Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R2 = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time. ; AIC‐D is a recipient of a BIO2016‐78150‐P grant funded by the Spanish Ministry of Economy and Competitiveness and Agencia Estatal de Investigación (MINECO/AEI) and Fondo Europeo de Desarrollo Regional (FEDER), and a European Research Council, ERC Consolidator Grant (ERC‐2015‐CoG – 683163). IB‐P is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport. DB‐E is funded by the ERC‐2015‐CoG – 683163 granted to the AIC‐D laboratory. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme (Grant Agreement No. 683163). This work was supported by the CERCA Programme from the Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (MINECO), through the 'Severo Ochoa Programme for Centres of Excellence in R&D' 2016–2019 (SEV‐2015‐0533)'. ; Peer reviewed
It is common practice to limit web survey access to individuals in the sample through the use of access codes such as personal identification numbers, user names, and passwords. Different technically equivalent methods exist to control survey access. However, these methods are not necessarily methodologically equivalent. In this study, an experimental design was set up to evaluate the effect of three login procedures: a manual, a semiautomatic, and an automatic login procedure. It was found that the automatic login produced the lowest data quality, whereas the manual and semiautomatic login produced data of a higher and comparable level of quality. Nevertheless, the manual and the semiautomatic login procedures differ from each other in certain respects. The study concludes that the semiautomatic login is a useful alternative to control web survey access.
Stereology is the tridimensional interpretation of bidimensional sections of a structure, widely used in fields such as mineralogy, medicine, and biology. This paper proposes a general software to do stereological analysis, called STERapp, with a friendly graphical interface to enable expert supervision. It includes a module to estimate fish fecundity (number of mature oocytes in the ovary), which has been used by experts in fish biology in two Spanish marine research centers since 2020 to estimate the fecundity of five fish species with different reproductive strategies and oocytes characteristics. This module encloses advanced computer vision and machine learning techniques to automatically recognize and classify the cells in histological images of fish gonads. The automatic recognition algorithm achieved a sensitivity of 55.6%, a specificity of 64.8%, and an average precision of 43.1%. The accuracies achieved for oocyte classification were 84.5% for the maturity stages and 78.5% for the classification regarding presence/absence of the nucleus. This facilitates the analysis and saves experts' time. Hence, the SUS questionnaire reported a mean score of 81.9, which means that the system was perceived from good to excellent to develop stereological analysis for the estimation of fish fecundity ; This work received financial support from the Xunta de Galicia (Centro singular de investigación de Galicia, accreditation 2020–2023) and the European Union (European Regional Development Fund—ERDF), Project MTM2016-76969-P, as well as from the National Program of collection, management, and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy (co-funded by the European Union through the European Maritime and Fisheries Fund) in the provision of histological images of Atlantic mackerel and Roughhead grenadier ; SI
Background: Assessment of drug and vaccine effects by combining information from different healthcare databases in the European Union requires extensive efforts in the harmonization of codes as different vocabularies are being used across countries. In this paper, we present a web application called CodeMapper, which assists in the mapping of case definitions to codes from different vocabularies, while keeping a transparent record of the complete mapping process. Methods: CodeMapper builds upon coding vocabularies contained in the Metathesaurus of the Unified Medical Language System. The mapping approach consists of three phases. First, medical concepts are automatically identified in a free-text case definition. Second, the user revises the set of medical concepts by adding or removing concepts, or expanding them to related concepts that are more general or more specific. Finally, the selected concepts are projected to codes from the targeted coding vocabularies. We evaluated the application by comparing codes that were automatically generated from case definitions by applying CodeMapper's concept identifica
