1,720,955 research outputs found
A 32-channel photon counting module with embedded auto/cross-correlators for real-time parallel fluorescence correlation spectroscopy
Get PDFFluorescence correlation spectroscopy (FCS) is a well-established technique to study binding interactions or the diffusion of fluorescently labeled biomolecules in vitro and in vivo. Fast FCS experiments require parallel data acquisition and analysis which can be achieved by exploiting a multi-channel Single Photon Avalanche Diode (SPAD) array and a corresponding multi-input correlator. This paper reports a 32-channel FPGA based correlator able to perform 32 auto/cross-correlations simultaneously over a lag-time ranging from 10 ns up to 150 ms. The correlator is included in a 32 × 1 SPAD array module, providing a compact and flexible instrument for high throughput FCS experiments. However, some inherent features of SPAD arrays, namely afterpulsing and optical crosstalk effects, may introduce distortions in the measurement of auto- and cross-correlation functions. We investigated these limitations to assess their impact on the module and evaluate possible workarounds
A simple and flexible FPGA based autocorrelator for afterpulse characterization of single-photon detectors
No full textSingle Photon Avalanche Diodes (SPADs) are widely employed for photon counting and timing in a variety of scientific and industrial applications. However they are affected by the afterpulsing effect, which can significantly increase the effective dark count rate of the detector. Being correlated with previous photon pulses, afterpulses can cause sharp distortions in photon correlation experiments. In this paper we exploit autocorrelation to characterize the afterpulsing of SPADs. A FPGA based autocorrelator has been specifically designed to this purpose, featuring a lag-time range from 10ns to more than 10ms, covering a range well beyond the longest expected trapped carrier lifetime
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Development of multi-channel FPGA-based correlators for parallel fluorescence correlation spectroscopy
No full textLa FCS (Fluorescence correlation spectroscopy) è una tecnica consolidata per studiare i legami molecolari ma permette anche di analizzare la diffusione delle molecole sia in-vitro che in-vivo. Tipicamente utilizza un microscopio confocale per rivelare le fluttuazioni nell’intensità di fluorescenza delle molecole in un piccolo volume (femtolitri) di osservazione. Tali fluttuazioni sono dovute ad una variazione del numero di molecole in tale volume. La funzione di autocorrelazione (ACF, autocorrelation function) dell’intensità di fluorescenza fornisce informazioni sia fisiche sia fotochimiche (dimensioni, concentrazione, blinking, tasso di legame) sulla molecole in esame. Per studiare queste fluttuazioni, la FCS deve essere svolta su campioni con concentrazioni nanomolari: i tempi di acquisizione variano da qualche secondo a parecchi minuti. Tuttavia, esistono casi particolari in cui è richiesta un’acquisizione molto più rapida, ad esempio quando si controllano fluidi ad alta densità (poiché è necessario avere misure simultanee su diverse parti del campione) o quando il sistema osservato evolve molto rapidamente (in questo caso i parametri in esame variano in funzione del tempo e vanno ricavati continuamente). Questo tipo di misura richiede sistemi paralleli, che permettono lo studio contemporaneo di diversi punti della stessa cellula. Tali sistemi impiegano matrici rivelatori e sistemi di eccitazione multi-spot, rendendo possibile l’acquisizione parallela di dati FCS. Tuttavia, l’acquisizione e l’elaborazione dei dati deve essere svolta anch’essa in parallelo, creando la necessità di correlatori multicanale ad alta efficienza. In queste tesi si descrive lo sviluppo di tali correlatori affinché sia possibile effettuare misure FCS multicanale.
Parecchi correlatori sono stati sviluppati e molti di essi sono disponibili sul mercato. Tradizionalmente si impiegano correlatori hardware per il calcolo real-time della funzione di autocorrelazione. Tuttavia sono necessarie diverse decadi di lag time per calcolare la funzione di autocorrelazione: uno spacing lineare dei canali di ritardo risulta difficilmente utilizzabile, mentre è più efficace ricorrere ad algoritmi multi-tau. Correlatori real-time multi-tau sono stati inizialmente impiegati come hardware per sistemi di elaborazione digitale veloce sia su ASIC (application-specific integrated circuit) sia, più recentemente, su FPGA (field programmable gate array). Oggigiorno, questi ultimi dispositivi sono realizzati in tecnologia CMOS a 28 nm e raggiungono alte densità di integrazione, consentendo così l’implementazione efficace di algoritmi molto complessi. Inoltre, offrono bassi costi fissi e velocizzano il time-to-market del prodotto rispetto appunto agli ASIC. Questa velocità al time-to-market è accenutata dai correlatori software, il cui design è ancora più rapido, estremamente flessibile. Essi tuttavia possono solo svolgere correlazioni offline. Difatti, per operazioni real-time sono poco efficienti poiché richiedono alla CPU un costo computazionale molto elevato,
impedendone l’utilizzo in sistemi FCS multicanale. Per questo motivo i correlatori che più si adattano alle necessità di questa tecnica sono quelli basati su FPGA, in particolare quelli real-time ad ampia dinamica di lag time.
