Statistical Reviewers Improve Reporting in Biomedical Articles: a Randomized Trial.

Background. Although peer review is widely considered to be the most credible way of selecting manuscripts and improving the quality of accepted papers in scientific journals, there is little evidence to support its use. Our aim was to estimate the effects on manuscript quality of either adding a statistical peer reviewer or suggesting the use of checklists such as CONSORT or STARD to clinical reviewers or both. Methodology and Principal Findings. Interventions were defined as 1) the addition of a statistical reviewer to the clinical peer review process, and 2) suggesting reporting guidelines to reviewers; with"no statistical expert" and"no checklist" as controls. The two interventions were crossed in a 262 balanced factorial design including original research articles consecutively selected, between May 2004 and March 2005, by the Medicina Clinica (Barc) editorial committee. We randomized manuscripts to minimize differences in terms of baseline quality and type of study (intervention, longitudinal, cross-sectional, others). Sample-size calculations indicated that 100 papers provide an 80% power to test a 55% standardized difference. We specified the main outcome as the increment in quality of papers as measured on the Goodman Scale. Two blinded evaluators rated the quality of manuscripts at initial submission and final post peer review version. Of the 327 manuscripts submitted to the journal, 131 were accepted for further review, and 129 were randomized. Of those, 14 that were lost to follow-up showed no differences in initial quality to the followed-up papers. Hence, 115 were included in the main analysis, with 16 rejected for publication after peer review. 21 (18.3%) of the 115 included papers were interventions, 46 (40.0%) were longitudinal designs, 28 (24.3%) cross-sectional and 20 (17.4%) others. The 16 (13.9%) rejected papers had a significantly lower initial score on the overall Goodman scale than accepted papers (difference 15.0, 95% CI: 4.6- 24.4). The effect of suggesting a guideline to the reviewers had no effect on change in overall quality as measured by the Goodman scale (0.9, 95% CI: 20.3+2.1). The estimated effect of adding a statistical reviewer was 5.5 (95% CI: 4.3-6.7), showing a significant improvement in quality. Conclusions and Significance. This prospective randomized study shows the positive effect of adding a statistical reviewer to the field-expert peers in improving manuscript quality. We did not find a statistically significant positive effect by suggesting reviewers use reporting guidelines.

In vivo electrochemical corrosion study of a CoCrMo biomedical alloy in human synovial fluids.

The present study was initiated with the aim to assess the in vivo electrochemical corrosion behaviour of CoCrMo biomedical alloys in human synovial fluids in an attempt to identify possible patient or pathology specific effects. For this, electrochemical measurements (open circuit potential OCP, polarization resistance Rp, potentiodynamic polarization curves, electrochemical impedance spectroscopy EIS) were carried out on fluids extracted from patients with different articular pathologies and prosthesis revisions. Those electrochemical measurements could be carried out with outstanding precision and signal stability. The results show that the corrosion behaviour of CoCrMo alloy in synovial fluids not only depends on material reactivity but also on the specific reactions of synovial fluid components, most likely involving reactive oxygen species. In some patients the latter were found to determine the whole cathodic and anodic electrochemical response. Depending on patients, corrosion rates varied significantly between 50 and 750mgdm(-2)year(-1).

Development of Customer Satisfaction Models for Electronics Engineering Company

Diplomityön tarkoituksena oli luoda ja kehittää kaksi asiakastyytyväisyysmallia asiakastyytyväisyyden mittaamisen aloittamiseksi ja toteuttamiseksi kohdeyrityksessä. Työ pohjautuu nykyisten tyytyväisyysprosessien analysointiin sekä työn teoriaosaan, joka käsittelee yksityiskohtaisesti niitä asioita, joita asiakastyytyväisyyden mittaamisessa ja prosessissa tulisi huomioida. Työssä tehdyn mallien tarkoituksen on auttaa kohdeyritystä hyödyntämään asiakastyytyväisyysmittauksen tuloksia paremmin liiketoiminnassa, sekä asiakkaiden keskuudessa. Työn yhtenä tavoitteena oli myös sopivan mittaustyökalun löytäminen ja suositteleminen kohdeyritykselle.Teorian ja analysoinnin pohjalta luotiin molemmat asiakastyytyväisyysmallit vastamaan kohdeyksiköiden tarpeita. Kun ulkoiset seikat, kuten mittaustavat, mittausinstrumentit, kyselylomakkeet ja vastaajaryhmät oli määritelty, keskityttiin tulosten analysointiin ja hyödyntämiseen, mikä korostui asiakassuuntautuneessa organisaatiossa. Työssä pohdittiin myös yhtenäisen asiakastyytyväisyysprosessin merkitystä ja etuja kohdeyrityksessä.