Potentiell allergene Proteine aus Hühnerei oder auch aus boviner Milch können für sensitive Verbraucher ein Problem darstellen. Da im Rahmen der Weinproduktion Proteine wie Lysozym aus Hühnerei zur Kontrolle der malolaktischen Gärung oder Ovalbumin beziehungsweise Casein zur Schönung eingesetzt werden, können Rückstände auch im Lebensmittel Wein verbleiben. Die Nutzung von Antikörpern für analytische Zwecke ermöglicht aufgrund der hohen Affinität und Spezifität der Bindung zum entsprechenden Antigen auch den Nachweis von Allergenspuren. Da die Produktion dieser Immunoglobuline jedoch stets Tiere beziehungsweise tierabhängige Methoden beinhaltet und gemäß der aktuellen Gesetzgebung der Einsatz von Tieren für wissenschaftliche Zwecke reduziert werden soll, wurden in der vorliegenden Arbeit Alternativen entwickelt. Da in den etablierten Methoden der entsprechende Antikörper lediglich einmal eingesetzt werden kann, wurde zur Reduktion des Verbrauches zunächst ein wiederverwendbares System auf Antikörperbasis entwickelt. Durch den Einsatz der Oberflächenplasmonenresonanzspektroskopie und Entwicklung einer Regenerationsprozedur ohne Beeinträchtigung der biologischen Aktivität konnte ein wiederverwendbarer Biosensor zur Detektion von Lysozym und Ovalbumin in Weißwein entwickelt werden. Die gesetzlich vorgeschriebenen Anforderungen (0,25 ppm Nachweisgrenze; 0,5 ppm Bestimmungsgrenze) sind durch eine direkte Messung von Proben und entsprechenden Kalibrierstandards innerhalb kürzester Zeit mit minimalem Personalaufwand realisierbar. Um eine vollständige Unabhängigkeit von Antikörpern zu erreichen, wurden auch die Einsatzmöglichkeiten von Aptameren zur Detektion von Allergenen im Kontext Wein untersucht. Diese einzelsträngigen Nukleinsäuren sind aufgrund des fehlenden Komplementärstrangs in der Lage mit unterschiedlichsten Zielmolekülen zu interagieren und werden durch einen Selektionsprozess vollständig in vitro generiert. Unter Nutzung eines teilautomatisierten Selektionsprozesses konnten in der vorliegenden Arbeit mehrere potentielle Sequenzen mit einer Affinität gegenüber Lysozym, Ovalbumin und den bovinen Caseinen identifiziert und in der Folge charakterisiert werden. Unter Berücksichtigung der nanomolaren Dissoziationskonstanten der Aptamer-Target-Komplexe wurden zunächst in Analogie zu den antikörperbasierten Biosensoren entsprechende Aptameranaloga entwickelt. Es zeigte sich bei der Analyse unterschiedlicher Proben, dass die Lysozym- und Ovalbuminaptamere zwar keine absolute Spezifität aufweisen und der Selektionsprozess diesbezüglich optimiert werden sollte, jedoch eine Detektion in Puffer und Realproben möglich ist. Die im Vergleich mit den Antikörpern hohe Stabilität der Nukleinsäuren gegenüber äußeren Einflüssen legt einen Einsatz in Vor-Ort-Methoden wie beispielsweise in LFDs (engl.: lateral flow devices) nahe. Unter Verwendung der selektierten Aptamere mit einer hohen Affinität zu Lysozym konnten entsprechende Systeme entwickelt und zur Detektion in Wein eingesetzt werden, um so beispielsweise die Einhaltung des gesetzlich vorgeschriebenen Höchstwertes (500 ppm) zu überprüfen. Des Weiteren wurden die genannten Aptamere genutzt, um eine bisher nicht in der Literatur beschriebene Möglichkeit der spezifischen Detektion nach einer HPTLC-Trennung (engl.: high performance thin layer chromatography) zu etablieren. Die Detektion unter Verwendung von fluoreszenzmarkierten Aptameren konnte auf unterschiedlichen stationären Phasen erfolgreich durchgeführt werden. Das entwickelte System konnte zur Untersuchung von Realproben und auch zur Beurteilung der Spezifität der Lysozym- und Caseinaptamere genutzt werden, wobei sich zeigte, dass die Lysozymaptamere in diesem Kontext eine hohe Spezifität aufweisen. ; Potentially allergenic proteins like lysozyme and ovalbumin originating from hen's egg or caseins from bovine milk could pose a risk for sensitive individuals. Since these proteins are used during the production of wine for stabilization (fining) or to control malolactic fermentation, residues can also be found in the final product. Multiple analytical methods for the assessment of allergenic risks have been developed under the use of antibodies, since these immunoglobulins are characterized by high affinity and specificity towards the corresponding antigen. A main drawback of antibodies is the production in animals or animal-dependent methods since current legislation demands a minimization of the use of animals for scientific purposes. In the currently established methods, the antibodies are often only used for one time. Therefore, the development of an analytical method using the biological receptors for multiple times could be a contribution to an overall reduction of antibody consumption. Using surface plasmon resonance spectroscopy and a non-denaturating regeneration procedure, it was possible to develop a biosensor for the detection of lysozyme and ovalbumin in white wine. The legislative requirements (limit of detection = 0.25 ppm, limit of quantification 