Study of using marker assisted selection on a beef cattle breeding program by model comparison

A data set of a commercial Nellore beef cattle selection program was used to compare breeding models that assumed or not markers effects to estimate the breeding values, when a reduced number of animals have phenotypic, genotypic and pedigree information available. This herd complete data set was composed of 83,404 animals measured for weaning weight (WW), post-weaning gain (PWG), scrotal circumference (SC) and muscle score (MS), corresponding to 116,652 animals in the relationship matrix. Single trait analyses were performed by MTDFREML software to estimate fixed and random effects solutions using this complete data. The additive effects estimated were assumed as the reference breeding values for those animals. The individual observed phenotype of each trait was adjusted for fixed and random effects solutions, except for direct additive effects. The adjusted phenotype composed of the additive and residual parts of observed phenotype was used as dependent variable for models' comparison. Among all measured animals of this herd, only 3160 animals were genotyped for 106 SNP markers. Three models were compared in terms of changes on animals' rank, global fit and predictive ability. Model 1 included only polygenic effects, model 2 included only markers effects and model 3 included both polygenic and markers effects. Bayesian inference via Markov chain Monte Carlo methods performed by TM software was used to analyze the data for model comparison. Two different priors were adopted for markers effects in models 2 and 3, the first prior assumed was a uniform distribution (U) and, as a second prior, was assumed that markers effects were distributed as normal (N). Higher rank correlation coefficients were observed for models 3_U and 3_N, indicating a greater similarity of these models animals' rank and the rank based on the reference breeding values. Model 3_N presented a better global fit, as demonstrated by its low DIC. The best models in terms of predictive ability were models 1 and 3_N. Differences due prior assumed to markers effects in models 2 and 3 could be attributed to the better ability of normal prior in handle with collinear effects. The models 2_U and 2_N presented the worst performance, indicating that this small set of markers should not be used to genetically evaluate animals with no data, since its predictive ability is restricted. In conclusion, model 3_N presented a slight superiority when a reduce number of animals have phenotypic, genotypic and pedigree information. It could be attributed to the variation retained by markers and polygenic effects assumed together and the normal prior assumed to markers effects, that deals better with the collinearity between markers. (C) 2012 Elsevier B.V. All rights reserved.

Multi-Country Event Study Methods

Which event study methods are best in non-U.S. multi-country samples? Nonparametric tests, especially the rank and generalized sign, are better specified and more powerful than common parametric tests, especially in multi-day windows. The generalized sign test is the best statistic but must be applied to buy-and-hold abnormal returns for correct specification. Market-adjusted and market-model methods with local market indexes, without conversion to a common currency, work well. The results are robust to limiting the samples to situations expected to be problematic for test specification or power. Applying the tests that perform best in simulation to merger announcements produces reasonable results.

Quality of experience in skype video calls

Skype is one of the well-known applications that has guided the evolution of real-time video streaming and has become one of the most used software in everyday life. It provides VoIP audio/video calls as well as messaging chat and file transfer. Many versions are available covering all the principal operating systems like Windows, Macintosh and Linux but also mobile systems. Voice quality decreed Skype success since its birth in 2003 and peer-to-peer architecture has allowed worldwide diffusion. After video call introduction in 2006 Skype became a complete solution to communicate between two or more people. As a primarily video conferencing application, Skype assumes certain characteristics of the delivered video to optimize its perceived quality. However in the last years, and with the recent release of SkypeKit1, many new Skype video-enabled devices came out especially in the mobile world. This forced a change to the traditional recording, streaming and receiving settings allowing for a wide range of network and content dynamics. Video calls are not anymore based on static ‘chatting’ but mobile devices have opened new possibilities and can be used in several scenarios. For instance, lecture streaming or one-to-one mobile video conferences exhibit more dynamics as both caller and callee might be on move. Most of these cases are different from “head&shoulder” only content. Therefore, Skype needs to optimize its video streaming engine to cover more video types. Heterogeneous connections require different behaviors and solutions and Skype must face with this variety to maintain a certain quality independently from connection used. Part of the present work will be focused on analyzing Skype behavior depending on video content. Since Skype protocol is proprietary most of the studies so far have tried to characterize its traffic and to reverse engineer its protocol. However, questions related to the behavior of Skype, especially on quality as perceived by users, remain unanswered. We will study Skype video codecs capabilities and video quality assessment. Another motivation of our work is the design of a mechanism that estimates the perceived cost of network conditions on Skype video delivery. To this extent we will try to assess in an objective way the impact of network impairments on the perceived quality of a Skype video call. Traditional video streaming schemes lack the necessary flexibility and adaptivity that Skype tries to achieve at the edge of a network. Our contribution will lye on a testbed and consequent objective video quality analysis that we will carry out on input videos. We will stream raw video files with Skype via an impaired channel and then we will record it at the receiver side to analyze with objective quality of experience metrics.