Robots and robotic systems for the electronics and telecommunication industry

Tämä diplomityö tutkii elektroniikka- ja telekommunikaatioteollisuutta sekä siihen läheisesti liittyviä robotteja ja robottijärjestelmiä. Tavoitteena on määrittää E&T-teollisuuden prosesseihin soveltuvien robottien testausmenetelmä. Tavoitteena on myös selvittää kahden ABB:n robotin soveltuvuutta E&T-teollisuuden tarpeisiin. Muutamia systemaattisia valmistusjärjestelmien suunnitteluun soveltuvia menetelmiä ja apuvälineitä on myös käsitelty. Alussa työ keskittyy elektroniikka- ja telekommunikaatioteollisuuden nykytilan tutkimiseen sekä siellä vallitsevien ja ennustettujen trendien kartoitukseen. Kohdat “Collaborative manufacturing” ja E&T-teollisuuden valmistusjärjestelmille asettamat vaatimukset käydään yksityiskohtaisesti läpi. Tutkimuksen pääkohteina ovat robotit, erityisesti ABB:n IRB 140 ja IRB 340 sekä robottien testausmenetelmän määrittäminen. Työssä käydään läpi IRB 340:llä suoritetut testit, jotka tehtiin sekä konenäköjärjestelmää apuna käyttäen että ilman. Myös TTKK:lla suoritetut robottitestit on käyty läpi. Robottien testituloksia on analysoitu ja vertailtu muihin robotteihin. Testausmenetelmät perustuvat ISO 9283 standardiin. Viimeinen osa työstä esittelee robottijärjestelmien systemaattiseen suunnitteluun soveltuvia menetelmiä ja apuvälineitä. Esillä ovat mm. Modular function deployment (MFD) ja The system design method (SDM).

Challenges in Supplier-Buyer Relationships in Electronics Industry

This thesis examines the supplier-buyer relationships in the Finnish electronics industry. The aim of the study was to increase understanding on the challenges that suppliers face in their relationship with the buyer. The research was conducted using qualitative methods because they allow more perspective for the research problem than quantitative methods would have. Choosing qualitative method also affected the selection of a research technique. Analysis of secondary data from written documents was chosen to give more perspective to a broad problem. The main findings of this research are that the relationships between supplier and buyer in electronics industry are challenging because supplier must understand and face three types of challenges. The challenges are: understanding the environment, choosing and implementing correct strategy and managing relationships. For the supplier it is important to understand the environment so it can adjust own strategy to fit to the environment. The supplier should also be careful not to be too dependent on the buyer.

A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.

Micro- and nanostructuring of poly(ethylene-2,6-naphthalate) surfaces, for biomedical applications, using polymer replication techniques

Here we investigate the formation of superficial micro- and nanostructures in poly(ethylene-2,6-naphthalate) (PEN), with a view to their use in biomedical device applications, and compare its performance with a polymer commonly used for the fabrication of these devices, poly(methyl methacrylate) (PMMA). The PEN is found to replicate both micro- and nanostructures in its surface, albeit requiring more forceful replication conditions than PMMA, producing a slight increase in surface hydrophilicity. This ability to form micro/nanostructures, allied to biocompatibility and good optical transparency, suggests that PEN could be a useful material for production of, or for incorporation into, transparent devices for biomedical applications. Such devices will be able to be autoclaved, due to the polymer's high temperature stability, and will be useful for applications where forceful experimental conditions are required, due to a superior chemical resistance over PMMA.