In questo progetto, lo studio di tali correlatori è iniziato sviluppando il VHDL per un correlatore a singolo canale. Il lag time massimo ha raggiunto 150 ms mentre il minimo bin vale 10 ns e, comparato con correlatori commerciali, è risultato più che affidabile. Il range di lag time è stato in seguito esteso da 5 ns a 80 s, per uniformare le prestazioni del correlatore a quelle dello stato dell’arte. Tale risultato è stato raggiunto dividendo il lag time in due parti, mantenendo così un calcolo real-time. È stato implementato anche un simulatore FPGA per verificarne il funzionamento. Oltre al correlatore hardware, ne è stato disegnato anche uno correlatore software, poiché l’applicazione richiede anche una correlazione offline. Questo correlatore impiega uno schema multi-tau ad algoritmo migliorato; Il segnale viene registrato in modalitá fotoni, ovvero misurando l’intervallo di tempo tra due impulsi. Infine, il correlatore completo è stato sviluppato, combinando il correlatore basato su FPGA per il calcolo on-line, con il registrazione del segnale in modalitá fotoni all’ interno della FPGA, e con l’interfaccia PC per la correlazione software e l’analisi offine. Il successo nello sviluppo del correlatore a singolo canale, ha portato al progetto di un correlatore a 32 canali, destinato ad essere inserito in un modulo di rivelazione che monta un array di 32 SPAD (Single Photon Avalanche Diode). Il modulo ha la stessa FPGA del correlatore singolo, le cui risorse sono limitate per la parallelizzazione, quindi lo schema di replicazione del correlatore è stato ottimizzato. Infine il modulo che integra SPAD e correlatori è stato predisposto per essere utilizzato in un setup FCS multicanale. Tuttavia, alcune caratteristiche degli SPAD, ovvero afterpulsing e crosstalk ottico, possono introdurre distorsioni nelle funzioni di auto- e cross-correlazione. Queste limitazioni sono state analizzate, valutandone l’impatto sulle prestazioni del modulo e studiandone possibili soluzioni.
Infine, date le risorse limitate dell’FPGA del modulo a 32 canali, non è stato possible apportare miglioramenti al correlatore, come ad esempio estendere il numero di canali o la durata del lag time. Per poterlo fare è quindi stato sviluppato un modulo apposito che monta una FPGA di una famiglia superiore. Essa consente di integrare fino a 64 correlatori con un lag time massimo circa 1 minuto. Il modulo ha anche il vantaggio di essere stand-alone e di poter essere collegato a due sistemi a 64 canali simili a quelli a 32 utilizzati in precedenza. Il correlatore consente di agire su tutti i dati campionati in parallelo effettuando 64 correlazioni che possono essere monitorate real-time grazie al modulo di trasferimento veloce inserito nel sistema. Il correlogramma di ogni SPAD può essere salvato su PC per successive correlazioni offline o per ulteriori analisi. Lo strumento sviluppato permette quindi il calcolo parallelo di 64 auto- o cross- correlazioni per un lungo lag time. Sistemi simili sono quasi introvabili in letteratura, pertanto quello presentato in questa tesi risulta di sicuro interesse per misure FCS multicanale.Fluorescence correlation spectroscopy (FCS) is a well-established technique to study binding interactions or the diffusion of fluorescently labeled biomolecules in-vitro and in-vivo. FCS is commonly implemented by using a confocal microscope to detect the fluctuations of fluorescence intensity arising from changes in the number of molecules diffusing through a small (~femtoliter) observation volume. The autocorrelation function (ACF) of fluorescence intensity fluctuations can yield physical as well as photochemical information (molecule size and concentration, blinking or binding/unbinding rates) about the diffusing molecules. To monitor the fluorescence fluctuations, FCS measurements need to be performed at nanomolar concentrations with typical acquisition times on the order of a few seconds to several minutes. However, faster acquisitions of FCS data are desirable in two cases: in high-content screening approaches, many molecules on reaction at different locations require simultaneous interrogation; also when observing fast evolving dynamic systems, diffusion parameters change as a function of time. It is thus important to develop FCS methods that enable simultaneous measurements at different locations within a living cell. Parallel FCS acquisition is then developed, with the help of multi-pixel detectors and multi-spot excitation generation technique, which maps each excitation spot onto every target pixel of the detector. Furthermore, simultaneous data acquisition and processing is needed, demanding for multi-input high efficiency correlators. Thereby this thesis describes design of multi-channel correlators for high throughput FCS experiments.
