OCR Correction Tool for Linguistic Corpora

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

HIMALDOC: A Tool for a Regional Open Repository on Sustainable Mountain Development Issues in the Hindu Kush Himalaya

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

The Human Communication Science Virtual Lab (HCS vLab): A repository microclimate in a rapidly evolving research-ecosystem

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Dual light barrier method for six degrees of freedom tool center point calibration of an industrial robot

Tool center point calibration is a known problem in industrial robotics. The major focus of academic research is to enhance the accuracy and repeatability of next generation robots. However, operators of currently available robots are working within the limits of the robot´s repeatability and require calibration methods suitable for these basic applications. This study was conducted in association with Stresstech Oy, which provides solutions for manufacturing quality control. Their sensor, based on the Barkhausen noise effect, requires accurate positioning. The accuracy requirement admits a tool center point calibration problem if measurements are executed with an industrial robot. Multiple possibilities are available in the market for automatic tool center point calibration. Manufacturers provide customized calibrators to most robot types and tools. With the handmade sensors and multiple robot types that Stresstech uses, this would require great deal of labor. This thesis introduces a calibration method that is suitable for all robots which have two digital input ports free. It functions with the traditional method of using a light barrier to detect the tool in the robot coordinate system. However, this method utilizes two parallel light barriers to simultaneously measure and detect the center axis of the tool. Rotations about two axes are defined with the center axis. The last rotation about the Z-axis is calculated for tools that have different width of X- and Y-axes. The results indicate that this method is suitable for calibrating the geometric tool center point of a Barkhausen noise sensor. In the repeatability tests, a standard deviation inside robot repeatability was acquired. The Barkhausen noise signal was also evaluated after recalibration and the results indicate correct calibration. However, future studies should be conducted using a more accurate manipulator, since the method employs the robot itself as a measuring device.

Radioactive fucose as a tool for studying glycoprotein secretion

The efficiency and reliability of radioactive fucose as a specific label for newly synthesized glycoproteins were investigated. Young adult male rabbits were injected intravitreally with [3H]-fucose, [3H]-galactose, [3H]-mannose, N-acetyl-[3H]-glucosamine or N-acetyl-[3H]-mannosamine, and killed 40 h after injection. In another series of experiments rabbits were injected with either [3H]-fucose or several tritiated amino acids and the specific activity of the vitreous proteins was determined. Vitreous samples were also processed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and histological sections of retina, ciliary body and lens (the eye components around the vitreous body) were processed for radioautography. The specific activity (counts per minute per microgram of protein) of the glycoproteins labeled with [3H]-fucose was always much higher than that of the proteins labeled with any of the other monosaccharides or any of the amino acids. There was a good correlation between the specific activity of the proteins labeled by any of the above precursors and the density of the vitreous protein bands detected by fluorography. This was also true for the silver grain density on the radioautographs of the histological sections of retina, ciliary body and lens. The contribution of radioautography (after [3H]-fucose administration) to the elucidation of the biogenesis of lysosomal and membrane glycoproteins and to the determination of the intracellular process of protein secretion was reviewed. Radioactive fucose is the precursor of choice for studying glycoprotein secretion because it is specific, efficient and practical for this purpose

Random amplified polymorphic DNA profiles as a tool for the characterization of Brazilian keratitis isolates of the genus Acanthamoeba

The genus Acanthamoeba comprises free-living amebae identified as opportunistic pathogens of humans and other animal species. Morphological, biochemical and molecular approaches have shown wide genetic diversity within the genus. In an attempt to determine the genetic relatedness among isolates of Acanthamoeba we analyzed randomly amplified polymorphic DNA (RAPD) profiles of 11 Brazilian isolates from cases of human keratitis and 8 American type culture collection (ATCC) reference strains. We found that ATCC strains belonging to the same species present polymorphic RAPD profiles whereas strains of different species show very similar profiles. Although most Brazilian isolates could not be assigned with certainty to any of the reference species, they could be clustered according to pattern similarities. The results show that RAPD analysis is a useful tool for the rapid characterization of new isolates and the assessment of genetic relatedness of Acanthamoeba spp. A comparison between RAPD analyses and morphological characteristics of cyst stages is also discussed.