Analisi di espressione di microRNA in Tumore a Cellule Giganti: identificazione dei target con ruolo di potenziali biomarcatori

Il Tumore a Cellule Giganti dell’osso (TCG) è una rara neoplasia che rappresenta il 5% dei tumori di natura ossea; sebbene venga considerato un tumore a decorso benigno può manifestare caratteri di aggressività locale dando origine a recidive locali nel 10-25% dei casi, e nel 2-4% dei casi metastatizza a livello polmonare. In questo studio è stata valutata l’espressione dei miRNA mediante miRNA microarray in 10 pazienti affetti da TCG, 5 con metastasi e 5 liberi da malattia; sono stati riscontrati miRNA differenzialmente espressi tra i 2 gruppi di pazienti e la successiva validazione mediante Real Time PCR ha confermato una differenza significativa per il miR-136 (p=0.04). Mediante analisi bioinformatica con il software TargetScan abbiamo identificato RANK e NF1B come target del miR-136 e ne abbiamo studiato l’espressione mediante Real Time PCR su una più ampia casistica di pazienti affetti da TCG, metastatico e non, evidenziando una maggior espressione di NF1B nel gruppo di pazienti metastatici, mentre RANK non ha dimostrato una differenza significativa. L’analisi di Western Blot ha rilevato una maggiore espressione di entrambe le proteine nei pazienti metastatici rispetto ai non metastatici. Successivamente è stato condotto uno studio di immunoistochimica su TMA di 163 campioni di pazienti affetti da TCG a diverso decorso clinico che ha dimostrato una maggiore e significativa espressione di entrambe i target nei pazienti con metastasi rispetto ai non metastatici; le analisi di popolazione mediante Kaplan-Meier hanno confermato la correlazione tra over-espressione di RANK, NF1B e ricaduta con metastasi (p=0.001 e p<0.0005 rispettivamente). Lo studio di immunoistochimica è stato ampliato alle proteine maggiormente coinvolte nell’osteolisi che risultano avere un significato prognostico; tuttavia mediante analisi di ROC, la co-over-espressione di RANK, RANKL e NF1B rappresenta il migliore modello per predire la comparsa di metastasi (AUC=0.782, p<0.0005).

La gestione dei beni fiscali da parte di Federico II di Svevia: Il "Quaternus excadenciarum capitinate". Edizione e commento

La ricerca è stata incentrata su di una fonte di grande importanza per una più puntuale comprensione della vita del regno di Federico II: il Quaternus excadenciarum Capitinate. Essa ha tenuto presenti le altre fonti coeve: Liber Augustalis, Registro della Cancelleria di Federico II degli anni 1239-1240, fonti cronachistiche. Il Quaternus è un inventario di talune particolari categorie di beni demaniali, le excadencie, la cui concessione è scaduta e pertanto ritornano al fisco. Tali beni sono situati in 33 località del Giustizierato di Capitanata. Senza data, è stato redatto tra il 1249 e il 1250 (risultano inseriti i beni confiscati a Pier della Vigna, bollato di tradimento nel febbraio 1249). Obiettivo della ricerca è stato duplice: 1) analizzare e approfondire le questioni di natura giuridico-istituzionale ed economica implicate nel documento e tentare di ricostruire uno spaccato della Capitanata del XIII sec.; 2) offrire una nuova e più corretta edizione del testo. La prima parte dello studio ha inteso inquadrare il documento nel contesto delle esigenze proprie delle monarchie del tempo di tenere sotto controllo i beni immobili di ciascun regno ed analizzare la politica economica fridericiana (capp. I, II). La seconda parte è stata dedicata agli approfondimenti innanzi ricordati. Essa è struttura in sette capitoli (I. Il Quaternus excadenciarum Capitinate; II. Beni e diritti costituenti le excadencie Capitinate; III. Il Quaternus come specchio di una politica dispotica; IV. La gestione delle excadencie; V. Pesi e misure; VI. Monete e valori; VII. Il Quaternus come documento sullo stato della Capitanata nel XIII secolo). In appendice: tabelle che offrono per ciascuna delle 33 località considerate, puntuali indicazioni dei beni e diritti censiti, dei nomi dei titolari delle concessioni (spesso personaggi di rango) e delle relative rendite.

