Measurement of acceleration while walking as an automated method for gait assessment in dairy cattle

The aims were to determine whether measures of acceleration of the legs and back of dairy cows while they walk could help detect changes in gait or locomotion associated with lameness and differences in the walking surface. In 2 experiments, 12 or 24 multiparous dairy cows were fitted with five 3-dimensional accelerometers, 1 attached to each leg and 1 to the back, and acceleration data were collected while cows walked in a straight line on concrete (experiment 1) or on both concrete and rubber (experiment 2). Cows were video-recorded while walking to assess overall gait, asymmetry of the steps, and walking speed. In experiment 1, cows were selected to maximize the range of gait scores, whereas no clinically lame cows were enrolled in experiment 2. For each accelerometer location, overall acceleration was calculated as the magnitude of the 3-dimensional acceleration vector and the variance of overall acceleration, as well as the asymmetry of variance of acceleration within the front and rear pair of legs. In experiment 1, the asymmetry of variance of acceleration in the front and rear legs was positively correlated with overall gait and the visually assessed asymmetry of the steps (r ≥0.6). Walking speed was negatively correlated with the asymmetry of variance of the rear legs (r=−0.8) and positively correlated with the acceleration and the variance of acceleration of each leg and back (r ≥0.7). In experiment 2, cows had lower gait scores [2.3 vs. 2.6; standard error of the difference (SED)=0.1, measured on a 5-point scale] and lower scores for asymmetry of the steps (18.0 vs. 23.1; SED=2.2, measured on a continuous 100-unit scale) when they walked on rubber compared with concrete, and their walking speed increased (1.28 vs. 1.22m/s; SED=0.02). The acceleration of the front (1.67 vs. 1.72g; SED=0.02) and rear (1.62 vs. 1.67g; SED=0.02) legs and the variance of acceleration of the rear legs (0.88 vs. 0.94g; SED=0.03) were lower when cows walked on rubber compared with concrete. Despite the improvements in gait score that occurred when cows walked on rubber, the asymmetry of variance of acceleration of the front leg was higher (15.2 vs. 10.4%; SED=2.0). The difference in walking speed between concrete and rubber correlated with the difference in the mean acceleration and the difference in the variance of acceleration of the legs and back (r ≥0.6). Three-dimensional accelerometers seem to be a promising tool for lameness detection on farm and to study walking surfaces, especially when attached to a leg.

Development of microdevices for proteome research and diagnosis

The basic goal of a proteomic microchip is to achieve efficient and sensitive high throughput protein analyses, automatically carrying out several measurements in parallel. A protein microchip would either detect a single protein or a large set of proteins for diagnostic purposes, basic proteome or functional analysis. Such analyses would include e.g. interactomics, general protein expression studies, detecting structural alterations or secondary modifications. Visualization of the results may occur by simple immunoreactions, general or specific labelling, or mass spectrometry. For this purpose we have manufactured chip-based proteome analysis devices that utilize the classical polymer gel electrophoresis technology to run one and two-dimensional gel electrophoresis separations of proteins in just a smaller size. In total, we manufactured three functional prototypes of which one performed a miniaturized one-dimensional gel electrophoresis (1-DE) separation, the second and third preformed two-dimensional gel electrophoresis (2-DE) separations. These microchips were successfully used to separate and characterize a set of predefined standard proteins, cell and tissue samples. Also, the miniaturized 2-DE (ComPress-2DE) chip presents a novel way of combining the 1st and 2nd dimensional separations, thus avoiding manual handling of the gels, eliminate cross-contamination, and make analyses faster and repeatability better. They all showed the advantages of miniaturization over the commercial devices; such as fast analysis, low sample- and reagent consumption, high sensitivity, high repeatability and inexpensive performance. All these instruments have the potential to be fully automated due to their easy-to-use set-up.