Salivary cortisol as a tool for physiological studies and diagnostic strategies

Salivary cortisol is an index of plasma free cortisol and is obtained by a noninvasive procedure. We have been using salivary cortisol as a tool for physiological and diagnostic studies, among them the emergence of circadian rhythm in preterm and term infants. The salivary cortisol circadian rhythm in term and premature infants was established between 8 and 12 postnatal weeks. In the preterm infants the emergence of circadian rhythm was parallel to the onset of sleep rhythm. We also studied the use of salivary cortisol for screening for Cushing's syndrome (CS) in control and obese outpatients based on circadian rhythm and the overnight 1 mg dexamethasone (DEX) suppression test. Salivary cortisol was suppressed to less than 100 ng/dl after 1 mg DEX in control and obese patients. A single salivary cortisol measurement at 23:00 h and again after 1 mg DEX above the 90th percentile of the obese group values had sensitivity and specificity of 93 and 93% (23:00 h), and 91 and 94% (after DEX), respectively. The sensitivity improved to 100% when we combined both parameters. We also studied 11 CS children and 21 age-matched primary obese children for whom salivary cortisol sensitivity and specificity were 100/95% (23:00 h), and 100/95% (1 mg DEX), respectively. Similar to adults, sensitivity and specificity of 100% were obtained by combining 23:00 h and 1 mg DEX. The measurement of salivary cortisol is a useful tool for physiological studies and for the diagnosis of CS in children and adults on an outpatient basis.

A Portuguese version of the Christo Inventory for Substance-Misuse Services: a simple outcome evaluation tool

The Christo Inventory for Substance-Misuse Services (CISS) is a single page outcome evaluation tool completed by drug alcohol service workers either on the basis of direct client interviews or of personal experience of their client supplemented by existing assessment notes. It was developed to assist substance misuse services to empirically demonstrate the effectiveness of their treatments to their respective funding bodies. Its 0 to 20 unidimensional scale consists of 10 items reflecting clients' problems with social functioning, general health, sexual/injecting risk behavior, psychological functioning, occupation, criminal involvement, drug/alcohol use, ongoing support, compliance, and working relationships. Good reliability and validity has already been demonstrated for the CISS [Christo et al., Drug and Alcohol Dependence 2000; 59: 189-197] but the original was written in English and a Portuguese version is presented here. The present review explores its applicability to a Brazilian setting, summarizes its characteristics and uses, and describes the process of translation to Portuguese. A pilot study conducted in a substance misuse service for adolescents indicated it is likely to be suitable for use among a Brazilian population. The simplicity, flexibility and brevity of the CISS make it a useful tool allowing comparison of clients within and between many different service settings.

Pharmacology of human experimental anxiety

This review covers the effect of drugs affecting anxiety using four psychological procedures for inducing experimental anxiety applied to healthy volunteers and patients with anxiety disorders. The first is aversive conditioning of the skin conductance responses to tones. The second is simulated public speaking, which consists of speaking in front of a video camera, with anxiety being measured with psychometric scales. The third is the Stroop Color-Word test, in which words naming colors are painted in the same or in a different shade, the incongruence generating a cognitive conflict. The last test is a human version of a thoroughly studied animal model of anxiety, fear-potentiated startle, in which the eye-blink reflex to a loud noise is recorded. The evidence reviewed led to the conclusion that the aversive conditioning and potentiated startle tests are based on classical conditioning of anticipatory anxiety. Their sensitivity to benzodiazepine anxiolytics suggests that these models generate an emotional state related to generalized anxiety disorder. On the other hand, the increase in anxiety determined by simulated public speaking is resistant to benzodiazepines and sensitive to drugs affecting serotonergic neurotransmission. This pharmacological profile, together with epidemiological evidence indicating its widespread prevalence, suggests that the emotional state generated by public speaking represents a species-specific response that may be related to social phobia and panic disorder. Because of scant pharmacological data, the status of the Stroop Color-Word test remains uncertain. In spite of ethical and economic constraints, human experimental anxiety constitutes a valuable tool for the study of the pathophysiology of anxiety disorders.

Business-Oriented IT Tool Development For Service Delivery Process

The target of this thesis is to evaluate a bid, project and resource management IT tool for service delivery process via proof-of-concept (POC) project to assess, if the tested software is an appropriate tool for the Case Company’s business requirements. Literature suggests that IT projects implementation is still a grey area in scientific research. Also, IT projects have a notably high rate of failure, one significant reason for this being insufficient planning. To tackle this risk, the Case Company decided to perform a POC project, which involved a hands-on testing period of the assessed system. End users from the business side feel that current, highly tailored project management tool is inflexible, difficult to use, and sets unnecessary limitations for the business. Semi-structured interviews and a survey form are used to collect information about current business practices and business requirements related to the IT tool. For the POC project, a project group involving members from each of the Case Company’s four business divisions was established to perform the hands-on testing. Based on data acquired during the interviews and the hands-on testing period, a target state was defined and a gap analysis was carried out by comparing the features provided by the current tool and the tested tool to the target state, which are, together with the current state description, the most important result of the thesis.