TNFα inhibits the development of osteoclasts through osteoblast-derived GM-CSF

Inflammatory cytokines such as tumor necrosis factor-alpha (TNFα) are potent stimulators of osteoclast formation and bone resorption and are frequently associated with pathologic bone metabolism. The cytokine exerts specific effects on its target cells and constitutes a part of the cellular microenvironment. Previously, TNFα was demonstrated to inhibit the development of osteoclasts in vitro via an osteoblast-mediated pathway. In the present study, the molecular mechanisms of the inhibition of osteoclastogenesis were investigated in co-cultures of osteoblasts and bone marrow cells (BMC) and in cultures of macrophage-colony stimulating factor (M-CSF) dependent, non-adherent osteoclast progenitor cells (OPC) grown with M-CSF and receptor activator of NF-κB ligand (RANKL). Granulocyte-macrophage colony stimulating factor (GM-CSF), a known inhibitor of osteoclastogenesis was found to be induced in osteoblasts treated with TNFα and the secreted protein accumulated in the supernatant. Dexamethasone (Dex), an anti-inflammatory steroid, caused a decrease in GM-CSF expression, leading to partial recovery of osteoclast formation. Flow cytometry analysis revealed that in cultures of OPC, supplemented with 10% conditioned medium (CM) from osteoblasts treated with TNFα/1,25(OH)(2)D(3), expression of RANK and CD11c was suppressed. The decrease in RANK expression may be explained by the finding, that GM-CSF and the CM from wt osteoblasts were found to suppress the expression of c-Fos, Fra-1, and Nfatc-1. The failure of OPC to develop into CD11c(+) dendritic cells suggests that cell development is not deviated to an alternative differentiation pathway, but rather, that the monocytes are maintained in an undifferentiated, F4/80(+), state. The data further implies possible interactions among inflammatory cytokines. GM-CSF induced by TNFα acts on early hematopoietic precursors, inhibiting osteoclastogenesis while acting as the growth factor for M-CSF independent inflammatory macrophages. These in turn may condition a microenvironment enhancing osteoclast differentiation and bone resorption upon migration of the OPC from circulation to the bone/bone marrow compartment.

Digital Commons @ Michigan Tech Content Policy

Content Policy outlining the acceptable content and file formats that can be deposited in Digital Commons @ Michigan Tech, as well as information pertaining to the organization of the digital repository, ownership and rights of content, privacy, and access.

Saliva suppresses osteoclastogenesis in murine bone marrow cultures.

Saliva can reach mineralized surfaces in the oral cavity; however, the relationship between saliva and bone resorption is unclear. Herein, we examined whether saliva affects the process of osteoclastogenesis in vitro. We used murine bone marrow cultures to study osteoclast formation. The addition of fresh sterile saliva eliminated the formation of multinucleated cells that stained positive for tartrate-resistant acid phosphatase (TRAP). In line with the histochemical staining, saliva substantially reduced gene expression of cathepsin K, calcitonin receptor, and TRAP. Addition of saliva led to considerably decreased gene expression of receptor activator of nuclear factor kappa-B (RANK) and, to a lesser extent, that of c-fms. The respective master regulators of osteoclastogenesis (c-fos and NFATc1) and the downstream cell fusion genes (DC-STAMP and Atp6v0d2) showed decreased expression after the addition of saliva. Among the costimulatory molecules for osteoclastogenesis, only OSCAR showed decreased expression. In contrast, CD40, CD80, and CD86-all costimulatory molecules of phagocytic cells-were increasingly expressed with saliva. The phagocytic capacity of the cells was confirmed by latex bead ingestion. Based on these in vitro results, it can be concluded that saliva suppresses osteoclastogenesis and leads to the development of a phagocytic cell phenotype.