0.5 ppm) are fulfilled by direct measurements without previous steps and on short notice. To reach full independence from antibodies, single-stranded nucleic acids, so-called aptamers, were evaluated regarding the possibility of allergen detection in wine. Therefore, a randomized nucleic acid library was used as starting point for in vitro-selection under white wine mimicking conditions. The selection processes using lysozyme, ovalbumin, and bovine caseins were performed using a semiautomatic procedure and yielded multiple sequences which where characterized afterwards. Using the aptamers which seem to build up the most stable aptamer-target-complexes, it was possible to establish aptamer-based SPR-biosensors with which detection of lysozyme and ovalbumin in white wine could be implemented. The comparably high stability of nucleic acids in comparison to antibodies suggests their use in in-field-methods like LFDs (lateral flow devices). Using the aptamers with an affinity towards lysozyme, it was possible to develop a test system which can be used to detect lysozyme exceeding maximum permissible levels (500 ppm). Furthermore, the identified aptamers have been used for the development of a new method for selective detection after separation via HPTLC (high performance thin layer chromatography). Using fluorescence-labelled aptamers it was possible to perform specific detection on various stationary phases. The procedure was named aptastaining and can be used for analysis of wine samples including a semiquantitative estimation and in addition to determine specificity of the used aptamers. Considering the results gained by the aptamer-based SPR-biosensor and the aptastaining procedures, it became apparent, that the specificity of the identified aptamers significantly depends on the operational purpose. This highlights that the field of application should be taken into account before the selection procedure starts.
Spatial data is the fundamental of borderland analysis of the geography, natural resources, demography, politics, economy, and culture. As the spatial region used in borderland researching usually covers several neighboring countries' borderland regions, the data is difficult to achieve by one research institution or government. VGI has been proven to be a very successful means of acquiring timely and detailed global spatial data at very low cost. Therefore VGI will be one reasonable source of borderland spatial data. OpenStreetMap (OSM) has been known as the most successful VGI resource. But OSM data model is far different from the traditional authoritative geographic information. Thus the OSM data needs to be converted to the scientist customized data model. With the real world changing fast, the converted data needs to be updated. Therefore, a dynamic integration method for borderland data is presented in this paper. In this method, a machine study mechanism is used to convert the OSM data model to the user data model; a method used to select the changed objects in the researching area over a given period from OSM whole world daily diff file is presented, the change-only information file with designed form is produced automatically. Based on the rules and algorithms mentioned above, we enabled the automatic (or semiautomatic) integration and updating of the borderland database by programming. The developed system was intensively tested.
Spatial data is the fundamental of borderland analysis of the geography, natural resources, demography, politics, economy, and culture. As the spatial region used in borderland researching usually covers several neighboring countries' borderland regions, the data is difficult to achieve by one research institution or government. VGI has been proven to be a very successful means of acquiring timely and detailed global spatial data at very low cost. Therefore VGI will be one reasonable source of borderland spatial data. OpenStreetMap (OSM) has been known as the most successful VGI resource. But OSM data model is far different from the traditional authoritative geographic information. Thus the OSM data needs to be converted to the scientist customized data model. With the real world changing fast, the converted data needs to be updated. Therefore, a dynamic integration method for borderland data is presented in this paper. In this method, a machine study mechanism is used to convert the OSM data model to the user data model; a method used to select the changed objects in the researching area over a given period from OSM whole world daily diff file is presented, the change-only information file with designed form is produced automatically. Based on the rules and algorithms mentioned above, we enabled the automatic (or semiautomatic) integration and updating of the borderland database by programming. The developed system was intensively tested.
