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RNF: a general framework to evaluate NGS read mappers

Karel Břinda, Valentina Boeva, Gregory Kucherov
2015 Bioinformatics  
team http://ga4gh.org/#/fileformats-team Read Naming Format • Evaluation tools had to be explicitly compatible with a used read simulatorCuReSim_eval, DwgSim_eval, Seq-Suite, WgSim_eval, … Formats for NGS  ... 
doi:10.1093/bioinformatics/btv524 pmid:26353839 pmcid:PMC4681991 fatcat:hqbyw2reh5cofnda6lc2mfcz6a

Inference with viral quasispecies diversity indices: clonal and NGS approaches

Josep Gregori, Miquel Salicrú, Esteban Domingo, Alex Sanchez, Juan I. Esteban, Francisco Rodríguez-Frías, Josep Quer
2014 Computer applications in the biosciences : CABIOS  
We propose solutions specific to each of the two sampling methods -CCSS and NGS -to guarantee statistically conforming conclusions as free of bias as possible.  ...  in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and Next Generation Sequencing (NGS  ...  Both the noise level and the confidence level may be modified as required. 0.5% and 90% are just given as examples, which fit our requirements on HCV NS3 samples, according to previous experience (Gregori  ... 
doi:10.1093/bioinformatics/btt768 pmid:24389655 fatcat:arpntvvm65cvxopkq3kulvr7va

Epidemic Exposure Notification with Smartwatch: A Proximity-Based Privacy-Preserving Approach [article]

Pai Chet Ng, Petros Spachos, Stefano Gregori, Konstantinos Plataniotis
2020 arXiv   pre-print
Businesses planning for the post-pandemic world are looking for innovative ways to protect the health and welfare of their employees and customers. Wireless technologies can play a key role in assisting contact tracing to quickly halt a local infection outbreak and prevent further spread. In this work, we present a wearable proximity and exposure notification solution based on a smartwatch that also promotes safe physical distancing in business, hospitality, or recreational facilities. Our
more » ... mity-based privacy-preserving contact tracing (P^3CT) leverages the Bluetooth Low Energy (BLE) technology for reliable proximity sensing, and an ambient signature protocol for preserving identity. Proximity sensing exploits the received signal strength (RSS) to detect the user's interaction and thus classifying them into low- or high-risk with respect to a patient diagnosed with an infectious disease. More precisely, a user is notified of their exposure based on their interactions, in terms of distance and time, with a patient. Our privacy-preserving protocol uses the ambient signatures to ensure that users' identities be anonymized. We demonstrate the feasibility of our proposed solution through extensive experimentation.
arXiv:2007.04399v1 fatcat:jl4uczqq75gqrpefgss5xhmh6y

Ultra fast tissue staining with chemical tags [article]

Johannes Kohl, Julian Ng, Sebastian Cachero, Michael-John Dolan, Ben Sutcliffe, Daniel Krüger, Shahar Frechter, Gregory SXE Jefferis
2014 bioRxiv   pre-print
Genetically encoded fluorescent proteins and immunostainings are widely used to detect cellular or sub-cellular structures in thick biological samples. However, each approach suffers from limitations, including low signal and limited spectral flexibility or slow speed, poor penetration and high background, respectively. Here we overcome these limitations by using transgenically expressed chemical tags for rapid, even and low-background labeling of thick biological tissues. We construct a
more » ... m of widely applicable transgenic Drosophila reporter lines, demonstrating that chemical labeling can accelerate staining of whole-mount fly brains by a factor of 100x. Together, this tag-based approach drastically improves the speed and specificity of labeling genetically marked cells in intact and/or thick biological samples.
doi:10.1101/005298 fatcat:allctydsmzbvhfrul5c7rfsyzy

Personal Devices for Contact Tracing: Smartphones and Wearables to Fight Covid-19 [article]

Pai Chet Ng, Petros Spachos, Stefano Gregori, Konstantinos Plataniotis
2021 arXiv   pre-print
We have made our collected dataset publicly available at https://github. com/pc-ng/rss HumanHuman. B.  ...  The final training and testing data for both sets are shared openly in https://github.com/pc-ng/rss smartwatch. C.  ... 
arXiv:2108.02008v1 fatcat:uvnucysq2jc5lltimjmzhhrvjy

Second Generation Drosophila Chemical Tags: Sensitivity, Versatility and Speed [article]

