Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Entwicklung eines routenbasierten Verkehrsumlegungsmodells

Transport assignment models play an important role in the research and practice of transport planning. Traditionally, transport assignment models are link-based, predicting traffic volumes on network links. However, route-based transport assignment models, which work with route sets and determine traffic volumes of routes, became more important in recent years. They support advanced analysis procedures that require route volumes as input, e.g. estimation of OD-matrices and evaluation of intelligent transport systems (ITS). The aim of this research is to develop a general framework for a route-based transport assignment, which emphasizes the quality of the resulting route sets. To achieve this goal, this framework differentiates the assignment procedure into two spate stages. In the first stage, it generates the route sets for all OD-pairs explicitly, and then in the second stage it distributes the travel demand between these routes. With this two-stage structure, a comprehensive route set generation procedure can be incorporated considering specific constraints. In order to generate realistic route sets, it is essential to have a clear definition of the quality of route sets. After examining the assumptions on the travellers’ behaviour in identifying and choosing routes, a set of indicators is introduced to quantify the quality of route sets. These indicators concern two aspects of the quality of route sets: the quality of individual routes and the composition of route sets. Constraints such as global detour factor, local detour factor, local optimal threshold for route sections and road hierarchical index are introduced to ensure the quality of individual routes while constraints such as choice set size and minimal dissimilarity address the composition of route sets. With these indicators in place, a two-stage route set generation procedure is developed to generate route sets whose quality satisfies certain constraints. The first stage employs the branch-and-bound technique to enforce the constraints on individual routes. For a given OD-pair, it enumerates all possible routes systematically and discards routes whose indicators do not satisfy the constraints. The second stage enforces the constraints on the route set composition. It produces route sets that contain a given number of routes where the routes are dissimilar with each other. Using the route set generation method a framework for distributing travel demand on given route sets is presented. It applies a nested logit model that takes advantages of the hierarchical structure of the route choice sets. For the feedback between route choice and route travel time it uses a simple convergence procedure based on successive average. A pilot implementation of this assignment framework is developed and some implementation issues such as network pre-processing are discussed. The pilot implementation is validated with a small test network and a larger test case in the Munich region. Here the generated route sets are compared with observed route sets. The result shows that the framework is capable of reproducing observed route sets with sufficient accuracy and that it is flexible enough to be calibrated for different situations.Für die Forschung und Praxis der Verkehrsplanung spielen Verkehrsumlegungsmodelle eine wichtige Rolle. Üblicherweise sind Verkehrsumlegungsmodelle streckenbasiert, d. h. sie prognostizieren die Verkehrsstärke für einzelne Strecken des Verkehrsnetzes. In den vergangenen Jahren haben routenbasierte Umlegungsmodelle an Bedeutung gewonnen, die Routenmengen generieren und die Verkehrsstärke jeder Route bestimmen. Sie sind Grundlage für weitere Verfahren, wie die Schätzung von Quelle-Ziel-Matrizen oder die Bewertung verkehrstelematischer Maßnahmen, die Routenbelastungen als Eingangsgrößen benötigen. Das Ziel dieser Arbeit ist es, ein allgemeines routenbasiertes Verkehrsumlegungsmodell zu entwickeln, bei dem die Qualität der verwendeten Routensets im Vordergrund steht. Zu diesem Zweck erfolgt die Umlegung in zwei getrennten Stufen: In der ersten Stufe werden die Routensets für alle Quelle-Ziel-Relationen in einem eigenständigen Verfahren generiert. In der zweiten Stufe wird die Verkehrsnachfrage dann auf diese Routen umgelegt. Die Trennung von Routengenerierung und Routenwahl ermöglicht eine Routengenerierung, die besondere Randbedingungen erfüllen kann. Die Generierung realistischer Routensets erfordert eine eindeutige Definition der Qualität von Routensets. Aufbauend auf einer Untersuchung der Annahmen zum Routenwahlverhalten von Verkehrsteilnehmern wird eine Reihe von Kenngrößen eingeführt, um die Qualität eines Routensets zu bewerten. Diese Kenngrößen bewerten zwei Aspekte der Qualität von Routensets: die Qualität der einzelnen Routen und die Zusammensetzung des gesamten Routensets. Die Qualität einzelner Routen wird durch die Vorgabe eines globalen und eines lokalen Umwegfaktors, eines lokalen Grenzwerts für Routenabschnitte und eines Straßenkategorieindexes sichergestellt. Die Zusammensetzung der Routensets wird durch die maximale Größe des Routensets und eine geringe Ähnlichkeit der Routen beeinflusst. Auf der Basis dieser Kenngrößen wird ein zweistufiges Verfahren zur Generierung von Routensets entwickelt, das Qualitätsgrenzwerte einhält. Die erste Stufe nutzt einen Branch-and-Bound Ansatz um die Grenzwerte für einzelne Routen einzuhalten. Für jede Quelle-Ziel-Relation werden alle möglichen Routen systematisch erzeugt, wobei Routen, deren Kenngrößen den Grenzwerten nicht entsprechen, aussortiert werden. In der zweiten Stufe wird die Zusammensetzung des Routensets anhand weiterer Grenzwerte überprüft, so dass Routensets mit einer vorgegebenen Anzahl von Routen generiert werden, deren Routen möglichst eigenständig sind. Aufbauend auf dem Routengenerierungsverfahren wird ein allgemeines Verfahren vorgestellt, mit dem die Nachfrage auf die Routen aufgeteilt werden kann. Es basiert auf einem Nested Logit Modell, das den hierarchischen Aufbau des Routensets nutzt. Für die Rückkopplung zwischen Routenwahl und belastungsabhängiger Fahrzeit wird ein einfaches Konvergenzverfahren basierend auf der Method of Successive Averages eingesetzt. Das Umlegungsverfahren wird als Prototyp implementiert und Fragen der Netzaufbereitung behandelt. Der Prototyp wird mithilfe eines kleinen Testnetzes und anhand eines größeren Testfalls in der Region München validiert. Die Ergebnisse zeigen, dass das Routengenerierungsverfahren die beobachteten Routensets mit angemessener Genauigkeit darstellen kann und dass es für unterschiedliche Anforderungen kalibriert werden kann