Individual predictors of adolescents' vocational interest stabilities

The study investigated the predictive utility of interest profile differentiation, coherence, elevation, congruence, and vocational identity commitment and career maturity (career planning and exploration) on the 10-month interest stability of 292 Swiss eighth-grade students: profile, rank, and level stabilities were assessed. Controlling for socio-demographic and vocational interest type variables, measures of differentiated and coherent vocational interests were significant predictors of profile stability. Interest elevation predicted more rank and level stability. The career development variables explained only a non-significant additional amount of variance in the different stability measures.

Small Cell Carcinoma of the Urinary Bladder: A Retrospective, Multicenter Rare Cancer Network Study of 107 Patients

PURPOSE Small cell carcinomas of the bladder (SCCB) account for fewer than 1% of all urinary bladder tumors. There is no consensus regarding the optimal treatment for SCCB. METHODS AND MATERIALS Fifteen academic Rare Cancer Network medical centers contributed SCCB cases. The eligibility criteria were as follows: pure or mixed SCC; local, locoregional, and metastatic stages; and age ≥18 years. The overall survival (OS) and disease-free survival (DFS) were calculated from the date of diagnosis according to the Kaplan-Meier method. The log-rank and Wilcoxon tests were used to analyze survival as functions of clinical and therapeutic factors. RESULTS The study included 107 patients (mean [±standard deviation, SD] age, 69.6 [±10.6] years; mean follow-up time, 4.4 years) with primary bladder SCC, with 66% of these patients having pure SCC. Seventy-two percent and 12% of the patients presented with T2-4N0M0 and T2-4N1-3M0 stages, respectively, and 16% presented with synchronous metastases. The most frequent curative treatments were radical surgery and chemotherapy, sequential chemotherapy and radiation therapy, and radical surgery alone. The median (interquartile range, IQR) OS and DFS times were 12.9 months (IQR, 7-32 months) and 9 months (IQR, 5-23 months), respectively. The metastatic, T2-4N0M0, and T2-4N1-3M0 groups differed significantly (P=.001) in terms of median OS and DFS. In a multivariate analysis, impaired creatinine clearance (OS and DFS), clinical stage (OS and DFS), a Karnofsky performance status <80 (OS), and pure SCC histology (OS) were independent and significant adverse prognostic factors. In the patients with nonmetastatic disease, the type of treatment (ie radical surgery with or without adjuvant chemotherapy vs conservative treatment) did not significantly influence OS or DFS (P=.7). CONCLUSIONS The prognosis for SCCB remains poor. The finding that radical cystectomy did not influence DFS or OS in the patients with nonmetastatic disease suggests that conservative treatment is appropriate in this situation.

Deployed military women: A second look at gender-specific infections

This descriptive, cross-sectional study addressed the relationship between variables of deployed military women and prevalence of gender-specific infections. The analysis of secondary data will look at the last deployment experience of 880 randomly selected U.S. military women who completed a mailed questionnaire (Deployed Female Health Practice Questionnaire (FHPQ)) in June 1998. The questionnaire contained 191 items with 80 data elements and one page for the subject's written comments. The broad categories of the questionnaire included: health practices, health promotion, disease prevention and treatment, reproduction, lifestyle management, military characteristics and demographics. The research questions are: (1) What is the prevalence of sexually transmitted diseases (STD), urinary tract infections (UTI) and vaginal infections (VI) related to demographic data, military characteristics, behavioral risk factors and health practices of military women during their last deployment? and (2) What are the differences between STD, UTI and VI related to the demographic data, military characteristics, behavioral risk factors and health practices of military women during their last deployment. The results showed that (1) STDs were found to be significantly associated with age and rank but not location of deployment or military branch; (2) UTI were found to be significantly associated with intrauterine device (IUD) use, prior UTI and type of items used for menses management, but not education or age; and (3) VI were significantly associated with age, rank and deployment location but not ethnicity or education. Although quantitative research exploring hygiene needs of deployed women continues, qualitative studies may uncover further “hidden” issues of importance. It cannot be said that the military has not made proactive changes for women, however, continued efforts to hone these changes are still encouraged. Mandatory debriefings of “seasoned” deployed women soldiers and their experiences would benefit leadership and newly deployed female soldiers with valuable “lessons learned.” Tailored hygiene education material, prevention education classes, easy access website with self-care algorithms, pre-deployment physicals, revision of military protocols for health care providers related to screening, diagnosing and treatment of gender-specific infections and process changes in military supply network of hygiene items for women are offered as recommendations. ^

