Versatile scanning tunneling microscopy with 120ps time resolution

We describe a fully ultra-high vacuum compatible scanning tunneling microscope (STM) optimized for radio-frequency signals. It includes in-situ exchangeable tips adapted to high frequency cabling and a standard sample holder, which offer access to the whole range of samples typically investigated by STM. We demonstrate a time resolution of 120 ps using the nonlinear I(V)-characteristic of the surface of highly oriented pyrolithic graphite. We provide atomically resolved images in pulse mode related to a spatially varying nonlinearity of the local density of states of the sample, thus, demonstrating the possible spatial resolution of the instrument in pulse mode. Analysis of the noise reveals that changes in the tunneling junction of 50 pA are dynamically detectable at 120 ps time resolution.Comment: 4 pages, 4 figure

Component based recognition of objects in an office environment

We present a component-based approach for recognizing objects under large pose changes. From a set of training images of a given object we extract a large number of components which are clustered based on the similarity of their image features and their locations within the object image. The cluster centers build an initial set of component templates from which we select a subset for the final recognizer. In experiments we evaluate different sizes and types of components and three standard techniques for component selection. The component classifiers are finally compared to global classifiers on a database of four objects

An ultrahigh-vacuum cryostat for simultaneous scanning tunneling microscopy and magneto-transport measurements down to 400mK

We present the design and calibration measurements of a scanning tunneling microscope setup in a 3He ultrahigh-vacuum cryostat operating at 400 mK with a hold time of 10 days. With 2.70 m in height and 4.70 m free space needed for assembly, the cryostat fits in a one-story lab building. The microscope features optical access, an xy table, in situ tip and sample exchange, and enough contacts to facilitate atomic force microscopy in tuning fork operation and simultaneous magneto-transport measurements on the sample. Hence, it enables scanning tunneling spectroscopy on microstructured samples which are tuned into preselected transport regimes. A superconducting magnet provides a perpendicular field of up to 14 T. The vertical noise of the scanning tunneling microscope amounts to 1 pmrms within a 700 Hz bandwidth. Tunneling spectroscopy using one superconducting electrode revealed an energy resolution of 120 mueV. Data on tip-sample Josephson contacts yield an even smaller feature size of 60 mueV, implying that the system operates close to the physical noise limit.Comment: 12 pages, 11 figure

Evidence for topological band inversion of the phase change material Ge2Sb2Te5

We present an angle-resolved photoemission study of a ternary phase change material, namely Ge2Sb2Te5, epitaxially grown on Si(111) in the metastable cubic phase. The observed upper bulk valence band shows a minimum at Gamma-bar being 0.3 eV below the Fermi level E_F and a circular Fermi contour around Gamma-bar with a dispersing diameter of 0.27-0.36 Anstroms^-1. This is in agreement with density functional theory calculations of the Petrov stacking sequence in the cubic phase which exhibits a topological surface state. The topologically trivial cubic KH stacking shows a valence band maximum at Gamma in line with all previous calculations of the hexagonal stable phase exhibiting the valence band maximum at Gamma for a trivial Z_2 topological invariant nu_0 and away from Gamma for non-trivial nu_0. Scanning tunneling spectroscopy exhibits a band gap of 0.4 eV around E_F

Isolation of soybean protein P34 from oil bodies using hydrophobic interaction chromatography

<p>Abstract</p> <p>Background</p> <p>Soybeans play a prominent role in allergologic research due to the high incidence of allergic reactions. For detailed studies on specific proteins it is necessary to have access to a large amount of pure substance.</p> <p>Results</p> <p>In this contribution, a method for purifying soybean (<it>Glycine max</it>) protein P34 (also called Gly m Bd 30 K or Gly m 1) using hydrophobic interaction chromatography is presented. After screening experiments using 1 mL HiTrap columns, Butyl Sepharose 4 FF was selected for further systematic investigations. With this stationary phase, suitable operation conditions for two-step gradient elution using ammonium sulphate were determined experimentally. The separation conditions obtained in a small column could be scaled up successfully to column volumes of 7.5 and 75 mL, allowing for high product purities of almost 100% with a yield of 27% for the chromatographic separation step. Conditions could be simplified further using a onestep gradient, which gave comparable purification in a shorter process time. The identity of the purified protein was verified using in-gel digestion and mass spectrometry as well as immunological techniques.</p> <p>Conclusion</p> <p>With the technique presented it is possible to produce, within a short timeframe, pure P34, suitable for further studies where an example antigen is needed.</p

Método de análisis biomecánico de la marcha en pacientes portadores de prótesis de rodilla