Readout electronics for low dark count pixel detectors based on geiger mode avalanche photodiodes fabricated in conventional CMOS technologies for future linear colliders

The high sensitivity and excellent timing accuracy of Geiger mode avalanche photodiodes makes them ideal sensors as pixel detectors for particle tracking in high energy physics experiments to be performed in future linear colliders. Nevertheless, it is well known that these sensors suffer from dark counts and afterpulsing noise, which induce false hits (indistinguishable from event detection) as well as an increase of the necessary area of the readout system. In this work, we present a comparison between APDs fabricated in a high voltage 0.35 µm and a high integration 0.13 µm commercially available CMOS technologies that has been performed to determine which of them best fits the particle collider requirements. In addition, a readout circuit that allows low noise operation is introduced. Experimental characterization of the proposed pixel is also presented in this work.

Distributed ControlArchitecture of Power Electronics Building-Block-Based Frequency Converters

The increasing power demand and emerging applications drive the design of electrical power converters into modularization. Despite the wide use of modularized power stage structures, the control schemes that are used are often traditional, in other words, centralized. The flexibility and re-usability of these controllers are typically poor. With a dedicated distributed control scheme, the flexibility and re-usability of the system parts, building blocks, can be increased. Only a few distributed control schemes have been introduced for this purpose, but their breakthrough has not yet taken place. A demand for the further development offlexible control schemes for building-block-based applications clearly exists. The control topology, communication, synchronization, and functionality allocationaspects of building-block-based converters are studied in this doctoral thesis. A distributed control scheme that can be easily adapted to building-block-based power converter designs is developed. The example applications are a parallel and series connection of building blocks. The building block that is used in the implementations of both the applications is a commercial off-the-shelf two-level three-phase frequency converter with a custom-designed controller card. The major challenge with the parallel connection of power stages is the synchronization of the building blocks. The effect of synchronization accuracy on the system performance is studied. The functionality allocation and control scheme design are challenging in the seriesconnected multilevel converters, mainly because of the large number of modules. Various multilevel modulation schemes are analyzed with respect to the implementation, and this information is used to develop a flexible control scheme for modular multilevel inverters.

Structural studies on enzymes of biotechnological and biomedical interest

Structural studies of proteins aim at elucidating the atomic details of molecular interactions in biological processes of living organisms. These studies are particularly important in understanding structure, function and evolution of proteins and in defining their roles in complex biological settings. Furthermore, structural studies can be used for the development of novel properties in biomolecules of environmental, industrial and medical importance. X-ray crystallography is an invaluable tool to obtain accurate and precise information about the structure of proteins at the atomic level. Glutathione transferases (GSTs) are amongst the most versatile enzymes in nature. They are able to catalyze a wide variety of conjugation reactions between glutathione (GSH) and non-polar components containing an electrophilic carbon, nitrogen or sulphur atom. Plant GSTs from the Tau class (a poorly characterized class) play an important role in the detoxification of xenobiotics and stress tolerance. Structural studies were performed on a Tau class fluorodifen-inducible glutathione transferase from Glycine max (GmGSTU4-4) complexed with GSH (2.7 Å) and a product analogue Nb-GSH (1.7 Å). The three-dimensional structure of the GmGSTU4-4-GSH complex revealed that GSH binds in different conformations in the two subunits of the dimer: in an ionized form in one subunit and a non-ionized form in the second subunit. Only the ionized form of the substrate may lead to the formation of a catalytically competent complex. Structural comparison between the GSH and Nb-GSH bound complexes revealed significant differences with respect to the hydrogen-bonding, electrostatic interaction pattern, the upper part of -helix H4 and the C-terminus of the enzyme. These differences indicate an intrasubunit modulation between the G-and Hsites suggesting an induced-fit mechanism of xenobiotic substrate binding. A novel binding site on the surface of the enzyme was also revealed. Bacterial type-II L-asparaginases are used in the treatment of haematopoietic diseases such as acute lymphoblastic leukaemia (ALL) and lymphomas due to their ability to catalyze the conversion of L-asparagine to L-aspartate and ammonia. Escherichia coli and Erwinia chrysanthemi asparaginases are employed for the treatment of ALL for over 30 years. However, serious side-effects affecting the liver and pancreas have been observed due to the intrinsic glutaminase activity of the administered enzymes. Structural studies on Helicobacter pylori L-asparaginase (HpA) were carried out in an effort to discover novel L-asparaginases with potential chemotherapeutic utility in ALL treatment. Detailed analysis of the active site geometry revealed structurally significant differences between HpA and other Lasparaginases that may be important for the biological activities of the enzyme and could be further exploited in protein engineering efforts.

