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A Dataset and an Approach for Identity Resolution of 38 Million Author IDs extracted from 2B Git Commits [article]

Tanner Fry, Tapajit Dey, Andrey Karnauch, Audris Mockus
2020 pre-print
We processed around 38 million author IDs and found around 14.8 million IDs to have an alias, which belong to 5.4 million different developers, with the median number of aliases being 2 per developer.  ...  In this paper, we propose a method that finds all author IDs belonging to a single developer in this entire dataset, and share the list of all author IDs that were found to have aliases.  ...  For the purpose of this analysis, we only use a single list of author IDs extracted from almost 2B commits in WoC.  ... 
doi:10.1145/3379597.3387500 arXiv:2003.08349v1 fatcat:26hxqjri6vh55nufuv2vidxcqa

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves higher resolution for research and breeding [article]

Jean-Marc Aury, Stefan Engelen, Benjamin Istace, Cécile Monat, Pauline Lasserre-Zuber, Caroline Belser, Corinne Cruaud, Hélène Rimbert, Philippe Leroy, Sandrine Arribat, Isabelle Dufau, Arnaud Bellec (+7 others)
2021 bioRxiv   pre-print
We provide the most contiguous and complete chromosome-scale assembly of a bread wheat genome to date, a resource that will be valuable for the crop community and will facilitate the rapid selection of  ...  AbstractThe sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years due to its large size (15.5 Gb), repeat content, and hexaploidy.  ...  We designed a dataset of 5.76 million ISBPs from CS assembly which represent 1 ISBP every 2.5 kb.  ... 
doi:10.1101/2021.08.24.457458 fatcat:yeinie63n5bitjp72i37r2ilku

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation [article]

Wai Y Low, Rick Tearle, Cynthia Liu, Sergey Koren, Arang Rhie, Derek M Bickhart, Benjamin D Rosen, Zev N Kroneberg, Sarah B Kingan, Elizabeth Tseng, Francoise Thibaud-Nissen, Fergal J Martin (+10 others)
2019 bioRxiv   pre-print
The high-quality genomes of economically important Angus and Brahman breeds were produced from an F1 cross using the trio binning approach and enabled us to identify structural and copy number variants  ...  About 4000 years ago, humans interbred indicine and taurine subspecies of cattle, most likely to cope with a multi-century drought.  ...  The input dataset for these analyses came from ~10x WGS short reads of 38 animals representing seven cattle breeds.  ... 
doi:10.1101/720797 fatcat:uyeemmxkdrhjflo66n3ty6nuta

Effective Data Versioning for Collaborative Data Analytics

Silu Huang
2020 Proceedings of the 2020 ACM SIGMOD International Conference on Management of Data  
Specifically, we build a system, OrpheusDB, on top of a relational database with a carefully designed data representation and an intelligent partitioning algorithm for fast version control operations.  ...  With the massive proliferation of datasets in a variety of sectors, data science teams in these sectors spend vast amounts of time collaboratively constructing, curating, and analyzing these datasets.  ...  In case of Git, we add and commit the files in the repository and then run a git repack -a -d --depth=50 --window=50 on the repository 2 .  ... 
doi:10.1145/3318464.3394027 dblp:conf/sigmod/Huang20 fatcat:cmqanfq5fvdbrjwdlo6dyq7uzy

Quantification of 3D spatial correlations between state variables and distances to the grain boundary network in full-field crystal plasticity spectral method simulations

Markus Tobias Kühbach, Franz Roters
2020 Modelling and Simulation in Materials Science and Engineering  
The individual strengths and limitations of these methods surplus the efficiency of their parallel implementation is assessed with an exemplary DAMASK large scale crystal plasticity study.  ...  This work contributes to the development of advanced such post-processing routines. Specifically, two grain reconstruction and three distancing methods are developed for solving above challenge.  ...  Acknowledgements The authors gratefully acknowledge the funding received from the German Research Foundation through project RO 2342/8-1.  ... 
doi:10.1088/1361-651x/ab7f8c fatcat:pxiigvzh7rflxmvcxsnbt7nuoq

AFQ-Browser: Supporting reproducible human neuroscience research through browser-based visualization tools [article]

Jason D. Yeatman, Adam Richie-Halford, Josh K. Smith, Anisha Keshavan, Ariel Rokem
2017 bioRxiv   pre-print
In an era where Big Data is playing an increasingly prominent role in scientific discovery, so will browser-based tools for exploring high-dimensional datasets, communicating scientific discoveries, sharing  ...  While scientists are generally aware that data sharing is an important component of reproducible research, it is not always clear how to usefully share data in a manner that allows other labs to understand  ...  Finally, we would like to thank the authors that contributed the public datasets discussed in this manuscript: Sarica A., Cerasa A., Valentino P., Trotta M., Barone S., Granata A., Nisticò R., Perrotta  ... 
doi:10.1101/182402 fatcat:ujpczwis3jewpolqnj5cnyxb2a

Deciphering TP53 mutant Cancer Evolution with Single-Cell Multi-Omics [article]

Alba Rodriguez-Meira, Ruggiero Norfo, Wei Xiong Wen, Agathe L. Chédeville, Haseeb Rahman, Jennifer O'Sullivan, Guanlin Wang, Eleni Louka, Warren W. Kretzschmar, Aimee Paterson, Charlotte Brierley, Jean-Edouard Martin (+16 others)
2022 bioRxiv   pre-print
Here, we carry out allelic resolution single-cell multi-omic analysis of haematopoietic stem/progenitor cells (HSPC) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary  ...  Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukaemia, and are of broader relevance to other cancer types.  ...  This collectively requires single-cell approaches which combine molecular and phenotypic analysis of HSPCs with allelic-resolution mutation detection, an approach recently enabled by the TARGET-seq technology  ... 
doi:10.1101/2022.03.28.485984 fatcat:xxwaqeegtzbs3cti7lmgnmufha