El análisis de la marcha ha adquirido en los últimos tiempos un extraordinario desarrollo. En la actualidad la ciencia biomecánica ofrece un gran campo de actuación para el estudio de la patología de la deambulación, aplicando los conocimientos anatómicos, las leyes físicas y la alta tecnología (ordenadores, video, plataformas de fuerza, etc ...) En este estudio, se comparan por medio del análisis del movimiento en tres dimensiones, la dinámica y el comportamiento articular de la marcha normal y de la marcha en el paciente portador de protesis de rodilla unilateral y bilateral, para analizar si se aprecian diferencias en las características generales de la marcha y los cambios evolutivos que provocan estas diferencias y sus posibles repercusiones patológicas. La marcha normal tiene una fase de balanceo, seguida de una fase de apoyo con: choque de talón, apoyo del retropié, apoyo de la planta, rodadura sobre el borde extremo, despegue del talón, despegue del primer dedo. Esta dinámica se acompaña de balanceo de las extremidades superiores para mantener el equilibrio y compensar los momentos de inercia provocados por la zancada

Thermogenic diagnosis of periprosthetic joint infection by microcalorimetry of synovial fluid

Background: Synovial fluid culture is the standard investigation for the preoperative diagnosis of periprosthetic joint infection (PJI). However, the culture has limited sensitivity and requires several days until result. We evaluated the value of isothermal microcalorimetry for real-time diagnosis of PJI based on heat produced by microbial growth in synovial fluid. Methods: Patients undergoing aspiration of prosthetic hip or knee joint before revision surgery were prospectively included between 2014 and 2015. The performance of microcalorimetry was compared to synovial fluid culture using McNemar’s chi-squared test. Pearson’s correlation coefficient was calculated for synovial fluid leukocyte count and microcalorimetric heat. Results: Of 107 included patients (58 knee and 49 hip prosthesis), PJI was diagnosed in 46 patients (43%) and aseptic failure in 61 patients (57%) according to institutional criteria. In 26 PJI cases (56%) the pathogen grew in synovial fluid and intra-operative cultures. The sensitivity of synovial fluid culture and microcalorimetry was both 39% and the results were concordant in 98 patients (92%). In patients with PJI, microcalorimetry missed 4 pathogens which grew in synovial fluid culture, whereas culture missed 4 pathogens detected by microcalorimetry. A linear correlation (r = 0.366) was found between leukocyte count and microcalorimetric heat in synovial fluid (p < 0.001). The median time to positivity of microcalorimetry was 9 h (range, 1–64 h) vs. 3 days for cultures (range, 1–14 days). Conclusion: Microcalorimetry of synovial fluid allows thermogenic diagnosis of periprosthetic joint infection in synovial fluid. The diagnostic performance of synovial fluid microcalorimetry is comparable to culture and delivers results considerably faster. Trial registration: This prospective study was registered on August 21, 2015 with the public clinical trial identification NCT02530229

Invasive and non-invasive assessment of upper airway obstruction and respiratory effort with nasal airflow and esophageal pressure analysis during sleep

