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MADX Demo: Elements
Deyan Ginev

Deyan Ginev

September 23, 2015
DEFINITION OF ELEMENTS
MADX Demo: Control
Deyan Ginev

Deyan Ginev

September 23, 2015
CONVENTIONS
PHYS321 Derivation
Larson Lovdal

Larson Lovdal

September 23, 2015
MOTIVATING THE DERIVATION In pursuit of an empirically determined value for the electron charge-to-mass e/m ratio we must guide electrons in a variable circular path using a homogeneous magnetic field. The Helmholtz configuration of two current-carrying coils with radius _R_ separated by a distance _d_ as shown in Fig. [fig1] provides the necessary field. To determine the magnetic field $}$ we will first find the magnetic field due to a single current-carrying loop using the Biot-Savart Law.
Summary of research for: “Local Radiation Hydrodynamic Simulations of Massive Star En...
Matteo Cantiello

Matteo Cantiello

September 21, 2015
This is a layman summary of “Local Radiation Hydrodynamic Simulations of Massive Star Envelopes at The Iron Opacity Peak” from Yan-Fei Jiang (姜燕飞), Matteo Cantiello , Lars Bildsten, Eliot Quataert and Omer Blaes. The full article can be downloaded from the arXiv. This layman summary is part of the Public Friendly Open Science initiative.
A Grateful Dead Analysis: The Relationship Between Concert and Listening Behavior
Alberto Pepe

Alberto Pepe

September 18, 2015
The Grateful Dead were an American band that was born out of the San Francisco, California psychedelic movement of the 1960s. The band played music together from 1965 to 1995 and is well known for concert performances containing extended improvisations and long and unique set lists. This article presents a comparative analysis between 1,590 of the Grateful Dead's concert set lists from 1972 to 1995 and 2,616,990 last.fm Grateful Dead listening events from August 2005 to October 2007. While there is a strong correlation between how songs were played in concert and how they are listened to by last.fm members, the outlying songs in this trend identify interesting aspects of the band and their fans 10 years after the band's dissolution.
Coupled Parametric Oscilators Proof of Concept in Radio Frequency
Leon Bello

Leon Bello

July 30, 2015
OVERVIEW Optical Paramteric Oscillators (OPO) oscillate at a specific frequency by means of a non-linear interaction. A pump input laser with frequency ωp is converted through the non-linear interaction into a signal and idler frequencies, such that ωp = ωi + ωs. Both frequencies can resonate in the cavity (doubly-resonant) or just one (singly-resonant).
Diffusion-Limited Aggregation
Leon Bello

Leon Bello

September 08, 2015
OVERVIEW Diffusion-Limited Aggregation (DLA) is a process whereby particles undergoing Brownian motion aggregate to form clusters of particles. “Diffusion” because the particles diffuse randomly before attaching themselves (“Aggregating”) to the structure. “Diffusion-limited” because the particles are considered to be in low concentrations so the structure grows one particle at a time. DLA can be observed in many natural phenomenon, such as the formation of snowflakes and the formation of electrically conducting regions in a dielectric breakdown. These clusters are an example of a fractal, i.e. a pattern that replicates itself in any scale.
Analysis and visualization of emerging zoonoses through temporal networks
Caitlin Rivers

Caitlin Rivers

January 16, 2014
I present case tree plots and checkerboard plots for visualizing contagions. The visualizations are best suited for diseases like SARS, MERS-CoV and H7N9 for which there are a limited (less than 200) number of cases, with data available on human to human transmission. They a) allow for easy estimation of epidemiological parameters like basic reproduction number b) indicate the frequency of introductory events, e.g. spillovers in the case of zoonoses c) represent patterns of case attributes like patient sex both by generation and over time.
The Environmental Footprints Explorer - a database for global sustainable accounting
Konstantin Stadler
Radek Lonka

Konstantin Stadler

and 4 more

March 02, 2015
Environmentally Extended Multi Regional Input Output tables and analysis (EE MRIOs) have emerged as one of the main tools to analyze resource use and environmental impacts across international supply chains. They provide insights into the life cycle impacts of the production and consumption of commodities world wide, taking into account the global supply chain of purchased commodities. Currently half a dozen EE MRIO databases are available which differ in their environmental and economic focus as well as in the level of detail. As these databases become more sophisticated, it has become increasingly difficult for the non-expert to access the most important attributes and results of basic calculations. Here we present an integrated web-platform, the Environmental Footprints Explorer (http://www.environmentalfootprints.com), designed to access indicator results calculated based on these databases. The main functionality of the web-platform include (1) exploring environmental accounts based on a single database (2) comparison between databases using a common classification system and (3) exporting analysis results visualization. The presented web-platform removes the obstacle for policy-makers and the public alike to access EE MRIO results.
Welcome to Authorea!
Enzo Grossi

