Genetic evaluation of mastitis liability and recovery through longitudinal analysis of transition probabilities

BACKGROUND: Many methods for the genetic analysis of mastitis use a cross-sectional approach, which omits information on, e.g., repeated mastitis cases during lactation, somatic cell count fluctuations, and recovery process. Acknowledging the dynamic behavior of mastitis during lactation and taking into account that there is more than one binary response variable to consider, can enhance the genetic evaluation of mastitis. METHODS: Genetic evaluation of mastitis was carried out by modeling the dynamic nature of somatic cell count (SCC) within the lactation. The SCC patterns were captured by modeling transition probabilities between assumed states of mastitis and non-mastitis. A widely dispersed SCC pattern generates high transition probabilities between states and vice versa. This method can model transitions to and from states of infection simultaneously, i.e. both the mastitis liability and the recovery process are considered. A multilevel discrete time survival model was applied to estimate breeding values on simulated data with different dataset sizes, mastitis frequencies, and genetic correlations. RESULTS: Correlations between estimated and simulated breeding values showed that the estimated accuracies for mastitis liability were similar to those from previously tested methods that used data of confirmed mastitis cases, while our results were based on SCC as an indicator of mastitis. In addition, unlike the other methods, our method also generates breeding values for the recovery process. CONCLUSIONS: The developed method provides an effective tool for the genetic evaluation of mastitis when considering the whole disease course and will contribute to improving the genetic evaluation of udder health

Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Although 58 genomic regions have been associated with CAD thus far, most of the heritability is unexplained, indicating that additional susceptibility loci await identification. An efficient discovery strategy may be larger-scale evaluation of promising associations suggested by genome-wide association studies (GWAS). Hence, we genotyped 56,309 participants using a targeted gene array derived from earlier GWAS results and performed meta-analysis of results with 194,427 participants previously genotyped, totaling 88,192 CAD cases and 162,544 controls. We identified 25 new SNP-CAD associations (P < 5 × 10(-8), in fixed-effects meta-analysis) from 15 genomic regions, including SNPs in or near genes involved in cellular adhesion, leukocyte migration and atherosclerosis (PECAM1, rs1867624), coagulation and inflammation (PROCR, rs867186 (p.Ser219Gly)) and vascular smooth muscle cell differentiation (LMOD1, rs2820315). Correlation of these regions with cell-type-specific gene expression and plasma protein levels sheds light on potential disease mechanisms

The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16–61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95–98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3′ end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes

Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species?

Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16× coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species

A Modular API for Intelligent Virtual Agents

This report proposes a modular Application Programmer's Interface (API) for handling the mental layer of intelligent virtual agents for a wide range of application types, with the aim of reducing the work required to program a completely new AI engine, and describes its implementation. One of the key elements and major difficulties in its design is the need to make it general enough to suit most types of applications, while preserving its usefulness and keeping it both efficient and reliable. A sample application interfacing with the API is created to demonstrate its capabilities, various AI algorithms are looked into and their respective suitability for the API is evaluated, and some techniques are implemented as modules in the API

Operatörsoberoende SMS-leverans med designmönstret Bridge

When different type of programs are developed one wants to make these adjustable to future changes and requirements. It must be done a good design of the program from the beginning to make it possible to continue development of it without having to redo big parts of it to high costs. In the area of object orientation there are design pattern, which can be used to design systems that can be adjusted to new changes in an easier way. I have in this thesis chosen to take a closer look at how to design a program that sends SMS to cell phones through a system of an operator. One requirement on the program is that it has to be possible to change what operator to send though in an easy way. I have chosen a design pattern named Bridge and investigate if a use of it makes a program operator independent. This thesis is for system developers who have basic knowledge of object orientation and have programmed in Java. The hypothesis that is tested is: &quot;If the design pattern Bridge is used to construct a program that sends SMS, then it will be a program where an operator&apos;s API easily can be replaced by another operator&apos;s API. The investigation was done by collecting a number of API&apos;s from different companies who offer the possibility to send SMS through themselves. Code was created for the classes that are part of the design pattern Bridge and specific code for every tested API were done and compiled and run. After that the possibility to switch between API&apos;s in an easy way was investigated. The result of the investigation was that it is possible to integrate some of the API&apos;s with Bridge and that the switching between API&apos;s is working. But to find out if Bridge can be used in a real program demands further investigations

A Modular API for Intelligent Virtual Agents

This report proposes a modular Application Programmer's Interface (API) for handling the mental layer of intelligent virtual agents for a wide range of application types, with the aim of reducing the work required to program a completely new AI engine, and describes its implementation. One of the key elements and major difficulties in its design is the need to make it general enough to suit most types of applications, while preserving its usefulness and keeping it both efficient and reliable. A sample application interfacing with the API is created to demonstrate its capabilities, various AI algorithms are looked into and their respective suitability for the API is evaluated, and some techniques are implemented as modules in the API

Sveriges televisions vänstervridning : En myt eller verklighet?

Syftet med den här uppsatsen är att undersöka om det finns en så kallad “vänstervridning” i Sveriges televisions nyhetsprogram. Det vill säga en favorisering av vänstern gentemot högern. Detta genom att undersöka nyhetsrapporteringen, i Rapport och Aktuellt, av i förväg valda ämnen

Large Swedish industrial companies : Farsightedness in business and sustainability strategies

Industry facilitates the economic development of nations and acquisition of human wealth. Parallel to the global spread of industry, the world is facing rapid population growth. Simultaneously, formerly impoverished populations are approaching middle class standards of living with corresponding increases in levels of consumption. If the populations and consumption levels of societies continue to grow at the expected pace we will face a future environmental crises in the long-term and the world’s environmental resources will not be adequate to meet coming needs. Societies, together with industry, must transform to become sustainable in order to tackle one of our world’s most pressing challenges.Governments and organizations are now pushing industrial companies to meet this challenge and integrate sustainability into their businesses in order to put the economy on the pathway to a sustainable transformation. The World Business Council for Sustainable Development has a vision with formulated conditions that must be met before year 2050 to meet this challenge. But in order to unlock the full potential of sustainable growth, one must also understand the farsightedness of company leaders. The aim of this study is to examine how farsighted Swedish industries are both related to business and sustainability strategies. The main questions for this thesis are: How farsighted are the longest-term strategies/tasks/visions of the Chief Executive Officers (CEOs)? How farsighted are the longest-term tasks that the CEO delegate to members of the management team? How farsighted are the longest-term sustainability strategy of the company? And finally, who in the organization is responsible for the longest-term sustainability strategy/task/vision?The thesis focuses on finding out if their farsightedness in sustainability strategies match with their other business strategies. Eight large Swedish industrial companies were investigated using interviews with their CEOs.The results show a very large difference between companies in the farsightedness measured with time-span of business strategy and sustainability strategy. The time-span of the tasks that the CEOs delegate to the management team also differ substantially between companies. Moreover, the study revealed that all of the studied companies place the ultimate responsibility for sustainability with the CEO and that the farsightedness in sustainability match with the companies’ business strategies. The research show that all eight companies do match their farsightedness in sustainability with business