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Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

William L Trimble, Kevin P Keegan, Mark D'Souza, Andreas Wilke, Jared Wilkening, Jack Gilbert, Folker Meyer
2012 BMC Bioinformatics  
Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations  ...  For error-containing short reads, FragGeneScan finds more prokaryotic coding regions than does MetaGeneAnnotator, MetaGeneMark, Orphelia, or Prodigal.  ...  Conclusions When annotating individual reads, sequencing errors cause a loss of predicted coding regions, leading to loss of signal.  ... 
doi:10.1186/1471-2105-13-183 pmid:22839106 pmcid:PMC3526449 fatcat:ya5j75lmsfd33ptoxcrmwdgoea

Not all phonological awareness deficits are created equal: evidence from a comparison between children with Otitis Media and poor readers

Julia M. Carroll, Helen L. Breadmore
2017 Developmental Science  
ACKNOWLEDGEMENTS We would like to thank all of the children, parents, teachers and research assistants involved in the research.  ...  Nonverbal IQ was not a significant covariate for Reading Comprehension (F(1, 55) = 0.08, p = .78, η 2 < .01), but it was a significant predictor of for Spelling (F(1, 59) = 2.12, p = .15, η 2 = .04).  ...  A "very mild" hearing loss would not normally be regarded as clinically significant. The patterns of parent responses and hearing profiles of the children are shown in .  ... 
doi:10.1111/desc.12588 pmid:28880490 pmcid:PMC5947145 fatcat:3kmyj6aqt5cxnbmnc3pp6afohm

Chapter Three Equalities [chapter]

2016 Everyday Women's and Gender Studies  
In addition to exploring each concept in detail, each chapter includes up to five short recently published readings that illuminate an aspect of that concept.  ...  The authors have done something remarkable in creating Everyday Women's and Gender Studies.  ...  , and two on her car; her husband has three flags on his van. equality does not mean total equality; it only means that some of us are more equal than others!  ... 
doi:10.4324/9781315643205-10 fatcat:ikiniciqyfcc5oaslgu2ouwsru

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development

Hong Zhang, Shengqian Dou, Feng He, Junjie Luo, Liping Wei, Jian Lu, Xuemei Chen
2018 PLoS Biology  
Upstream open reading frames (uORFs) play important roles in regulating the main coding DNA sequences (CDSs) via translational repression.  ...  Moreover, mutations that destroy existing uORFs or create new ones are known to cause human disease. Although PLOS Biology | https://doi.org/10.1371/journal.pbio.  ...  Jianrong Yang, Xuerui Yang, Cheng Li, Jianzhi Zhang, and Allen Zhu for constructive comments on this manuscript and the Biodynamic Optical Imaging Center from Peking University for providing sequencing  ... 
doi:10.1371/journal.pbio.2003903 pmid:30028832 pmcid:PMC6070289 fatcat:7hguxvqi6bgdtomtt4rfkgs2pe

Calibration of image persistence in HgCdTe photodiodes

Roger M. Smith, Maximilian Zavodny, Gustavo Rahmer, Marco Bonati, David A. Dorn, Andrew D. Holland
2008 High Energy, Optical, and Infrared Detectors for Astronomy III  
We describe the suppression of persistence by signal in the current frame and begin to examine the superposition of the decay curves from multiple stimuli.  ...  For several Teledyne 1.7 µm cutoff HgCdTe detectors tested, persistence is linear over most of the normal signal range.  ...  Fig. 17 shows that the suppression is about 90% complete for signals of equal intensity in the current and previous frames.  ... 
doi:10.1117/12.789619 fatcat:rdbsmaflzrdgvfk2uoctkydmga

Low bit-rate speech coders for multimedia communication

R.V. Cox, P. Kroon
1996 IEEE Communications Magazine  
Its frame size of 30 ms and one-way algorithmic codec delay o f 37.5 ms allow for a further reduction in bit rate compared to the 6.729 coder.  ...  Annex A of Rec. G.729 is a reduced-complexity version of the CS-ACELP coder.  ...  What happens when there are channel errors during transmission? These errors could be individual bit errors or the loss of entire frames. Are the errors detected or undetected?  ... 
doi:10.1109/35.556484 fatcat:ha2gxhkvazgkvi2rqlbqxzptfa

Time-domain coding of (near) toll quality speech at rates below 16 KB/S

Peter Kroon
1985 Signal Processing  
Each sequence of 40 candidate excitation samples is scaled in such a way that the energy of the excitation sequence is equal to the energy of the prediction error after both short and long delay prediction  ...  Figure 2 . 9 . 29 Cascade of short-time predictor and long-time predictor. The parameters {ft,} and M are chosen to minimize the mean squared error E'.  ...  How ever, if the position of the right-most pulse is, say, equal to 40, then locating the 7th pulse at position 70 would create a second critical distance.  ... 
doi:10.1016/0165-1684(85)90136-7 fatcat:cdh3wpjqpncy5k7hbx77dflyuu

Fully automated assessment of the severity of Parkinson's disease from speech

Alireza Bayestehtashk, Meysam Asgari, Izhak Shafran, James McNames
2015 Computer Speech and Language  
Our results show that the severity of the disease can be inferred from speech with a mean absolute error of about 5.5, explaining 61% of the variance and consistently well-above chance across all clinics  ...  More recent studies have adopted a machine learning approach where a large number of potential features are extracted and the models are learned automatically from the data.  ...  Diadokinetic and reading tasks are better predictors and the combination of all three tasks gives the best results.  ... 
doi:10.1016/j.csl.2013.12.001 pmid:25382935 pmcid:PMC4222054 fatcat:rd74rse6cnfyrajojqm6qlsbca

lncRNA-MFDL: identification of human long non-coding RNAs by fusing multiple features and using deep learning