Measuring Cost of Poor Quality in Industrial Electronics

Quality is not only free but it can be a profit maker. Every dollar that is not spent on doing things wrong becomes a dollar right on the bottom line. The main objective of this thesis is to give an answer on how cost of poor quality can be measured theoretically correctly. Different calculation methods for cost of poor quality are presented and discussed in order to give comprehensive picture about measurement process. The second objective is to utilize the knowledge from the literature review and to apply it when creating a method for measuring cost of poor quality in supplier performance rating. Literature review indicates that P-A-F model together with ABC methodology provides a mean for quality cost calculations. These models give an answer what should be measured and how this measurement should be carried out. However, when product or service quality costs are incurred when quality character derivates from target value, then QLF seems to be most appropriate methodology for quality cost calculation. These methodologies were applied when creating a quality cost calculation method for supplier performance ratings.

Thermal Stress in a Roll-to-Roll Printed Electronics Substrate

The Roll-to-Roll process makes it possible to print electronic products continuously onto a uniform substrate. Printing components on flexible surfaces can bring down the costs of simple electronic devices such as RFID tags, antennas and transistors. The possibility of quickly printing flexible electronic components opens up a wide array of novel products previously too expensive to produce on a large scale. Several different printing methods can be used in Roll-to-Roll printing, such as gravure, spray, offset, flexographic and others. Most of the methods can also be mixed in one production line. Most of them still require years of research to reach a significant commercial level. The research for this thesis was carried out at the Konkuk University Flexible Display Research Center (KU-FDRC) in Seoul, Korea. A system using Roll-to-Roll printing requires that the motion of the web can be controlled in every direction in order to align different layers of ink properly. Between printers the ink is dried with hot air. The effects of thermal expansion on the tension of the web are studied in this work, and a mathematical model was constructed on Matlab and Simulink. Simulations and experiments lead to the conclusion that the thermal expansion of the web has a great influence on the tension of the web. Also, experimental evidence was gained that the particular printing machine used for these experiments at KU-FDRC may have a problem in controlling the speeds of the cylinders which pull the web.

A Method for reducing throughput-time in industrial electronics

Lyhyet toimitusajat tuovat yrityksille kilpailuetua nopeasti muuttuvassa teollisuusympäristössä. Tämän diplomityön ensisijaisena tavoitteena on löytää kirjallisuuden avulla yrityksen käyttöön soveltuva menetelmä, joka soveltuu systemaattiseen läpimenoaikojen lyhentämiseen. Tärkeää on myös varmistaa valitun menetelmän soveltuvuus kohdeyrityksen ympäristöön. Työn toisena tavoitteena on ymmärtää, että minkälaisella panostuksella yhden päivän läpimenoaika voidaan saavuttaa. Kirjallisuustutkimuksen avulla on valittu tarkoitukseen sopiva toimintamalli. Menetelmä on testattu yhdellä tuotantolinjalla ja saadut tulokset sekä palaute osoittavat, että se näyttäisi soveltuvan kohdeyrityksen käyttöön. Tuotantolinjalle on tehty toimintasuunnitelma yhden päivän toimitusajan saavuttamiseksi vuoden 2013 aikana. Haasteen laajuutta koko kohdeyrityksessä on tutkittu erillisessä ideointisessiossa. Session tulosten perusteella on tehty prioriteettilista, joka antaa käsityksen toimitusajan merkittävän lyhentämisen vaatimuksista. Yleisesti ottaen kysynnän vaihtelun hallinta on suurin haaste, mutta useita ratkaisuvaihtoehtoja tämän hallitsemiseksi on tunnistettu.