Enzo Grossi

August 31, 2015
Oh, an empty article! You can get started by double clicking this text block and begin editing. You can also click the Insert button below to add new block elements. Or you can drag and drop an image right onto this text!
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Deyan Ginev

Deyan Ginev

July 29, 2015
Let’s try: testing here. Here is an attempt: testing 1 + 2 = 3 here.
The Skeleton of the Milky Way
Catherine Zucker
Alyssa Goodman

Catherine Zucker

and 2 more

June 19, 2014
Recently, argued that the very long, very thin infrared dark cloud “Nessie” lies directly in the Galactic midplane and runs along the Scutum-Centaurus arm in position-position-velocity (_p-p-v_) space as traced by lower density CO and higher density NH₃ gas. Nessie was presented as the first “bone” of the Milky Way, an extraordinarily long, thin, high-contrast filament that can be used to map our Galaxy’s ”skeleton.“ Here, we present evidence for additional bones in the Milky Way Galaxy, arguing that Nessie is not a curiosity but one of several filaments that could potentially trace Galactic structure. Our ten bone candidates are all long, filamentary, mid-infrared extinction features which lie parallel to, and no more than twenty parsecs from, the physical Galactic mid-plane. We use CO, N₂H+, HCO+ and NH₃ radial velocity data to establish the three-dimensional location of the candidates in _p-p-v_ space. Of the ten candidates, six also: have a projected aspect ratio of ≥50: 1; run along, or extremely close to, the Scutum-Centaurus arm in _p-p-v_ space; _and_ exhibit no abrupt shifts in velocity. Evidence suggests that these candidates are marking the locations of significant spiral features, with the bone called filament 5 (”BC_18.88-0.09") being a close analog to Nessie in the Northern Sky. As molecular spectral-line and extinction maps cover more of the sky at increasing resolution and sensitivity, we seek to find more bones in future studies, ultimately to create a global-fit to the Galaxy’s spiral arms by piecing together individual skeletal features.
ProCS15: A DFT-based chemical shift predictor for backbone and C\(\beta\) atoms in pr...
Jan Jensen
Lars Andersen Bratholm

Jan Jensen

and 3 more

May 17, 2015
ABSTRACT We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values below 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms respectively. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each protein. The maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.
Acronym test
Deyan Ginev

Deyan Ginev

August 19, 2015
Acronym: Again: [H₂O]water
White paper
Timea Bagosi
Koen Hindriks

Timea Bagosi

and 2 more

May 26, 2015
Hey, welcome. Double click anywhere on the text to start writing. In addition to simple text you can also add text formatted in BOLDFACE, _italic_, and yes, math too: E = mc²! Add images by drag’n’drop or click on the “Insert Figure” button. Citing other papers is easy. Voilà: or . Click on the cite button in the toolbar to search articles and cite them. Authorea also comes with a powerful commenting system. Highlight the text you want to discuss or click the comment button. Find out more about using Authorea on our help page.
Giant anterior sacral meningocele repaired through a posterior approach.
Juan Patino
Awaiting Activation

Juan Patino

and 3 more

January 13, 2015
Anterior sacral meningoceles are rare forms of spinal dysraphism produced by herniation of the thecal sac through a bone defect in the anterior sacral wall. The patients may remain asymptomatic or present with nonspecific symptoms such as long-term constipation, urinary dysfunction, lower back pain, or perineal hypoalgesia These lesions are difficult to diagnose without a strong suspicion due to the multiple range of nonspecific symptoms such as low lumbar pain, obstetric problems, and bowel and bladder difficulties. Special care should be taken in order to avoid erroneous diagnoses that may expose the patient to unnecessary surgical procedures. Because these lesions usually do not regress spontaneously, surgical treatment is mandatory for symptomatic or growing masses. The dural defect can be repaired with a variety of anterior transabdominal or posterior transsacral approaches. We present the case of a 82-year-old female patient with a giant anterior sacral meningocele that was initially confused with various entities such as inguinal hernia and an ovarian cyst. Once the anterior sacral meningocele was conffirmed through a MRI-scan she was successfully treated using a posterior transsacral approach. We present a brief review of the current literature and discuss the surgical treatment options. _KEYWORDS:_ _Anterior sacral meningocele, posterior approach, abdominal pain._
Nara Desert, Pakistan
Rahmatullah