A Phase Model for Building a Customer Value Based Sales Tool – Case Mining and Metals Industry

The objective of this research is to observe the state of customer value management in Outotec Oyj, determine the key development areas and develop a phase model with which to guide the development of a customer value based sales tool. The study was conducted with a constructive research approach with the focus of identifying a problem and developing a solution for the problem. As a basis for the study, the current literature involving customer value assessment and solution and customer value selling was studied. The data was collected by conducting 16 interviews in two rounds within the company and it was analyzed by coding openly. First, seven important development areas were identified, out of which the most critical were “Customer value mindset inside the company” and “Coordination of customer value management activities”. Utilizing these seven areas three functionality requirements, “Preparation”, “Outotec’s value creation and communication” and “Documentation” and three development requirements for a customer value sales tool were identified. The study concluded with the formulation of a phase model for building a customer value based sales tool. The model included five steps that were defined as 1) Enable customer value utilization, 2) Connect with the customer, 3) Create customer value, 4) Define tool to facilitate value selling and 5) Develop sales tool. Further practical activities were also recommended as a guide for executing the phase model.

The powerful high pressure tool for protein conformational studies

The pressure behavior of proteins may be summarized as a the pressure-induced disordering of their structures. This thermodynamic parameter has effects on proteins that are similar but not identical to those induced by temperature, the other thermodynamic parameter. Of particular importance are the intermolecular interactions that follow partial protein unfolding and that give rise to the formation of fibrils. Because some proteins do not form fibrils under pressure, these observations can be related to the shape of the stability diagram. Weak interactions which are differently affected by hydrostatic pressure or temperature play a determinant role in protein stability. Pressure acts on the 2º, 3º and 4º structures of proteins which are maintained by electrostatic and hydrophobic interactions and by hydrogen bonds. We present some typical examples of how pressure affects the tertiary structure of proteins (the case of prion proteins), induces unfolding (ataxin), is a convenient tool to study enzyme dissociation (enolase), and provides arguments to understand the role of the partial volume of an enzyme (butyrylcholinesterase). This approach may have important implications for the understanding of the basic mechanism of protein diseases and for the development of preventive and therapeutic measures.

Balance between education- and research-oriented publications from a Brazilian University Hospital

We analyzed the trends of scientific output of the University Hospital, Federal University of Rio de Janeiro. A total of 1420 publications were classified according to pattern and visibility. Most were non-research publications with domestic visibility. With time, there was a tendency to shift from non-research (or education-oriented) publications with domestic visibility to research publications with international visibility. This change may reflect new academic attitudes within the institution concerning the objectives of the hospital and the establishment of scientific research activities. The emphasis of this University Hospital had been on the training of new physicians. However, more recently, the production of new knowledge has been incorporated as a new objective. The analysis of the scientific production of the most productive sectors of the hospital also showed that most are developing non-research studies devoted to the local public while a few of the sectors are carrying out research studies published in journals with international status. The dilemma of quality versus quantity and of education versus research-oriented publication seems, however, to continue to exist within the specialized sectors. The methodology described here to analyze the scientific production of a university hospital can be used as a tool to better understand the evolution of medical research in Brazil and also to help formulate public policies and new strategies to include research among the major objectives of University Hospitals.

Nichesourcing the Uralic Languages for the Benefit of Research and Societies

Presentation of Jussi-Pekka Hakkarainen, held at the Emtacl15 conference on the 20th of April 2015 in Trondheim, Norway.

FANCD2 Western blot as a diagnostic tool for Brazilian patients with Fanconi anemia

Fanconi anemia is a rare hereditary disease showing genetic heterogeneity due to a variety of mutations in genes involved in DNA repair pathways, which may lead to different clinical manifestations. Phenotypic variability makes diagnosis difficult based only on clinical manifestations, therefore laboratory tests are necessary. New advances in molecular pathogenesis of this disease led researchers to develop a diagnostic test based on Western blot for FANCD2. The objective of the present study was to determine the efficacy of this method for the diagnosis of 84 Brazilian patients with Fanconi anemia, all of whom tested positive for the diepoxybutane test, and 98 healthy controls. The FANCD2 monoubiquitinated isoform (FANCDS+/FANCD2L-) was not detected in 77 patients (91.7%). In 2 patients (2.4%), there was an absence of both the monoubiquitinated and the non-ubiquitinated proteins (FANCD2S-/FANCD2L-) and 5 patients (5.9%) had both isoforms (FANCD2S+/FANCD2L+). This last phenotype suggests downstream subtypes or mosaicism. All controls were diepoxybutane negative and were also negative on the FANCD2 Western blot. The Western blot for FANCD2 presented a sensitivity of 94% (79/84) and specificity of 100% (98/98). This method was confirmed as an efficient approach to screen Brazilian patients with deleterious mutations on FANCD2 (FANCD2S-/FANCD2L-) or other upstream genes of the FA/BRCA pathway (FANCDS+/FANCD2L-), to confirm the chromosome breakage test and to classify patients according to the level of FA/BRCA pathway defects. However, patients showing both FANCD2 isoforms (FANCD2S+/FANCD2L+) require additional studies to confirm mutations on downstream Fanconi anemia genes or the presence of mosaicism.