Genotyping for genetic association studies: Methods and applications

In this thesis, two separate single nucleotide polymorphism (SNP) genotyping techniques were set up at the Finnish Genome Center, pooled genotyping was evaluated as a screening method for large-scale association studies, and finally, the former approaches were used to identify genetic factors predisposing to two distinct complex diseases by utilizing large epidemiological cohorts and also taking environmental factors into account. The first genotyping platform was based on traditional but improved restriction-fragment-length-polymorphism (RFLP) utilizing 384-microtiter well plates, multiplexing, small reaction volumes (5 µl), and automated genotype calling. We participated in the development of the second genotyping method, based on single nucleotide primer extension (SNuPeTM by Amersham Biosciences), by carrying out the alpha- and beta tests for the chemistry and the allele-calling software. Both techniques proved to be accurate, reliable, and suitable for projects with thousands of samples and tens of markers. Pooled genotyping (genotyping of pooled instead of individual DNA samples) was evaluated with Sequenom s MassArray MALDI-TOF, in addition to SNuPeTM and PCR-RFLP techniques. We used MassArray mainly as a point of comparison, because it is known to be well suited for pooled genotyping. All three methods were shown to be accurate, the standard deviations between measurements being 0.017 for the MassArray, 0.022 for the PCR-RFLP, and 0.026 for the SNuPeTM. The largest source of error in the process of pooled genotyping was shown to be the volumetric error, i.e., the preparation of pools. We also demonstrated that it would have been possible to narrow down the genetic locus underlying congenital chloride diarrhea (CLD), an autosomal recessive disorder, by using the pooling technique instead of genotyping individual samples. Although the approach seems to be well suited for traditional case-control studies, it is difficult to apply if any kind of stratification based on environmental factors is needed. Therefore we chose to continue with individual genotyping in the following association studies. Samples in the two separate large epidemiological cohorts were genotyped with the PCR-RFLP and SNuPeTM techniques. The first of these association studies concerned various pregnancy complications among 100,000 consecutive pregnancies in Finland, of which we genotyped 2292 patients and controls, in addition to a population sample of 644 blood donors, with 7 polymorphisms in the potentially thrombotic genes. In this thesis, the analysis of a sub-study of pregnancy-related venous thromboses was included. We showed that the impact of factor V Leiden polymorphism on pregnancy-related venous thrombosis, but not the other tested polymorphisms, was fairly large (odds ratio 11.6; 95% CI 3.6-33.6), and increased multiplicatively when combined with other risk factors such as obesity or advanced age. Owing to our study design, we were also able to estimate the risks at the population level. The second epidemiological cohort was the Helsinki Birth Cohort of men and women who were born during 1924-1933 in Helsinki. The aim was to identify genetic factors that might modify the well known link between small birth size and adult metabolic diseases, such as type 2 diabetes and impaired glucose tolerance. Among ~500 individuals with detailed birth measurements and current metabolic profile, we found that an insertion/deletion polymorphism of the angiotensin converting enzyme (ACE) gene was associated with the duration of gestation, and weight and length at birth. Interestingly, the ACE insertion allele was also associated with higher indices of insulin secretion (p=0.0004) in adult life, but only among individuals who were born small (those among the lowest third of birth weight). Likewise, low birth weight was associated with higher indices of insulin secretion (p=0.003), but only among carriers of the ACE insertion allele. The association with birth measurements was also found with a common haplotype of the glucocorticoid receptor (GR) gene. Furthermore, the association between short length at birth and adult impaired glucose tolerance was confined to carriers of this haplotype (p=0.007). These associations exemplify the interaction between environmental factors and genotype, which, possibly due to altered gene expression, predisposes to complex metabolic diseases. Indeed, we showed that the common GR gene haplotype associated with reduced mRNA expression in thymus of three individuals (p=0.0002).

Search for the associated production of the standard-model Higgs boson in the all-hadronic channel

"We report on a search for the standard-model Higgs boson in pp collisions at s=1.96 TeV using an integrated luminosity of 2.0 fb(-1). We look for production of the Higgs boson decaying to a pair of bottom quarks in association with a vector boson V (W or Z) decaying to quarks, resulting in a four-jet final state. Two of the jets are required to have secondary vertices consistent with B-hadron decays. We set the first 95% confidence level upper limit on the VH production cross section with V(-> qq/qq('))H(-> bb) decay for Higgs boson masses of 100-150 GeV/c(2) using data from run II at the Fermilab Tevatron. For m(H)=120 GeV/c(2), we exclude cross sections larger than 38 times the standard-model prediction."