Rahmatullah

August 10, 2015
Hey, welcome. Double click anywhere on the text to start writing. In addition to simple text you can also add text formatted in BOLDFACE, _italic_, and yes, math too: E = mc²! Add images by drag’n’drop or click on the “Insert Figure” button.
A Moral Imperative: Open Science in the Ebola Crisis
Jace Harker
Alberto Pepe

Jace Harker

and 3 more

August 08, 2015
Last June, a dedicated global team of Ebola researchers began an ambitious project to track the virus using large-scale genome sequencing. Their research, published June 18 in _Cell_, reveals critical information about how the virus traveled and spread over seven months of the recent Ebola outbreak. The team, which included researchers from over a dozen institutions, made a conscious decision to pursue Open Science practices for this project. One choice they made was to write their paper on Authorea, a new science editing and publishing website. The full working version of the paper is now available to the public on Authorea. By using the “History” feature, readers can get a behind-the-scenes look at how the research came together, including every edit and change from the writing process. “When we were kicking off the study, we discussed how much we would open up what we’re doing,” said co-lead author Danny Park. “Our team comes out of the Human Genome Project, so culturally we come from the open science ’put everything out there’ background. And especially in this kind of emergency situation there’s a moral imperative” to publish the data openly and quickly, he said. The team chose Authorea in order to make the writing process transparent. Authorea’s History feature allows the public to view every change made during the writing process. Because key technical sentences were revised and words chosen carefully over time, the evolution of the document can be educational, said Dr. Park. Authorea was just one of many tools used by the research team to publish their work as quickly and openly as possible. The team: - Published their raw genome data to the GenBank database and Virological.org online forum as soon as it was collected, so that other research teams could use and discuss the data immediately - Released demographic and clinical metadata on a special website to enable other researchers to spot important trends - Set up a new website to gather and visualize data from multiple research groups - Published a Comment in Nature strongly advocating open sharing of data during this and future outbreaks - Chose Authorea as a platform to write and edit their draft manuscript, allowing readers to view the writing process with full transparency - Published their article as fully Open Access in _Cell_ “One of the most rewarding aspects of working in this outbreak response is the connections we have made with so many extraordinary individuals through open data sharing”, said senior author Pardis Sabeti. The goal of Open Science principles is to produce stronger, more reproducible, transparent scientific results as quickly as possible. It’s a virtuous circle: openness begets collaboration begets more openness. And in a serious outbreak like the recent Ebola epidemic, more open research can quite literally save lives. ABOUT AUTHOREA: Authorea is an online word processor that makes research writing and publishing faster and easier. Created by scientists, for scientists, Authorea encourages and supports Open Science, transparency, and collaboration. With over 41000 users and a weekly growth rate that has doubled in the past nine months, Authorea is currently the fastest-growing science publishing platform in the world. OTHER RESOURCES _AUTHOREA CONTACTS_ - Alberto Pepe, co-founder and CEO, Authorea: alberto@authorea.com, +1 (310) 600-3929 - Jace Harker, Growth and Community: jace@authorea.com, +1 585-737-6459 - Tanya Anderson, Outreach: tanya@authorea.com _KEY AUTHOR CONTACTS_ - Danny Park: dpark@broadinstitute.org
(*Out of date*) On the Fluxes and Rates of Fast Radio Bursts
Casey Law

Casey Law

June 26, 2014
INTRODUCTION The “fast radio burst” (FRB) is a new class of transient found in a variety of single-dish pulsar surveys . FRBs are identified by their large dispersion measure (DM), which has been observed as high as 1100 pc cm−3, an order of magnitude larger than expected from the Galaxy. The simplest explanation for this large DM is that the bursts are dispersed by the intergalactic medium (IGM), implying that they originate at distances up to z∼1. If FRBs are cosmological, then they could be used to probe the intergalactic medium and study processes for their formation \citep[e.g., double neutron star mergers][]{2013PASJ...65L..12T}. However, terrestrial phenomena known as perytons have been discovered at the same telescopes finding FRBs . Perytons are impulsive radio transients with a width of tens of ms and an apparent DM of a few hundred, partially overlapping with characteristics expected of extragalactic radio transients. suggest that perytons and FRBs are the same, terrestrial process seen in different optical regimes of the telescopes. It will be critical to distinguish these populations to be certain that FRBs are are astrophyiscal. One way to understand their nature is to build statistical tests... Euclidean distribution... Rate constraint for future observing campaigns... We are in the midst of a large survey with the Karl G. Jansky Very Large Array (VLA) to detect an FRB \citep[results in][]{law2014a}. The nondetection in that survey inspired us to reanalyze published rates in an attempt to make a reliable prediction for FRB rates for any given survey. Here, we present our estimate of the apparent flux distribution of FRBs to determine if they are consistent with an astrophysical population. We then use a Bayesian technique to estimate the FRB rate for a given telescope flux limit.
The Linked Paleo Data framework: a common tongue for paleoclimatology
Nick McKay
Julien Emile-Geay