Four-dimensional (4D) flow magnetic resonance imaging (4D Flow MRI) enables acquisition of time-resolved three-directional velocity data in the entire heart and all major thoracic vessels. The segmentation of these tissues is typically performed using semi-automatic methods. Some of which primarily rely on the velocity data and result in a segmentation of the vessels only during the systolic phases. Other methods, mostly applied on the heart, rely on separately acquired balanced Steady State Free Precession (b-SSFP) MR images, after which the segmentations are superimposed on the 4D Flow MRI. While b-SSFP images typically cover the whole cardiac cycle and have good contrast, they suffer from a number of problems, such as large slice thickness, limited coverage of the cardiac anatomy, and being prone to displacement errors caused by respiratory motion. To address these limitations we propose a multi-atlas segmentation method, which relies only on 4D Flow MRI data, to automatically generate four-dimensional segmentations that include the entire thoracic cardiovascular system present in these datasets. The approach was evaluated on 4D Flow MR datasets from a cohort of 27 healthy volunteers and 83 patients with mildly impaired systolic left-ventricular function. Comparison of manual and automatic segmentations of the cardiac chambers at end-systolic and end-diastolic timeframes showed agreements comparable to those previously reported for automatic segmentation methods of b-SSFP MR images. Furthermore, automatic segmentation of the entire thoracic cardiovascular system improves visualization of 4D Flow MRI and facilitates computation of hemodynamic parameters. ; Funding details: 310612; Funding details: FP7, Seventh Framework Programme; Funding details: 621-2014-6191, VR, Vetenskapsrådet; Funding details: 223615; Funding details: 20140398; Funding text: This work was partially funded by the FP7-funded project DOPPLER-CIP [grant number 223615]; the European Union's Seventh Framework Programme ( FP7/2007-2013 ) [grant number 310612 ]; the Swedish Research Council [grant number 621-2014-6191 ]; and the Swedish Heart and Lung Foundation [grant number 20140398 ].
Legal and public policies concerning youth gun violence tend to rely heavily on crime reports, survey data, and statistical methods. Rarely is attention given to the young voices belonging to those who carry high-powered semiautomatic handguns. In Language of the Gun, Bernard E. Harcourt recounts in-depth interviews with youths detained at an all-malecorrectional facility, exploring how they talk about guns and what meanings they ascribe to them in a broader attempt to understand some of the assumptions implicit in current handgun policies. In the process, Harcourt redraws the relationships am
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The paper presents a method of the determining a mandibular cortical width on dental panoramic radiographs. Cortical width of lower border of mandible may potentially be associated with recognition of osteoporosis in postmenopausal women. An algorithm to perform a semiautomatic cortical width measurement in a given region of interest was developed. The algorithm is based on separate extraction of lower and upper boundaries of cortical bone. Results of boundaries extraction performed on 34 panoramic radiographs of healthy and osteoporotic individuals are presented, together with automatic measurements of particular distances. They were compared with results of hand-made measurements done by two maxillofacial radiologists. Presented algorithm may potentially be useful for screening patients with osteoporosis.