Ben Sutcliffe, Julian Ng, Thomas O. Auer, Mathias Pasche, Richard Benton, Gregory S. X. E. Jefferis, Sebastian Cachero
2016 bioRxiv   pre-print
Labeling and visualizing cells and sub-cellular structures within thick tissues, whole organs and even intact animals is key to studying biological processes. This is particularly true for studies of neural circuits where neurons form sub-micron synapses but have arbors that may span millimeters in length. Traditionally labeling is achieved by immunofluorescence; however diffusion of antibody molecules (>100 kDa) is slow and often results in uneven labeling with very poor penetration into the
more » ... ntre of thick specimens; these limitations can be partially addressed by extending staining protocols to over a week (Drosophila brain) and months (mice). Recently we developed an alternative approach using genetically encoded chemical tags CLIP, SNAP, Halo and TMP for tissue labeling; this resulted in >100 fold increase in labeling speed in both mice and Drosophila, at the expense of a considerable drop in absolute sensitivity when compared to optimized immunofluorescence staining. We now present a second generation of UAS and LexA responsive CLIP, SNAP and Halo chemical labeling reagents for flies. These multimerized tags with translational enhancers have up to 64 fold increase in sensitivity over first generation reagents. In addition we developed a suite of conditional reporters (4xSNAP tag and CLIP-SNAP-Halo) that are activated by the DNA recombinase Bxb1. Our new reporters can be used with weak and strong GAL4 and LexA drivers and enable stochastic, intersectional and multicolor Brainbow labeling. These improvements in sensitivity and experimental versatility, while still retaining the substantial speed advantage that is a signature of chemical labeling, should significantly increase the scope of this technology.
doi:10.1101/095398 fatcat:bbhkmfe5urfxjpu3s6wwroyxni

59.1: Invited Paper: A Display Simulation Toolbox

Joyce Farrell, Gregory Ng, Kevin Larson, Brian Wandell
2008 SID Symposium Digest of Technical Papers  
The Display Simulation Toolbox (DST) is an integrated suite of software tools that help the user characterize the key properties of display devices and predict the radiance of displayed images. Assuming that pixel emissions are independent, the DST uses the sub-pixel point spread functions, spectral power distributions, and gamma curves to calculate display image radiance. For LCD displays, the assumption of pixel independence assumption is reasonably accurate. For CRT displays it is not.
doi:10.1889/1.3069818 fatcat:2g436cnuazezblk5kmhe2e6adq

Major Thrombotic Event Despite Anticoagulation in a Patient With COVID-19

Basma Ataallah, Aman Sharma, Sharmiz Tamanna, Joseph Ng, Gregory Haggerty
2020 Cureus  
During the course of his ICU stay, an elevated D-dimer level was observed at more than 5,000 ng/mL.  ... 
doi:10.7759/cureus.8896 pmid:32742863 pmcid:PMC7389143 fatcat:h6wpglfwxfei3h37nwq563zlee

Enabling Intuitive Human-Robot Teaming Using Augmented Reality and Gesture Control [article]

Jason M. Gregory, Christopher Reardon, Kevin Lee, Geoffrey White, Ki Ng, Caitlyn Sims
2019 arXiv   pre-print
Human-robot teaming offers great potential because of the opportunities to combine strengths of heterogeneous agents. However, one of the critical challenges in realizing an effective human-robot team is efficient information exchange - both from the human to the robot as well as from the robot to the human. In this work, we present and analyze an augmented reality-enabled, gesture-based system that supports intuitive human-robot teaming through improved information exchange. Our proposed
more » ... requires no external instrumentation aside from human-wearable devices and shows promise of real-world applicability for service-oriented missions. Additionally, we present preliminary results from a pilot study with human participants, and highlight lessons learned and open research questions that may help direct future development, fielding, and experimentation of autonomous HRI systems.
arXiv:1909.06415v1 fatcat:qqxezeqflrfnxcnu3pc6452lve

A fast solution to NGS library preparation with low nanogram DNA input

Pingfang Liu, Gregory JS Lohman, Eric Cantor, Bradley W Langhorst, Erbay Yigit, Lynne M Apone, Daniela B Munafo, Christine Sumner, Fiona J Stewart, Thomas C Evans, Nicole M Nichols, Eileen T Dimalanta (+1 others)
2012 BMC Proceedings  
This method enables library construction from an amount of DNA as low as 5 ng, and can be used for both intact and fragmented DNA. Moreover, the workflow is compatible with multiple NGS platforms.  ...  By delivering massive DNA sequences at unprecedented speed and cost, NGS promises to make personalized medicine a reality in the foreseeable future.  ...  This method enables library construction from an amount of DNA as low as 5 ng, and can be used for both intact and fragmented DNA. Moreover, the workflow is compatible with multiple NGS platforms.  ... 
doi:10.1186/1753-6561-6-s6-p26 pmcid:PMC3467472 fatcat:evjt2adivbdf5amf7ltu6qbqvm

Unbound Form of Tomato Inhibitor-II Reveals Interdomain Flexibility and Conformational Variability in the Reactive Site Loops

