicate that two very similar organs of male reproductive system do not respond to DNA damage similarly. The differentiated, non - replicating cells of both tissues were able to recognize DSBs, but under proliferation human prostate epithelial cells had deficient activation of the DNA damage response. This suggests that prostate epithelium is most vulnerable to accumulating genomic aberrations under conditions where it needs to proliferate, for example after inflammatory cellular damage.