Various correlators have been developed, some are commercially available. The hardware correlators have been traditionally employed for real-time calculation of correlation functions over a certain dynamic range. Since in typical FCS measurements the correlation function spans over several decades of lag times, linear channel spacing is impractical and the multi-tau algorithm is used. Real-time, multi-tau correlators were formerly implemented on custom high-speed digital signal-processing hardware, either application-specific integrated circuits (ASICs) or, lately, field-programmable gate arrays (FPGAs). Nowadays, FPGAs can be manufactured in 28 nm CMOS processes and have reached integration densities that allow cost efficient implementation of even complex and resource intensive DSP algorithms. They offer lower non-recurring engineering costs and faster time to market than more customized approaches such as full-custom VLSI or ASIC design. On the other hand, software correlators are also available; they have fast design cycle, flexible structure and can provide offline operations. However for online computations, they could lack efficiency due to the high CPU utilization rate which prevents their application in high-throughput FCS experiments. As a result, FPGA based correlators providing multiple channels, high dynamic lag time range and online operations, are very promising for highly paralleled FCS experiments.
A single-channel FPGA based correlator was first designed employing the multi-tau algorithm. It features a maximum lag time of 150 ms while minimum time bin being 10 ns. This correlator is adopted to characterize afterpulsing effect of Single Photon Avalanche Diodes (SPADs), whose results are verified by a commercial correlator. So as to meet state-of-art standards, lag time range of the FPGA based correlator was then extended upwards to 80 s with minimum time bin being 5 ns. This long lag time correlator is divided into two parts to maintain real time display. Apart from the FPGA based correlators, a PC based software correlator exploiting an improved multi-tau scheme was designed for offline analysis. The signal trace for the software correlator is recorded in photon mode which counts the time interval between two pulses. Combining the FPGA based correlator for online correlation computation, with photon mode recording of the signal traces in FPGA, and PC interface integrated with software correlator for intercommunication and offline analysis, a complete single-channel correlator was developed.
Based on the successful design of single channel correlators, a 32-channel correlator is then implemented which is intended to be directly contained in a photon detection module mounted with a 32 × 1 SPAD array. The module has a same FPGA as the one used for the single-channel design. In order to fully utilize the limited FPGA resources, the replication scheme for the 32-channel correlator is redesigned. The photon detection module together with the multi-channel correlator as a compact module can be applied in FCS experiments providing direct signal detection and analysis path. However, some inherent features of SPAD arrays, namely afterpulsing and optical crosstalk effects, may introduce distortions in the measurement of auto- and cross-correlation functions. These limitations are investigated to assess their impact on the module and evaluate possible workarounds. The photon detection module and the PC interface are shown in the following figure.
In order to further upgrade the 32-channel correlator and enable correlation computation between modules, a standalone cross-correlator module has been developed. It employs larger FPGA, faster data transfer interface, able to hold 64-channel FPGA based cross-correlator with maximum lag time around 1 min. The module can connect with two external multi-channel SPAD array modules, receiving up to 128 channels of photon counting signals. The correlator system can execute instant signal-trace recording and fast online FPGA based correlation computation with real time display of all the 64 correlograms. The signal track from each SPAD pixel can be stored in PC for offline correlation calculation or other analysis. According both to literature and commercial products, few of them are able to accommodate high number of input channels while still maintaining large lag time range with low minimum time bin. Thus this complete correlator module would be of great interest for high-throughput FCS experiments.DIPARTIMENTO DI ELETTRONICA, INFORMAZIONE E BIOINGEGNERIAElectronics26GERACI, ANGELOFIORINI, CARLO ETTOR
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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