Public Articles
When the Obstacle is the Course: Job Security in Academia
This post is part of the series called Obstacles in Academia, which aims to highlight the many challenges young scientists face today.
Authorea Partners with Italian Doctoral Association
and 1 collaborator
What Really Happened: Darwin's Finches
The Decline of Accuracy in Science Communication: Who is to Blame?
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FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET
and 4 collaborators
Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores.
While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date.
In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis.
We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community.
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Relatório 2 Detetive Ecológico
and 5 collaborators
Ferramentas do Detetive Ecológico: uso e avaliação de modelos com detecção imperfeita
Paulo Inácio de Knegt López de Prado
Instituto de Biociências, Universidade de São Paulo
Carlos Ernesto Candia-Gallardo, Pós-graduação em Ecologia IB–USP
Cristiane Honoran Millán, mestre em Ecologia
Gregório Menezes, consultor autônomo
Gustavo Mattos Accacio, consultor autônomo
Gustavo Requena, Pós-doutorado IB–USP
Leonardo Liberali Wedekin, Pós-doutorado IB–USP
Rodolpho Credo Rodrigues, Pós-graduação em Ecologia IB–USP
Melina de Souza Leite, Especialista em Laboratório, IB–USP
2013/19250-7 Auxílio Pesquisa - Regular
01/02/2014 a 31/01/2016
01/02/2015 a 31/10/2015
Radiative properties of ordered and disordered porous ceria particle clouds under solar irradiation
and 1 collaborator
We study the radiative behavior of particle clouds consisting of two types of highly porous spherical ceria particles under direct solar irradiation—one with a templated three-dimensionally ordered macroporous (3DOM) structure and the other with pores randomly located within the structure. Individual radiative properties—the scattering efficiency factor, absorption efficiency factor, and the scattering phase function—of the randomly porous particles are numerically predicted in this work for comparison against existing 3DOM data. Clouds of monodisperse particles with a spatially uniform particle density are studied for each case. Solutions are compared to results based on individual particle scattering properties obtained from an effective medium theory combined with Mie theory results. It is found that the high degree of order in 3DOM particles does not significantly change the radiative properties of the cloud. However *something interesting*.
Thesis: Machine Learning-based Indoor Localization for Micro Aerial Vehicles
\label{chap:introduction}
In the world of automation, micro aerial vehicles (MAVs) provide unprecedented perspectives for domestic and industrial applications. They can serve as mobile surveillance cameras, flexible transport platforms, or even as waiters in restaurants. However, indoor employment of these vehicles is still hindered by the lack of real-time positions estimates. The focus of this thesis is, thus, the development of accurate and fast indoor localization for MAVs combining computer vision and machine learning techniques.
How to Bring Science Publishing into the 21st Century
A new collaborative tool could revolutionize scientific authorship. Originally published by Scientific American
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The Night of the Shooting Stars
During the night of August 11th, a meteor shower called ’Perseids’ might put up a memorable show. After the moon sets, which occurs around 1:00 AM local time, it might be possible to see up to 200 ’shooting stars’ per hour. Below, what you need to know about this astronomical event.
Despite their name, shooting stars are actually small rocks (meteoroids) falling towards the Earth due to our planet’s gravitational attraction. As they move rapidly through the atmosphere, they reach very high temperatures due to friction with air particles. This makes them burn and become visible to the human eye. The trail they leave is called ’Meteor’. Due to their tiny size, they usually almost completely burn in a fraction of a second. In some very exceptional cases, large meteors can continue the hot descent and hit the ground. If they also survive the crash, they get promoted immediately to the ’meteorites’ class. Generally speaking a meteoroid producing a meteor needs to be at least as large as a marble to reach the Earth and eventually become a meteorite. Some Burning facts:
Average meteorite velocity: 30000 miles/hour (48000 km/h)
Max temperature: 3000 F (1650 C)
The Meteor Crater in Arizona was formed 50000 years ago by an object 160 feet (50 meters) across
... yes, impacts like the one that produced the Meteor Crater are extremely rare
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Tokenizing an arXiv.org article with LLaMaPUn
The Cornell preprint contains roughly a million scientific papers, making it a treasure trove for natural language processing (NLP) experiments.
However, a big difference from mainstream NLP corpora is the presence of mathematical formulas, citations and other language modalities specific to scientific discourse. A second, and in practice just as significant challenge is that the majority of documents are authored in LaTeX, making them very irregular for naive automated mining.
At the research group at Jacobs University we have invested a lot of work in trying to regularize the dataset and make it available for NLP research, which is a large topic in its own right. I wrote an entry-level blog post about that effort here.
In this blog post, I want to briefly introduce the newest incarnation of the NLP library for scientific documents, backed up by a running example of word tokenization on an average preprint from the dataset.
Have there been aliens? Will there be aliens?
The fact we are alive and pondering a vast Universe from spaceship Earth raises a number of fascinating questions. Astrophysicist are now asking why “here” and why “now”. What is the chance of life emerging around a star like the Sun, about 12-13 billion years after our Universe was born?
The SKV Algorithm as a Tool in Image Processing
The skv algorithm was introduced as a method of identifying onsets and offsets in a model of auditory signal processing \cite{Coath_2005} and it is also an integral part of a model of auditory feature extraction \cite{Denham_2005} \cite{Coath_2007}. It has been found to exhibit a range of desirable properties, as well as some features that make it biophysically plausible. The method has subsequently been used in a range of contexts including auditory salience detection \cite{Kovacs_2015}, beat tracking \cite{Coath_2009}, and studies of infant speech production \cite{Warlaumont_2016}.
It has also been shown that the important features of the skv response can be captured in the output of an artificial neural network \cite{Kovacs_2013}. These results demonstrate that the approach is suitable for parallel distributed programming and, possibly, other ’neuromorphic’ implementations.
The abbreviation skv when applied to auditory signals was derived from skewness over variable time, reflecting the measure of asymmetry (the skewness or third normalized moment) and the technique of varying the time window over which this value was calculated \cite{Coath_2005}. For image processing the v will stand instead for ’variable spatial frequency’, which also relates to the size of the window used.
VLASS Pilot Survey Design
and 5 collaborators
This document describes the design for the VLA Sky Survey (VLASS) Pilot Survey which will be carried out in the 27 May – 5 Sep 2016 time-frame.
Dear Social Media, Get DNA Chirality *Right*
and 1 collaborator
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