Xiao-Nan Fan, Shao-Wu Zhang
2015 Molecular Biosystems  
By fusing multiple features and using deep learning algorithms, a lncRNA-MFDL predictor was developed to identify lncRNAs, which is much more effective and robust.  ...  reading frames (ORFs) and are less homologous with protein-coding genes 13 .  ...  However, they are not suitable for identifying long noncoding RNAs (lncRNAs), 45 because lncRNAs may contain long putative ORFs or short protein-like sub-sequences 14, 15 .  ... 
doi:10.1039/c4mb00650j pmid:25588719 fatcat:cfwssdwe2nac7hx2ufcnyrgr2a

Introduction to Digital Speech Processing

Lawrence R. Rabiner, Ronald W. Schafer
2007 Foundations and Trends® in Signal Processing  
The breadth of this subject does not allow us to discuss any aspect of speech processing to great depth; hence our goal is to provide a useful introduction to the wide range of important concepts that  ...  We present a comprehensive overview of digital speech processing that ranges from the basic nature of the speech signal, through a variety of methods of representing speech in digital form, to applications  ...  Of course, we are responsible for any weaknesses or inaccuracies that remain in this text.  ... 
doi:10.1561/2000000001 fatcat:j3eqhs7rvbb6noom4lqwury2xq

Cross-Domain Adaptation of Spoken Language Identification for Related Languages: The Curious Case of Slavic Languages

Badr M. Abdullah, Tania Avgustinova, Bernd Möbius, Dietrich Klakow
2020 Interspeech 2020  
State-of-the-art spoken language identification (LID) systems, which are based on end-to-end deep neural networks, have shown remarkable success not only in discriminating between distant languages but  ...  In this paper, we present a set of experiments to investigate the impact of domain mismatch on the performance of neural LID systems for a subset of six Slavic languages across two domains (read speech  ...  We observe that balanced accuracy scores highly correlate with equal error rate (EER) and average cost (Cavg), which we do not report for the sake of conciseness.  ... 
doi:10.21437/interspeech.2020-2930 dblp:conf/interspeech/AbdullahAMK20 fatcat:f4kmope3qnhzfovn5qx65q7cly

Cross-Domain Adaptation of Spoken Language Identification for Related Languages: The Curious Case of Slavic Languages [article]

Badr M. Abdullah, Tania Avgustinova, Bernd Möbius, Dietrich Klakow
2020 arXiv   pre-print
State-of-the-art spoken language identification (LID) systems, which are based on end-to-end deep neural networks, have shown remarkable success not only in discriminating between distant languages but  ...  In this paper, we present a set of experiments to investigate the impact of domain mismatch on the performance of neural LID systems for a subset of six Slavic languages across two domains (read speech  ...  We observe that balanced accuracy scores highly correlate with equal error rate (EER) and average cost (Cavg), which we do not report for the sake of conciseness.  ... 
arXiv:2008.00545v2 fatcat:fjr6ntv3vzgrva2fevoqzkpuxi

Proteogenomics to discover the full coding content of genomes: A computational perspective

Natalie Castellana, Vineet Bafna
2010 Journal of Proteomics  
Examples include confirmation of translation, reading-frame determination, identification of gene and exon boundaries, evidence for post-translational processing, identification of splice-forms including  ...  While there are many different techniques for separating peptides, ionizing fragments, and mass analysis, all producing different results, we consider an end product of this process: the tandem mass spectrum  ...  Coding signals, based on hexamer compositions, are not sufficient to determine frame in short exons [16] , and sometimes cause annotators to miss the exon completely.  ... 
doi:10.1016/j.jprot.2010.06.007 pmid:20620248 pmcid:PMC2949459 fatcat:qsi4iul35razxhepwkybg4dj3e

Predicting Mean Ribosome Load for 5'UTR of any length using Deep Learning [article]

Alexander Karollus, Ziga Avsec, Julien Gagneur
2020 bioRxiv   pre-print
However, this model is restricted to sequence lengths investigated in the reporter assay and therefore cannot be applied to the majority of human sequences without a substantial loss of information.  ...  Here, we introduced frame pooling, a novel neural network operation that enabled the development of an MRL prediction model for 5'UTRs of any length.  ...  Despite not having position-specific weights, the frame pooling model captures almost as much signal as Optimus on the short MPRA sequences.  ... 
doi:10.1101/2020.06.15.152728 fatcat:2ehb2b23pratnjtbdsx6qgadx4

Speckle Noise Detection and Removal for Laser Speech Measurement Systems

Yahui Wang, Wenxi Zhang, Zhou Wu, Xinxin Kong, Hongxin Zhang
2021 Applied Sciences  
This makes it possible to detect the position of noise through a combination of the average short-time energy and kurtosis.  ...  The method not only precisely locates small clicks (with a duration of just a few samples), but also finds the location of longer bursts and scratches (with a duration of up to a hundred samples).  ...  Informed Consent Statement: Not applicable. Data Availability Statement: Not applicable. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/app11219870 fatcat:wv3o54a2kvbbjlh5groerlnuna
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