Diseño gráfico de etiquetas para envases de vino : definición de descriptores para un análisis de componentes sintácticas

Las gráficas de etiquetas para envases de vino son diseñadas a partir de características sintácticas, semánticas y pragmáticas. Este trabajo tiene por objetivos realizar una recopilación, clasificación, análisis y jerarquización de los componentes de la configuración de etiquetas de vino, y además, proveer un instrumento que permita un análisis de estas piezas gráficas, de manera individual, con carácter de sistema o en comparación. Podrá ser aplicado por los profesionales que diseñan etiquetas y envases, por docentes en el campo del diseño y en guías para el público usuario. (…) “los diseñadores nos convertimos en el nexo simbólico entre la calidad de los productos elaborados por nuestros clientes y la calidad de vida de aquéllos que los disfrutan. Somos los que preparamos la logística simbólica que explicita estéticamente lo que un buen vino necesita para llamar la atención. Se trata de crear la imagen que represente fielmente al conjunto de atributos del vino, y de resaltar visualmente esta red de placeres que están presentes en él. Sólo así se logra una relación de confianza con la marca". (Santiago Zemma, 2005).

Influencia de la maquinaria agrícola sobre la variabilidad espacial de la compactación del suelo. Aplicación de la metodología geoestadística-fractal

El cultivo de la caña de azúcar es uno de los más importantes en muchos países del mundo. Los suelos dedicados a este cultivo son usualmente compactados por el tránsito de la maquinaria en el proceso de cosecha. El uso combinado de la geoestadística con el análisis fractal ha demostrado ser útil para el estudio de los mismos. El objetivo del trabajo fue determinar los cambios espaciales de la resistencia a la penetración del suelo debido a la influencia del tránsito de la maquinaria en el proceso de cosecha de la caña de azúcar en un Vertisol, aplicando la metodología geoestadística-fractal. La investigación se llevó a cabo en el período de cosecha 2008-2009. Se evaluó la resistencia a la penetración en dos momentos, antes y después de la cosecha. El muestreo se realizó sistemáticamente en cuadrícula y en transecto, seleccionando 144 y 100 observaciones antes y después de la cosecha, respectivamente, y 221 para el transecto en diagonal. También se determinó el contenido de humedad del suelo por el método gravimétrico, para lo que se tomaron 288 muestras aleatorias en todo el campo. Los resultados demuestran que los valores de resistencia a la penetración (RP) presentaron una distribución normal a partir de los 5 cm de profundidad, el tránsito de la maquinaria agrícola para la cosecha de la caña de azúcar provocó concentración de la variabilidad espacial a escalas inferiores a la del muestreo (el efecto pepita aumentó), un aumento del rango de correlación espacial y una redistribución de las zonas de compactación (las variaciones de los mapas de Krigeaje). También indujo anti-persistencia y anisotropía en algunas direcciones horizontales. Se observó un comportamiento irregular de (RP) verticalmente en el transecto, donde no solamente influyó la maquinaria, sino que también otros factores influyeron como: la hilera, borde de la hilera y grietas. ABSTRACT The cultivation of the cane of sugar is one of the most important in many countries of the world. The soils dedicated to this cultivation are usually compacted by the traffic of the machinery in the harvest process. The combined use of the geostatistics with the fractal analysis has demonstrated to be useful for the study of the same ones. The objective of the work was to determine the space changes from the resistance to the penetration of the floor due to the influence of the traffic of the machinery in the harvest process of harvest of the cane of sugar in a Vertisol applying the geostatistic-fractal methodology. The investigation was carried out in the period of harvest 2008-2009. The resistance to the penetration at two moments was evaluated, before and after the harvest. The sampling was realized systematically in grid and transect, selecting 144 and 100 observations before and after the harvest, respectively, and 221 for transect in diagonal. Also the soil moisture content of the ground by the gravimetric method was determined, so 288 random samples in the entire field were taken. The results shown that resistance to penetration values presented a normal distribution deeper than 5 cm before and after harvest. The transit of the agricultural machinery for sugar cane harvest concentrated the space variability at lower distances than the sampling one, reflected an increase in the nugget effect. At the same time, an increase space correlation rank and a redistribution of compaction areas were observed studying the variations in kriging maps. Another effect of the agricultural machinery transit was to induce antipersistence and anisotropy in some horizontal directions. However, in vertical direction of the longest transect an irregular behaviour was induced not only by the machinery as by another factors such as soil cracks, crop rows and allocation.