Isabelle H. Barrette-Ng, Kenneth K.-S. Ng, Maia M. Cherney, Gregory Pearce, Usman Ghani, Clarence A. Ryan, Michael N. G. James
2003 Journal of Biological Chemistry  
The Potato II (Pot II) family of proteinase inhibitors plays important roles in the constitutive and inducible defense of plants against predation by a wide range of pests. The structural basis of inhibition by a multidomain Pot II family inhibitor was revealed recently by the structure of the ternary complex between the twoheaded tomato inhibitor-II (TI-II) and two molecules of subtilisin Carlsberg. Here we report the 2.15-Å resolution crystal structure of the unbound form of TI-II that
more » ... significant conformational flexibility in the absence of bound proteinase molecules. The four independent copies of unbound TI-II in the asymmetric unit of the unit cell display a range of different conformations when compared with the bound form of the inhibitor, most strikingly in the orientations of the inhibitory domains and in the conformations of the reactive site loops. One of the two linker segments (residues 74 to 79) between the two domains as well as the adjacent ␤-strand in Domain I (residues 80 -85) is well ordered in all four copies of the unbound inhibitor, even though this region appeared to be disordered in the structure of the ternary complex. Conformational flexibility seen in the reactive site loops of unbound TI-II suggests a mechanism by which the inhibitor can balance the need for tight binding with the need for broad inhibitory function.
doi:10.1074/jbc.m304562200 pmid:12788916 fatcat:haukx7j7ynh3xklsndneklqe4m

Purulent pericarditis and mediastinal abscess in a young infant

Khuen Foong Ng, Ashanti Sham Bala Krishnan, Gregory J Skinner, Premkumar Christian Bakia Sundaram
2020 BMJ Case Reports  
Figure 2 2 Second chest X-ray showed widened mediastinum, globular heart, right chest wall swelling and right pleural effusion.2 Ng KF, et al. BMJ Case Rep 2020;13:e237315. doi:10.1136/bcr-2020-237315  ...  ORCID iD Khuen Foong Ng http:// orcid. org/ 0000-0002-8767-3974  ... 
doi:10.1136/bcr-2020-237315 pmid:32843391 fatcat:rpx2vwedujgplgpwxggavk5ijm

Global Health Training in US Graduate Psychiatric Education

Alexander C. Tsai, Gregory L. Fricchione, Rochelle P. Walensky, Courtney Ng, David R. Bangsberg, Vanessa B. Kerry
2014 Academic Psychiatry  
Objective-Global health training opportunities have figured prominently into medical students' residency program choices across a range of clinical specialties. To date, however, the national scope of global mental health education has not heretofore been systematically assessed. We therefore sought to characterize the distribution of global health training opportunities in U.S. graduate psychiatric education. Methods-We examined the web pages of all U.S. psychiatry residency training programs,
more » ... along with search results from a systematic Google query designed to identify global health training opportunities. Results-Of the 183 accredited U.S. psychiatry residency programs, we identified 17 programs (9.3%) offering 28 global health training opportunities in 64 countries. Ten psychiatry residency programs offered their residents opportunities to participate in one or more elective-based rotations, eight offered research activities, and six offered extended field-based training. Most global health training opportunities occurred within the context of externally administered, institution-wide initiatives generally available to residents from a range of clinical specialties, rather than within internally administered departmental initiatives specifically tailored for psychiatry residents. Conclusions-There are relatively few global health training opportunities in U.S. graduate psychiatric education. These activities have a clear role in enhancing mastery of Accreditation Council for Graduate Medical Education core competencies, but important challenges related to program funding and evaluation remain. Keywords International; Public Health; Cross-Cultural Psychiatry; World Health -psychiatry residents U.S. medical trainees have increasingly expressed interest in global health programs at all levels of training, ranging from university pre-medical education (1) to undergraduate (2) and graduate (3, 4) medical education. Global health training opportunities have figured prominently into medical students' residency program choices in such varied disciplines as emergency medicine (5) , family medicine (6), internal medicine (7, 8), and pediatrics (9).
doi:10.1007/s40596-014-0092-0 pmid:24664609 pmcid:PMC4111765 fatcat:rcrzjrfee5a2fptgg55uo4cava

Digital correction of lens aberrations in light field photography

Ren Ng, Pat Hanrahan, G. Groot Gregory, Joseph M. Howard, R. John Koshel
2007 International Optical Design Conference 2006  
More details about the prototype camera are available in Ng [5] . This kind of a camera is sometimes called a plenoptic camera [8] , and it is based on integral photography techniques [9, 10] .  ... 
doi:10.1117/12.692290 fatcat:halb5bl3q5ek5fl775kjrox6fm

Structural Basis of Inhibition Revealed by a 1:2 Complex of the Two-headed Tomato Inhibitor-II and Subtilisin Carlsberg

Isabelle H. Barrette-Ng, Kenneth K.-S. Ng, Maia M. Cherney, Gregory Pearce, Clarence A. Ryan, Michael N. G. James
2003 Journal of Biological Chemistry  
Barrette-Ng and M. N. G. James, unpublished observations. FIG. 4 . 4 Conformations of the reactive site loops. A, stereoscopic view of a superposition of the reactive site loops of both domains.  ... 
doi:10.1074/jbc.m302020200 pmid:12684499 fatcat:kyosyih62bb3dh3e3wmenl6q4y
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