Paper for printed electronics and functionality

Mass-produced paper electronics (large area organic printed electronics on paper-based substrates, “throw-away electronics”) has the potential to introduce the use of flexible electronic applications in everyday life. While paper manufacturing and printing have a long history, they were not developed with electronic applications in mind. Modifications to paper substrates and printing processes are required in order to obtain working electronic devices. This should be done while maintaining the high throughput of conventional printing techniques and the low cost and recyclability of paper. An understanding of the interactions between the functional materials, the printing process and the substrate are required for successful manufacturing of advanced devices on paper. Based on the understanding, a recyclable, multilayer-coated paper-based substrate that combines adequate barrier and printability properties for printed electronics and sensor applications was developed in this work. In this multilayer structure, a thin top-coating consisting of mineral pigments is coated on top of a dispersion-coated barrier layer. The top-coating provides well-controlled sorption properties through controlled thickness and porosity, thus enabling optimizing the printability of functional materials. The penetration of ink solvents and functional materials stops at the barrier layer, which not only improves the performance of the functional material but also eliminates potential fiber swelling and de-bonding that can occur when the solvents are allowed to penetrate into the base paper. The multi-layer coated paper under consideration in the current work consists of a pre-coating and a smoothing layer on which the barrier layer is deposited. Coated fine paper may also be used directly as basepaper, ensuring a smooth base for the barrier layer. The top layer is thin and smooth consisting of mineral pigments such as kaolin, precipitated calcium carbonate, silica or blends of these. All the materials in the coating structure have been chosen in order to maintain the recyclability and sustainability of the substrate. The substrate can be coated in steps, sequentially layer by layer, which requires detailed understanding and tuning of the wetting properties and topography of the barrier layer versus the surface tension of the top-coating. A cost competitive method for industrial scale production is the curtain coating technique allowing extremely thin top-coatings to be applied simultaneously with a closed and sealed barrier layer. The understanding of the interactions between functional materials formulated and applied on paper as inks, makes it possible to create a paper-based substrate that can be used to manufacture printed electronics-based devices and sensors on paper. The multitude of functional materials and their complex interactions make it challenging to draw general conclusions in this topic area. Inevitably, the results become partially specific to the device chosen and the materials needed in its manufacturing. Based on the results, it is clear that for inks based on dissolved or small size functional materials, a barrier layer is beneficial and ensures the functionality of the printed material in a device. The required active barrier life time depends on the solvents or analytes used and their volatility. High aspect ratio mineral pigments, which create tortuous pathways and physical barriers within the barrier layer limit the penetration of solvents used in functional inks. The surface pore volume and pore size can be optimized for a given printing process and ink through a choice of pigment type and coating layer thickness. However, when manufacturing multilayer functional devices, such as transistors, which consist of several printed layers, compromises have to be made. E.g., while a thick and porous top-coating is preferable for printing of source and drain electrodes with a silver particle ink, a thinner and less absorbing surface is required to form a functional semiconducting layer. With the multilayer coating structure concept developed in this work, it was possible to make the paper substrate suitable for printed functionality. The possibility of printing functional devices, such as transistors, sensors and pixels in a roll-to-roll process on paper is demonstrated which may enable introducing paper for use in disposable “onetime use” or “throwaway” electronics and sensors, such as lab-on-strip devices for various analyses, consumer packages equipped with product quality sensors or remote tracking devices.

Readout Electronics for Gas Electron Multiplier Detectors

The European Organization for Nuclear Research (CERN) operates the largest particle collider in the world. This particle collider is called the Large Hadron Collider (LHC) and it will undergo a maintenance break sometime in 2017 or 2018. During the break, the particle detectors, which operate around the particle collider, will be serviced and upgraded. Following the improvement in performance of the particle collider, the requirements for the detector electronics will be more demanding. In particular, the high amount of radiation during the operation of the particle collider sets requirements for the electronics that are uncommon in commercial electronics. Electronics that are built to function in the challenging environment of the collider have been designed at CERN. In order to meet the future challenges of data transmission, a GigaBit Transceiver data transmission module and an E-Link data bus have been developed. The next generation of readout electronics is designed to benefit from these technologies. However, the current readout electronics chips are not compatible with these technologies. As a result, in addition to new Gas Electron Multiplier (GEM) detectors and other technology, a new compatible chip is developed to function within the GEMs for the Compact Muon Solenoid (CMS) project. In this thesis, the objective was to study a data transmission interface that will be located on the readout chip between the E-Link bus and the control logic of the chip. The function of the module is to handle data transmission between the chip and the E-Link. In the study, a model of the interface was implemented with the Verilog hardware description language. This process was simulated by using chip design software by Cadence. State machines and operating principles with alternative possibilities for implementation are introduced in the E-Link interface design procedure. The functionality of the designed logic is demonstrated in simulation results, in which the implemented model is proven to be suitable for its task. Finally, suggestions that should be considered for improving the design have been presented.