Combination of Tevatron Searches for the Standard Model Higgs Boson in the W+W- Decay Mode

We combine searches by the CDF and D0 collaborations for a Higgs boson decaying to W+W-. The data correspond to an integrated total luminosity of 4.8 (CDF) and 5.4 (D0) fb-1 of p-pbar collisions at sqrt{s}=1.96 TeV at the Fermilab Tevatron collider. No excess is observed above background expectation, and resulting limits on Higgs boson production exclude a standard-model Higgs boson in the mass range 162-166 GeV at the 95% C.L.

Inclusive Search for Standard Model Higgs Boson Production in the WW Decay Channel using the CDF II Detector

We present a search for standard model (SM) Higgs boson production using ppbar collision data at sqrt(s) = 1.96 TeV, collected with the CDF II detector and corresponding to an integrated luminosity of 4.8 fb-1. We search for Higgs bosons produced in all processes with a significant production rate and decaying to two W bosons. We find no evidence for SM Higgs boson production and place upper limits at the 95% confidence level on the SM production cross section (sigma(H)) for values of the Higgs boson mass (m_H) in the range from 110 to 200 GeV. These limits are the most stringent for m_H > 130 GeV and are 1.29 above the predicted value of sigma(H) for mH = 165 GeV.

Search for the associated production of the standard-model Higgs boson in the all-hadronic channel

"We report on a search for the standard-model Higgs boson in pp collisions at s=1.96 TeV using an integrated luminosity of 2.0 fb(-1). We look for production of the Higgs boson decaying to a pair of bottom quarks in association with a vector boson V (W or Z) decaying to quarks, resulting in a four-jet final state. Two of the jets are required to have secondary vertices consistent with B-hadron decays. We set the first 95% confidence level upper limit on the VH production cross section with V(-> qq/qq('))H(-> bb) decay for Higgs boson masses of 100-150 GeV/c(2) using data from run II at the Fermilab Tevatron. For m(H)=120 GeV/c(2), we exclude cross sections larger than 38 times the standard-model prediction."

Search for standard model Higgs boson production in association with a W boson using a neural network discriminant at CDF

We present a search for standard model Higgs boson production in association with a W boson in proton-antiproton collisions at a center of mass energy of 1.96 TeV. The search employs data collected with the CDF II detector that correspond to an integrated luminosity of approximately 1.9 inverse fb. We select events consistent with a signature of a single charged lepton, missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with a secondary vertex tagging method, a jet probability tagging method, and a neural network filter. We use kinematic information in an artificial neural network to improve discrimination between signal and background compared to previous analyses. The observed number of events and the neural network output distributions are consistent with the standard model background expectations, and we set 95% confidence level upper limits on the production cross section times branching fraction ranging from 1.2 to 1.1 pb or 7.5 to 102 times the standard model expectation for Higgs boson masses from 110 to $150 GeV/c^2, respectively.

Searching the inclusive ℓγE̸T+b-quark signature for radiative top quark decay and non-standard-model processes

In a search for new phenomena in a signature suppressed in the standard model of elementary particles (SM), we compare the inclusive production of events containing a lepton, a photon, significant transverse momentum imbalance (MET), and a jet identified as containing a b-quark, to SM predictions. The search uses data produced in proton-antiproton collisions at 1.96 TeV corresponding to 1.9 fb-1 of integrated luminosity taken with the CDF detector at the Fermilab Tevatron. We find 28 lepton+photon+MET+b events versus an expectation of 31.0+4.1/-3.5 events. If we further require events to contain at least three jets and large total transverse energy, simulations predict that the largest SM source is top-quark pair production with an additional radiated photon, ttbar+photon. In the data we observe 16 ttbar+photon candidate events versus an expectation from SM sources of 11.2+2.3/-2.1. Assuming the difference between the observed number and the predicted non-top-quark total is due to SM top quark production, we estimate the ttg cross section to be 0.15 +- 0.08 pb.