Introduction to the third edition of Shooting Incident Reconstruction -- Introduction to the second edition by Michael Haag -- Introduction to the first edition by Lucien C. (Luke) Haag -- Further reading -- 1 Case approach, philosophy, and objectives -- Why this book? -- Reconstruction-the ultimate goal of criminalistics -- Basic kills and approach to casework -- Qualifications -- General philosophy -- The scientific method -- Specific considerations -- 5058 Ask yourself these key questions -- Concluding comments -- Shooting reconstruction objectives -- Case decisions related to the admissibility of scientific evidence -- Chapter knowledge -- Further reading -- 2 Working shooting scenes -- Authors' notes -- The team -- Working the scene -- Shooting scene photography -- Ammunition components -- Photography of firearms at shooting incident scenes -- Revolvers -- Semiautomatic pistols -- Investigation teams and laboratory work -- New, not-so-new, and emerging techniques in shooting scene investigations -- Case examples -- Emerging technology -- Summary
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A semiautomatic radar surveillance system was simulated using a time-compressed, real-time cathode-ray tube display. Subjects were required to detect targets entering the surveillance area, initiate automatic tracking of these targets, and reinitiate lost tracks when automatic tracking failed. A within-subject response surface methodology (RSM) central-composite design was employed which permitted simultaneous investigation of the effects of five system parameters on surveillance operator performance. Response surface fits (second-order polynomials) were obtained and analyses of variance were conducted to describe these effects on two dependent measures of performance. Results support the contention that operator performance may be dependent upon complex relationships among the five system parameters tested. Furthermore, an RSM central-composite design provided an efficient method for obtaining data and quantifying these relationships.
The process of technical change from the economist's viewpoint may be broken down into three phases: invention, innovation, and diffusion. Invention, or the increase in technological possibilities, is the discovery or perception of new configurations of technical processes or principles that alter the array of possible production functions. An innovation consists of using any given production function for the "first" time. Diffusion is basically imitative and involves the gradual replacement of old methods by the new. One example will suffice to illustrate these distinctions. The invention of the automatic bottle machine consisted of the conception, experimentation, and model-building activities of Michael J. Owens; the pioneering efforts of the entrepreneurs at Toledo, Ohio, to demonstrate that the new production function was both practical and economically feasible constituted the innovational phase; and the gradual replacement of hand-blown and semiautomatic machine methods by the new process in both American and foreign markets involved diffusion.
Moderate resolution remote sensing data, as provided by MODIS, can be used to detect and map active or past wildfires from daily records of suitable combinations of reflectance bands. The objective of the present work was to develop and test simple algorithms and variations for automatic or semiautomatic detection of burnt areas from time series data of MODIS biweekly vegetation indices for a Mediterranean region. MODIS-derived NDVI 250m time series data for the Valencia region, East Spain, were subjected to a two-step process for the detection of candidate burnt areas, and the results compared with available fire event records from the Valencia Regional Government. For each pixel and date in the data series, a model was fitted to both the previous and posterior time series data. Combining drops between two consecutive points and 1-year average drops, we used discrepancies or jumps between the pre and post models to identify seed pixels, and then delimitated fire scars for each potential wildfire using an extension algorithm from the seed pixels. The resulting maps of the detected burnt areas showed a very good agreement with the perimeters registered in the database of fire records used as reference. Overall accuracies and indices of agreement were very high, and omission and commission errors were similar or lower than in previous studies that used automatic or semiautomatic fire scar detection based on remote sensing. This supports the effectiveness of the method for detecting and mapping burnt areas in the Mediterranean region. ; This work was supported by the research projects FEEDBACK (CGL2011-30515- C02-01), funded by the Spanish Ministry of Innovation and Science, CASCADE (GA283068), funded by European Commission under the Seventh Framework Program, and GVPRE/2008/310, funded by the Valencia Regional Government (Generalitat Valenciana).
Abstract. When floods hit inhabited areas, great losses are usually registered in terms of both impacts on people (i.e., fatalities and injuries) and economic impacts on urban areas, commercial and productive sites, infrastructures, and agriculture. To properly assess these, several parameters are needed, among which flood depth is one of the most important as it governs the models used to compute damages in economic terms. This paper presents a simple yet effective semiautomatic approach for deriving very precise inundation depth. First, precise flood extent is derived employing a change detection approach based on the normalized difference flood index computed from high-resolution synthetic aperture radar imagery. Second, by means of a high-resolution lidar digital elevation model, water surface elevation is estimated through a statistical analysis of terrain elevation along the boundary lines of the identified flooded areas. Experimental results and quality assessment are given for the flood that occurred in the Veneto region, northeastern Italy, in 2010. In particular, the method proved fast and robust and, compared to hydrodynamic models, it requires sensibly less input information.