La estimación del esfuerzo respiratorio durante el sueño es de una importancia crítica para la identificación correcta de eventos respiratorios en los trastornos respiratorios del sueño (TRS), el diagnóstico correcto de las patologías relacionadas con los TRS y las decisiones sobre la terapia correspondiente. Hoy en día el esfuerzo respiratorio suele ser estimado mediante la polisomnografía (PSG) nocturna con técnicas imprecisas y mediante la evaluación manual por expertos humanos, lo cual es un proceso laborioso que conlleva limitaciones significativas y errores en la clasificación. El objetivo principal de esta tesis es la presentación de nuevos métodos para la estimación automático, invasiva y no-invasiva del esfuerzo respiratorio y cambios en la obstrucción de las vías aéreas superiores (VAS). En especial, la aplicación de estos métodos debería permitir, entre otras cosas, la diferenciación automática invasiva y no-invasiva de eventos centrales y obstructivos durante el sueño. Con este propósito se diseñó y se obtuvo una base de datos de PSG nocturna completamente nueva de 28 pacientes con medición sistemática de presión esofágica (Pes). La Pes está actualmente considerada como el gold-standard para la estimación del esfuerzo respiratorio y la identificación de eventos respiratorios en los TRS. Es sin embargo una técnica invasiva y altamente compleja, lo cual limita su uso en la rutina clínica. Esto refuerza el valor de nuestra base de datos y la dificultad que ha implicado su adquisición. Todos los métodos de procesado propuestos y desarrollados en esta tesis están consecuentemente validados con la señal gold-standard de Pes para asegurar su validez.En un primer paso, se presenta un sistema automático invasivo para la clasificación de limitaciones de flujo inspiratorio (LFI) en los ciclos inspiratorios. La LFI se ha definido como una falta de aumento en flujo respiratorio a pesar de un incremento en el esfuerzo respiratorio, lo cual suele resultar en un patrón de flujo respiratorio característico (flattening). Un total de 38,782 ciclos respiratorios fueron automáticamente extraídos y analizados. Se propone un modelo exponencial que reproduzca la relación entre Pes y flujo respiratorio de una inspiración y permita la estimación objetiva de cambios en la obstrucción de las VAS. La capacidad de caracterización del modelo se estima mediante tres parámetros de evaluación: el error medio cuadrado en la estimación de la resistencia en la presión pico, el coeficiente de determinación y la estimación de episodios de LFI. Los resultados del modelo son comparados a los de los dos mejores modelos en la literatura. Los resultados finales indican que el modelo exponencial caracteriza la LFI y estima los niveles de obstrucción de las VAS con la mayor exactitud y objetividad. Las anotaciones gold-standard de LFI obtenidas, fueron utilizadas para entrenar, testear y validar un nuevo clasificador automático y no-invasivo de LFI basa en la señal de flujo respiratorio nasal. Se utilizaron las técnicas de Discriminant Analysis, Support Vector Machines y Adaboost para la clasificación no-invasiva de inspiraciones con las características extraídas de los dominios temporales y espectrales de los patrones de flujo inspiratorios. Este nuevo clasificador automático no-invasivo también identificó exitosamente los episodios de LFI, alcanzando una sensibilidad de 0.87 y una especificidad de 0.85. La diferenciación entre eventos respiratorios centrales y obstructivos es una de las acciones más recurrentes en el diagnostico de los TRS. Sin embargo únicamente la medición de Pes permite la diferenciación gold-standard de este tipo de eventos. Recientemente se han propuesto nuevas técnicas para la diferenciación no-invasiva de apneas e hipopneas. Sin embargo su adopción ha sido lenta debido a su limitada validación clínica, ya que la creación manual por expertos humanos de sets gold-standard de validación representa un trabajo laborioso. En esta tesis se propone un nuevo sistema para la diferenciación gold-standard automática y objetiva entre hipopneas obstructivas y centrales. Expertos humanos clasificaron manualmente un total de 769 hypopneas en 28 pacientes para crear un set de validación gold-standard. Como siguiente paso se extrajeron características específicas de cada hipopnea para entrenar y testear clasificadores (Discriminant Analysis, Support Vector Machines y adaboost) para diferenciar entre hipopneas centrales y obstructivas mediante la señal gold-standard Pes. El sistema de diferenciación automática alcanzó resultados prometedores, obteniendo una sensibilidad, una especificad y una exactitud de 0.90. Por lo tanto este sistema parece prometedor para la diferenciación automática, gold-standard de hipopneas centrales y obstructivas. Finalmente se propone un sistema no-invasivo para la diferenciación automática de hipopneas centrales y obstructivas. Se propone utilizar la señal de flujo respiratorio para la diferenciación utilizando características de los ciclos inspiratorios de cada hipopnea, entre ellos los patrones flattening. Este sistema automático no-invasivo es una combinación de los sistemas anteriormente presentados y se valida mediante las anotaciones gold-standard obtenidas mediante la señal de Pes por expertos humanos. Los resultados de este sistema son comparados a los resultados obtenidos por expertos humanos que utilizaron un nuevo algoritmo no-invasivo para la diferenciación manual de hipopneas. Los resultados del sistema automático no-invasivo son prometedores y muestran la viabilidad de la metodología empleada. Una vez haya sido validado extensivamente, se ha propuesto este algoritmo para su utilización en dispositivos de terapia de TRS desarrollados por uno de los socios cooperantes en este proyecto.The assessment of respiratory effort during sleep is of major importance for the correct identification of respiratory events in sleep-disordered breathing (SDB), the correct diagnosis of SDB-related pathologies and the consequent choice of treatment. Currently, respiratory effort is usually assessed in night polysomnography (NPSG) with imprecise techniques and manually evaluated by human experts, resulting in a laborious task with significant limitations and missclassifications.The main objective of this thesis is to present new methods for the automatic, invasive and non-invasive assessment of respiratory effort and changes in upper airway (UA) obstruction. Specifically, the application of these methods should, in between others, allow the automatic invasive and non-invasive differentiation of obstructive and central respiratory events during sleep.For this purpose, a completely new NPSG database consisting of 28 patients with systematic esophageal pressure (Pes) measurement was acquired. Pes is currently considered the gold-standard to assess respiratory effort and identify respiratory events in SDB. However, the invasiveness and complexity of Pes measurement prevents its use in clinical routine, underlining the importance of this new database. . . All the processing methods developed in this thesis will consequently be validated with the gold-standard Pes-signal in order to ensure their clinical validity.In a first step, an (invasive) automatic system for the classification of inspiratory flow limitation (IFL) in the inspiratory cycles is presented.IFL has been defined as a lack of increase in airflow despite increasing respiratory effort, which normally results in a characteristic inspiratory airflow pattern (flattening). A total of 38,782 breaths were extracted and automatically analyzed. An exponential model is proposed to reproduce the relationship between Pes and airflow of an inspiration and achieve an objective assessment of changes in upper airway obstruction. The characterization performance of the model is appraised with three evaluation parameters: mean-squared-error when estimating resistance at peakpressure,coefficient of determination and assessment of IFL episodes. The model's results are compared to the two best-performing models in the literature. The results indicated that the exponential model characterizes IFL and assesses levels of upper airway obstruction with the highest accuracy and objectivity.The obtained gold-standard IFL annotations were then employed to train, test and validate a new automatic, non-invasive IFL classification system by means of the nasal airflow signal. Discriminant Analysis, Support Vector Machines and Adaboost algorithms were employed to objectively classify breaths non-invasively with features extracted from the time and frequency domains of the breaths' flow patterns. The new non-invasive automatic classification system also succeeded identifying IFL episodes, achieving a sensitivity of 0.87 and a specificity of 0.85.The differentiation between obstructive and central respiratory events is one of the most recurrent tasks in the diagnosis of sleep disordered breathing, but only Pes measurement allows the gold-standard differentiation of these events. Recently new techniques have been proposed to allow the non-invasive differentiation of hypopneas. However, their adoption has been slow due to their limited clinical validation, as the creation of manual, gold-standard validation sets by human experts is a cumbersome procedure. In this study, a new system is proposed for an objective automatic, gold-standard differentiation between obstructive and central hypopneas with the esophageal pressure signal. An overall of 769 hypopneas of 28 patients were manually scored by human experts to create a gold-standard validation set. Then, features were extracted from each hypopnea to train and test classifiers (Discriminant Analysis, Support Vector Machines and adaboost classifiers) to differentiate between central and obstructive hypopneas with the gold-standard esophageal pressure signal. The automatic differentiation system achieved promising results, with a sensitivity of 0.82, a specificity of 0.87 and an accuracy of 0.85. Hence, this system seems promising for an automatic, goldstandard differentiation between obstructive and central hypopneas.Finally, a non-invasive system is proposed for the automatic differentiation of central and obstructive hypopneas. Only the airflow signal is used for the differentiation, as features of the inspiratory cycles of the hypopnea, such as the flattening patterns, is used. The automatic, non-invasive system represents a combination of the systems that have been presented before and it was validated with the gold-standard scorings obtained with the Pes-signal by human experts. The outcome is compared to the results obtained by human scorers that applied a new non-invasive algorithm for the manual differentiation of hypopneas. The non-invasive system's results are promising and show the viability of this technique. Once validated, this algorithm has been proposed to be used in therapy devices developed by one of the partner institutions cooperating in this project