ISO 13567 - The Proposed International Standard for Structuring Layers in Computer Aided Building Design

Layering is a widely used method for structuring data in CAD-models. During the last few years national standardisation organisations, professional associations, user groups for particular CAD-systems, individual companies etc. have issued numerous standards and guidelines for the naming and structuring of layers in building design. In order to increase the integration of CAD data in the industry as a whole ISO recently decided to define an international standard for layer usage. The resulting standard proposal, ISO 13567, is a rather complex framework standard which strives to be more of a union than the least common denominator of the capabilities of existing guidelines. A number of principles have been followed in the design of the proposal. The first one is the separation of the conceptual organisation of information (semantics) from the way this information is coded (syntax). The second one is orthogonality - the fact that many ways of classifying information are independent of each other and can be applied in combinations. The third overriding principle is the reuse of existing national or international standards whenever appropriate. The fourth principle allows users to apply well-defined subsets of the overall superset of possible layernames. This article describes the semantic organisation of the standard proposal as well as its default syntax. Important information categories deal with the party responsible for the information, the type of building element shown, whether a layer contains the direct graphical description of a building part or additional information needed in an output drawing etc. Non-mandatory information categories facilitate the structuring of information in rebuilding projects, use of layers for spatial grouping in large multi-storey projects, and storing multiple representations intended for different drawing scales in the same model. Pilot testing of ISO 13567 is currently being carried out in a number of countries which have been involved in the definition of the standard. In the article two implementations, which have been carried out independently in Sweden and Finland, are described. The article concludes with a discussion of the benefits and possible drawbacks of the standard. Incremental development within the industry, (where ”best practice” can become ”common practice” via a standard such as ISO 13567), is contrasted with the more idealistic scenario of building product models. The relationship between CAD-layering, document management product modelling and building element classification is also discussed.

United We Stand - Divided We Fall : A Standard Model of Unit Cohesion

Research on unit cohesion has shown positive correlations between cohesion and valued outcomes such as strong performance, reduced stress, less indiscipline, and high re-enlistment intentions. However, the correlations have varied in strength and significance. The purpose of this study is to show that taking into consideration the multi-component nature of cohesion and relating the most applicable components to specific outcomes could resolve much of the inconsistency. Unit cohesion is understood as a process of social integration among members of a primary group with its leaders, and with the larger secondary groups of which they are a part. Correspondingly, included in the framework are four bonding components: horizontal (peer) and vertical (subordinate and leader) and organizational and institutional, respectively. The data were collected as part of a larger research project on cohesion, leadership, and personal adjustment to the military. In all, 1,534 conscripts responded to four questionnaires during their service in 2001-2002. In addition, sociometric questionnaires were given to 537 group members in 47 squads toward the end of their service. The results showed that platoons with strong primary-group cohesion differed from other platoons in terms of performance, training quality, secondary-group experiences, and attitudes toward refresher training. On the sociometric level it was found that soldiers who were chosen as friends by others were more likely to have higher expected performance, better performance ratings, more positive attitudes toward military service, higher levels of well-being during conscript service, and fewer exemptions from duty during it. On the group level, the selection of the respondents own group leader rather than naming a leader from outside (i.e., leader bonding) had a bearing not only on cohesion and performance, but also on the social, attitudinal, and behavioral criteria. Overall, the aim of the study was to contribute to the research on cohesion by introducing a model that takes into account the primary foci of bonding and their impact. The results imply that primary-group and secondary-group bonding processes are equally influential in explaining individual and group performance, whereas the secondary-group bonding components are far superior in explaining career intentions, personal growth, avoidance of duty, and attitudes toward refresher training and national defense. This should be considered in the planning and conducting of training. The main conclusion is that the different types of cohesion components have a unique, positive, significant, but varying impact on a wide range of criteria, confirming the need to match the components with the specific criteria.