Prime+Probe 1, JavaScript 0: Overcoming Browser-based Side-Channel Defenses [article]

Anatoly Shusterman, Ayush Agarwal, Sioli O'Connell, Daniel Genkin, Yossi Oren, Yuval Yarom
2021 arXiv   pre-print
A common approach for countermeasures is to disable or restrict JavaScript features deemed essential for carrying out attacks.  ...  To assess the effectiveness of this approach, in this work we seek to identify those JavaScript features which are essential for carrying out a cache-based attack.  ...  The authors thank Jamil Shusterman for his assistance in bringing up the measurement setup.  ... 
arXiv:2103.04952v1 fatcat:gmfmfyfew5aunkv7zwmiisfw7m

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees [article]

Briana E Mittleman, Sebastian Pott, Shane Warland, Kenneth Barr, Claudia Cuevas, Yoav Gilad
2020 bioRxiv   pre-print
To begin addressing this gap, we studied APA in lymphoblastoid cell lines from six humans and six chimpanzees, and estimated usage for 44,432 polyadenylation sites (PAS) in 9,518 genes in both species.  ...  In particular, differences in APA between humans and chimpanzees can explain a subset of observed inter-species protein expression differences that do not display corresponding differences at the transcript  ...  Gonzales for comments on the manuscript. We thank Y. Li, M. Ward, and G. Housman for useful discussion.  ... 
doi:10.1101/2020.08.27.270686 fatcat:5v5xvgji6zgw3iban2z4rcnfwq

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Kristoffer Sahlin, Botond Sipos, Phillip L. James, Paul Medvedev
2021 Nature Communications  
We are able to obtain a median accuracy of 98.9–99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.  ...  When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis  ...  We want to thank Botond Sipos for several substantially helpful discussions regarding data analysis, and Philip L James for producing the biological sequencing data.  ... 
doi:10.1038/s41467-020-20340-8 pmid:33397972 fatcat:2zeglpw2kneuzdhhge5dtlnzkm

PARTHENOS D2.1 Report on User Requirements

Sebastian Drude, Sara Di Giorgio, Paola Ronzino, Petra Links, Annelies van Nispen, Karolien Verbrugge, Emiliano Degl'Innocenti, Jenny Oltersdorf, Juliane Stiller, Claus Spiecker
2016 Zenodo  
It contains a comprehensive report based on a review of literature produced by previous relevant projects, supplemented with additional direct input from PARTHENOS partners.  ...  This document is the final, updated, version of deliverable D2.1 of the PARTHENOS project, which addresses user requirements and needs.  ...  Could include or just be an ID-number.  ... 
doi:10.5281/zenodo.2204560 fatcat:imvwnzcalzeqvetrpgrnkegjqq

CARS 2016—Computer Assisted Radiology and Surgery Proceedings of the 30th International Congress and Exhibition Heidelberg, Germany, June 21–25, 2016

2016 International Journal of Computer Assisted Radiology and Surgery  
'', and Amazon Inc., for providing valuable computing resources through an ''AWS in Education Research'' grant.  ...  Acknowledgments The authors wish to thank Fundación CEIBA and Alcaldía Mayor de Bogotá, for the financial support of Ricardo Mendoza's PhD studies through the scholarship program ''Becas Rodolfo Llinás  ...  For 3D model-based approaches, however, building the 3D shape model from a training data set of segmented instances of an object is a major challenge and currently remains an open problem.  ... 
doi:10.1007/s11548-016-1412-5 pmid:27206418 fatcat:uk5r46n2xvhedkfjzmeiweyneq

Money and Trust in Metaverses, Bitcoin and Stablecoins in global social XR [article]

John Joseph O'Hare, Allen Fairchild, Umran Ali
2022 arXiv   pre-print
Bitcoin is selected as the best contender for value transfer in metaverses because of it's free and open source nature, and network effect. Challenges and risks of this approach are identified.  ...  A high level overview of Web3 technologies leads to a description of blockchain, and the Bitcoin network is specifically selected for detailed examination.  ...  So, the VM will have the following Network Devices: commit save Inspiration for the above was taken from: https://bertvv.github.io/cheat-sheets/VyOS.html @todo: hardening, IDS, IPS Install and configure  ... 
arXiv:2207.09460v2 fatcat:l2zcoloatvhvzmta4cw52ggdju

Towards an open digital audio workstation for live performance [article]

Smilen Dimitrov
2015 Ph.d.-serien for Det Teknisk-Naturvidenskabelige Fakultet, Aalborg Universitet  
Towards an open digital audio workstation for live performance: the development of an open soundcard. Aalborg Universitetsforlag. Ph.d.  ...  PDF, also known as Version of record Link to publication from Aalborg University Citation for published version (APA): Dimitrov, S. (2015).  ...  The authors would like to thank the Medialogy department at Aalborg University in Copenhagen, for the support of this work as a part of a currently ongoing PhD project.  ... 
doi:10.5278/vbn.phd.engsci.00028 fatcat:5ox6vssazjgrdghqboopj6c6vq

Studies in Analytical Reproducibility: the Conquaire Project

Philipp Cimiano, Christian Pietsch, Cord Wiljes
2020
The book concludes with recommendations and lessons learned from the practical attempt to reproduce a number of published results.  ...  This book is a direct result of the Conquaire (Continuous Quality Control for Research Data to Ensure Reproducibility) project, which was funded by the DFG between 2016 and 2019.  ...  the support of Lukas Biermann and Fabian Herrmann for helping with implementation of the scripts and data analysis.  ... 
doi:10.4119/unibi/2942780 fatcat:7ttrcrd4ajgdhi6kyigw7iabkq
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