Nick McKay

and 1 more

February 20, 2015
A document by Nick McKay, written on Authorea.
Transferability Study of Video Tracking Optimization for Traffic Data Collection and...
Philip Morse
Paul St-Aubin

Philip Morse

and 3 more

May 28, 2015
Despite the extensive studies on the performance of video sensors and computer vision algorithms, calibration of these systems is usually done by trial and error using small datasets and incomplete metrics such as brute detection rates. There is a widespread lack of systematic calibration of tracking parameters in the literature. This study proposes an improvement in automatic traffic data collection through the optimization of tracking parameters using a genetic algorithm by comparing tracked road user trajectories to manually annotated ground truth data with Multiple Object Tracking Accuracy and Multiple Object Tracking Precision as primary measures of performance. The optimization procedure is first performed on training data and then validated by applying the resulting parameters on non-training data. A number of problematic tracking and visibility conditions are tested using five different camera views selected based on differences in weather conditions, camera resolution, camera angle, tracking distance, and camera site properties. The transferability of the optimized parameters is verified by evaluating the performance of the optimization across these data samples. Results indicate that there are significant improvements to be made in the parametrization. Winter weather conditions require a specialized and distinct set of parameters to reach an acceptable level of performance, while higher resolution cameras have a lower sensitivity to the optimization process and perform well with most sets of parameters. Average spot speeds are found to be insensitive to MOTA while traffic counts are strongly affected.
Informe Final SIN IMAGENES Química de Superficies y Coloides Licenciatura en Química...
Juan Allegretto
Aldo

Juan Allegretto

and 3 more

July 12, 2015
INTRODUCCIÓN El presente informe, resume los distintos trabajos experimentales realizados durante el curso de Quimica de Superficies y Coloides, de la Licenciatura en Quimica, de la Facultad de Ciencias Exactas, UNLP. En la asignatura, se nos consignó reproducir algunos trabajos publicados en el Journal of Chemical Education[1], a fin de abordar un tópico de actualidad científica y cercano, a su vez, al trabajo de grado. Una vez seleccionados los trabajos, se debió planificar qué técnicas se iban a aplicar a cada sistema, en función de sus características. Es sabido que no todo trabajo publicado es perfectamente reproducible: Las condiciones y/o variables que afectan a un sistema no siempre son perfectamente conocidas o identificadas, debido a que ciertos tópicos no pueden abundar en los detalles de experiencias ya descriptos en otros trabajos, o se omiten por causas varias. Esto, sin lugar a dudas, creó la incertidumbre que motivó la búsqueda bibliográfica complementaria y constituyó gran parte del interés (posteriormente desarrollado) en la comprensión del sistema de estudio. [1] http://pubs.acs.org/journal/jceda8
Design of a Silicon based Mach-Zehnder Interferometer and Two-stage optical filter...
German Vargas

German Vargas

July 18, 2015
INTRODUCTION This design proposal is about the study of an optical device known as the Mach-Zehnder interferometer (MZI) via simulation and to verify its operation experimentally. The device will be fabricated using Silicon over Insulator (SOI) technology. These types of interferometers are commonly employed in telecommunications applications such as switches, modulators and filters. Also, in sensing applications, MZI’s are commonly employed to allow one of the arms of a interferometer to interact with an analyte via a waveguide’s evanescent field. In this draft design, two devices were chosen. The first is a simple MZI with different path length differences ΔL. An explanation of a MZI operation is thus presented. The second device is a basic filter based on two cascaded interferometers. Also, the basic theory of a lossless two stage MZI filter is presented. Here in this report simulations in terms of optical component and circuit device are shown, which later on will be compared with experimental results after device fabrication.
Object Localization by Smart Floors
Jakub Hvizdos

Jakub Hvizdos

July 14, 2015
The abstract goes here. Smartfloor and intelligent space.
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