AVALIAÇÃO DA COMPRESSÃO DA IMAGEM DIGITAL DA TELERRADIOGRAFIA LATERAL NA REPRODUTIBILIDADE DA MARCAÇÃO DE PONTOS CEFALOMÉTRICOS

A imagem digital adquirida pelo sistema da placa de fósforo foto ativada é visualizada no monitor do computador em um formato denominado DICOM. Este formato ocupa muito espaço para armazenamento, o que dificulta o arquivamento e transmissão da imagem pela Internet. O objetivo deste estudo foi avaliar a influência da compressão JPEG, nos Fatores de Qualidade 100, 80 e 60 na reprodutibilidade da marcação de pontos cefalométricos em imagens de telerradiografias em norma lateral comparadas com o formato DICOM. A amostra consistiu de 120 imagens de telerradiografias em norma lateral obtidas a partir de 30 indivíduos, dos quais se obteve uma radiografia digital no formato DICOM. Essas imagens foram convertidas para o formato JPEG. Após o cegamento e randomização da amostra, três Ortodontistas calibrados marcaram a localização de 12 pontos cefalométricos em cada imagem utilizando o sistema de coordenadas X e Y. Esse procedimento foi repetido após 1 mês. A reprodutibilidade intra e inter observador foi calculada usando o teste de correlação intraclasse. Para comparação entre os grupos de compressão e DICOM na reprodutibilidade de marcação dos pontos utilizou se a Análise de Variância (ANOVA) a um critério para medidas repetidas. Os resultados mostraram que as marcações dos pontos cefalométricos foram bastante reprodutíveis, exceto para o ponto Órbita na coordenada X. Os diferentes formatos de arquivo mostraram estatisticamente iguais para cada ponto e eixo aferido. As compressões JPEG estudadas das imagens de telerradiografias em norma lateral não tiveram efeito na reprodutibilidade da marcação dos pontos cefalométricos testados.

AVALIAÇÃO DA COMPRESSÃO DA IMAGEM DIGITAL DA TELERRADIOGRAFIA LATERAL NA REPRODUTIBILIDADE DA MARCAÇÃO DE PONTOS CEFALOMÉTRICOS

A imagem digital adquirida pelo sistema da placa de fósforo foto ativada é visualizada no monitor do computador em um formato denominado DICOM. Este formato ocupa muito espaço para armazenamento, o que dificulta o arquivamento e transmissão da imagem pela Internet. O objetivo deste estudo foi avaliar a influência da compressão JPEG, nos Fatores de Qualidade 100, 80 e 60 na reprodutibilidade da marcação de pontos cefalométricos em imagens de telerradiografias em norma lateral comparadas com o formato DICOM. A amostra consistiu de 120 imagens de telerradiografias em norma lateral obtidas a partir de 30 indivíduos, dos quais se obteve uma radiografia digital no formato DICOM. Essas imagens foram convertidas para o formato JPEG. Após o cegamento e randomização da amostra, três Ortodontistas calibrados marcaram a localização de 12 pontos cefalométricos em cada imagem utilizando o sistema de coordenadas X e Y. Esse procedimento foi repetido após 1 mês. A reprodutibilidade intra e inter observador foi calculada usando o teste de correlação intraclasse. Para comparação entre os grupos de compressão e DICOM na reprodutibilidade de marcação dos pontos utilizou se a Análise de Variância (ANOVA) a um critério para medidas repetidas. Os resultados mostraram que as marcações dos pontos cefalométricos foram bastante reprodutíveis, exceto para o ponto Órbita na coordenada X. Os diferentes formatos de arquivo mostraram estatisticamente iguais para cada ponto e eixo aferido. As compressões JPEG estudadas das imagens de telerradiografias em norma lateral não tiveram efeito na reprodutibilidade da marcação dos pontos cefalométricos testados.