Automated extraction of temporal motor activity signals from video recordings of neonatal seizures based on adaptive block matching

Abstract-This paper presents a new method for tracking features in video. This method estimates the displacement of a feature between two successive frames by minimizing an error function defined in terms of the feature intensities at these frames. The minimization problem is made analytically tractable by approximating the error function using a second-order Taylor expansion. The displacement between two successive frames is computed in an iterative fashion using gradient descent. The improved reliability of the proposed method is illustrated by its application in the extraction of temporal motor activity signals from video recordings of neonatal seizures. successive frames is estimated by minimizing an error function defined in terms of the intensity functions at these frames. In the proposed procedure, the error function is approximated by using a second-order Taylor expansion for the intensity function at the next frame. The proposed feature tracking method is used to extract motor activity signals from video recordings of neonatal seizures. Motor activity signals can be extracted by projecting the location of selected anatomical sites to the horizontal and vertical axes. As the seizure progresses in time, these projections will produce temporal signals recording motor activity of the body parts of interest. Extraction of Temporal Motor Activity Signals From Video Recordings of Keywords-Feature tracking, motor activity signal, translation motion mode

Chromatograph Skeleton Components of Feng-flavor Baijiu during Different Production Stages

Production of Feng-flavor baijiu includes six stages (first fermented stage, second fermented stage, third fermented stage, normal fermented stage and quitting fermented stage, ending of fermented stage). Each stage of the base liquor has its own style. The main chromatogram structure components were analyzed by gas chromatography (GC), to explore the characteristics of base baijiu during different production stages, which can provide a reference for classification storage and body design of baijiu

The Influence of Hydrothermal Activity on the Long-Distance Migration and Accumulation of Hydrocarbons: A Case Study from the Y8 Area in the Songnan-Baodao Sag of Qiongdongnan Basin

The Qiongdongnan (QDN) basin in the northwestern South China Sea has been shown to be rich in petroleum resources and has significant exploration potential for deepwater oil and gas resources. Therefore, it is of great significance to clarify the gas accumulation process in the deepwater area of the QDN basin, specifically the Y8 area. In this study, fluid inclusion analysis, including the identification and localization of fluid inclusions under a microscope, laser Raman spectrum analysis and homogenization temperature (Th) measurement, reconstruction of the thermal evolution burial history, geochemical analysis, and typical seismic section analysis were comprehensively used to interpret the gas accumulation process of the Y8 area. The laser Raman spectrum analysis results of fluid inclusions verified the existence of methane and confirmed the hydrocarbon charging event in this area. However, the Th of fluid inclusions in the reservoir, the mixed compositions of hydrothermal compositions (H2S + SO2) and hydrocarbons (methane) in the fluid inclusions, and the low Tmax values of some wells in the Y8 area comprehensively confirmed that the coincidence of hydrothermal activity with the accumulation process affected the long-distance gas accumulation of the Y8 area. The hydrothermal activity was also confirmed by the presence of fluid diapirs in seismic profiles of the Y8 area. Furthermore, the hydrocarbon accumulation process was reconstructed using the modified thermal evolution history considering the effect of hydrothermal activity. Overall, this study attributed the high Th of fluid inclusions in the reservoirs of the Y8 area to hydrothermal activity and proposed a long-distance migration model of hydrocarbon accumulation coinciding with hydrothermal activity, both of which are beneficial to understanding the accumulation process of the Y8 area

Blackwell Publishing, Inc. C ○ 2005 International League Against Epilepsy Computerized Motion Analysis of Videotaped Neonatal Seizures of Epileptic Origin

development of automated video processing and analysis procedures aimed at the recognition and characterization of the types of neonatal seizures. The long-term goal of this research is the integration of these computational procedures into the development of a stand-alone automated system that could be used as a supplement in the neonatal intensive care unit (NICU) to provide 24-h per day noninvasive monitoring of infants at risk for seizures. Methods: We developed and evaluated a variety of computational tools and procedures that may be used to carry out the three essential tasks involved in the development of a seizure recognition and characterization system: the extraction of quantitative motion information from video recordings of neonatal seizures in the form of motion-strength and motor-activity signals, the selection of quantitative features that convey som