Value of multiplex PCR for detection of antimicrobial resistance in samples retrieved from patients with orthopaedic infections

Background: The performance of multiplex PCR (mPCR) for detection of antimicrobial resistance from clinical isolates is unknown. We assessed the ability of mPCR to analyse resistance genes directly from clinical samples. Patients with orthopedic infections were prospectively included. Phenotypical and genotypical resistance was evaluated in clinical samples (synovial and sonication fluid) where identical pathogens were identified by culture and mPCR. Result: A total of 94 samples were analysed, including 60 sonication fluid and 34 synovial fluid samples. For coagulase-negative staphylococcus strains, mPCR detected resistance to oxacillin in 10 of 23 isolates (44%) and to rifampin in none of 6 isolates. For S. aureus isolates, detection rate of oxacillin and rifampin-resistance was 100% (2/2 and 1/1, respectively). Fluoroquinolone-resistance was confirmed by mPCR in all 3 isolates of Enterobacteriaceae, in enterococci resistance to aminoglycoside-high level was detected in 1 of 3 isolates (33%) and in streptococci resistance to macrolides/lincosamides in none of 2 isolates. The overall sensitivity for different pathogens and antimicrobials was 46% and specificity 95%, the median concordance was 80% (range, 57–100%). Full agreement was observed for oxacillin in S. aureus, vancomycin in enterococci, carbapenems/cephalosporins in Enterobacteriaceae and rifampin in Cutibacterium species. Conclusion: The overall sensitivity for detection of antimicrobial resistance by mPCR directly from clinical samples was low. False-negative mPCR results occurred mainly in coagulase-negative staphylococci, especially for oxacillin and rifampin. However, the specificity of mPCR was high and a positive result reliably predicted antimicrobial resistance. Including universal primers in the PCR test assay may improve the detection rate but requires additional sequencing step. Trial registration: www.clinicaltrials.gov No. NCT02530229, registered at 21 August 2015 (retrospectively registered)