scholarly journals The time substructure of jets and boosted object tagging

2021 ◽  
Author(s):  
Matthew Klimek
Keyword(s):  
Standard Model ◽  
Velocity Distribution ◽  
Time Scale ◽  
False Positive ◽  
Charged Hadron ◽  
Next Generation ◽  
Arrival Times ◽  
Hadronization Process ◽  
Jet Energy ◽  
Object Tagging

Abstract We propose the study of the time substructure of jets, motivated by the fact that the next generation of detectors at particle colliders will resolve the time scale over which jet constituents arrive. This effect is directly related to the fragmentation and hadronization process, which transforms partons into massive hadrons with a distribution of velocities. We review the basic predictions for the velocity distribution of jet hadrons, and suggest an application for this information in the context of boosted object tagging. By noting that the velocity distribution is determined by the properties of the color string which ends on the parton that initiates the jet, we observe that jets originating from boosted color singlets, such as Standard Model electroweak bosons, will exhibit velocity distributions that are boosted relative to QCD jets of similar jet energy. We find that by performing a simple cut on the corresponding distribution of charged hadron arrival times at the detector, we can discriminate against QCD jets that would otherwise give a false positive under a traditional spatial substructure based boosted object tagger.

scholarly journals Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers

2020 ◽  
Vol 5 (4) ◽  
pp. 2473011420S0002
Author(s):  
Yoonjung Choi ◽  
Irvin Oh
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Bacterial Genome ◽  
Rrna Gene ◽  
Next Generation ◽  
Antibiotic Resistant ◽  
Streptococcus Species ◽  
Resistant Genes ◽  
Standard Culture ◽  
Generation Sequencing

Category: Other Introduction/Purpose: Foot infections are often polymicrobial with diverse microbiomes. Accurate identification of the main pathogen in diabetic foot ulcer (DFU) remain challenging due to contamination or negative cultures often leading to ineffective post-surgical antibiotic treatment. Application of molecular diagnostics, such as next generation sequencing (NGS) has been explored as an alternative to standard culture in orthopaedic infections. NGS is highly sensitive and detects an entire bacterial genome along with pharmacologic resistant genes in a given sample. We sought to investigate the potential use of NGS for accurate diagnosis and quantification of various species in infected DFU. We hypothesize that NGS will provide a more accurate means of diagnosing and profiling microorganisms in infected DFU compared to the standard culture method. Methods: We investigated 30 infected DFU patients who underwent surgical treatment by a single academic orthopaedic surgeon from October 2018 to September 2019. The average age of the patient was 60.4 (range 33-82) years-old. Surgical procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Quantitative PCR was performed to determine the bacterial burden present in the sample. DNA was amplified by PCR from a highly conserved region of the rRNA gene in the bacteria (16S rRNA). Once a high level of DNA was generated and determined, it was compared against NIH GenBank database. Concordance between the standard culture and NGS was assessed. Results: In 28 of 29 patients, pathogens were identified by both NGS and culture, with complete consistency of organisms in 13 cases (concordance rate: 43.3%). NGS provided relative quantitative measures and the presence of antibiotic resistant genes for each pathogen. In NGS, Anaerococcus species (79.3%) was the most common organism, followed by Streptococcus species (44.8%), Prevotella species (44.8%), Finegoldia magna (44.8%). In culture, S. aureus (58.6%) was the most common, followed by Streptococcus species (34.5%), coagulase-negative Staphylococci (24.1%), Corynebacterium species (20.7%). On average, NGS revealed 5.1 (1-11) number of pathogens, whereas standard culture revealed 2.6 (1-6) pathogens in a given sample. NGS identified 2 cases with false positive standard culture and detected antibiotic resistant organisms in 15 specimens. Conclusion: NGS is an emerging method of microbial identification in orthopedic infection. It is particularly helpful in profiling diverse microbes in polymicrobial infected DFU. It can identify major pathogens and may correct false positive or false negative culture. NGS may allow a faster invitation of postoperative targeted antibiotic therapy. [Table: see text]

scholarly journals Magnetic Field Decay, or Just Period-Dependent Beaming?

2004 ◽  
Vol 218 ◽  
pp. 41-44 ◽  
Author(s):  
Joeri van Leeuwen ◽  
Frank Verbunt
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Velocity Distribution ◽  
Neutron Stars ◽  
Time Scale ◽  
Radio Pulsar ◽  
New Born ◽  
Field Decay ◽  
The Magnetic Field

Several recent papers conclude that radio-pulsar magnetic fields decay on a time-scale of 10 Myr, apparently contradicting earlier results. We have implemented the methods of these papers in our code and show that this preference for rapid field decay is caused by the assumption that the beaming fraction does not depend on the period. When we do include this dependence, we find that the observed pulsar properties are reproduced best when the modeled field does not decay. When we assume that magnetic fields of new-born neutron stars are from a distribution sufficiently wide to explain magnetars, the magnetic field and period distributions we predict for radio are pulsars wider than observed. Finally we find that the observed velocities overestimate the intrinsic velocity distribution.

scholarly journals Optical Timing of the Crab Nebula Pulsar NP 0532

1971 ◽  
Vol 46 ◽  
pp. 151-151
Author(s):  
Jerry Nelson ◽  
Richard Hills ◽  
David Cudaback ◽  
Joseph Wampler
Keyword(s):  
Time Scale ◽  
Crab Nebula ◽  
Rate Of Change ◽  
Arrival Times ◽  
Average Value ◽  
Mean Shape ◽  
The Mean ◽  
The Difference ◽  
The Crab Nebula ◽  
Pulse Arrival

Accurate pulse arrival times have been measured for NP 0532 during the period 15 December 1969 to 3 May 1970, and have been fitted to simple models of the pulsar braking mechanism. A good fit could not be obtained to all the data at once, because of deviations on a time scale of several days. However it was possible to divide the observing period into four shorter intervals in such a way that the data within each deviated only slightly from smoothly varying functions. The difference in the parameters of these four functions may indicate sudden events in the pulsar producing changes of order of 1 part in 109 in the pulsar frequency and 4 parts in 105 in the rate of change of frequency. In each case the difference in frequency from one interval to the next implies a slowdown of the pulsar.We found that the average value of the ‘braking parameter’ n in the equation dE/dt = -Aωn was 3.63, but dividing the data into shorter intervals gave values between 0 and 5. We found no changes in the mean shape of the pulses, or the phase of the interpulse relative to the main pulse.

Detection of false positive mutations in BRCA gene by next generation sequencing

2016 ◽  
Vol 16 (3) ◽  
pp. 311-317 ◽  
Author(s):  
Moushumi Suryavanshi ◽  
Dushyant Kumar ◽  
Manoj Kumar Panigrahi ◽  
Meenakshi Chowdhary ◽  
Anurag Mehta
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Next Generation ◽  
Brca Gene ◽  
Generation Sequencing

scholarly journals Learnings From Precision Clinical Trial Matching for Oncology Patients Who Received NGS Testing

2021 ◽  
pp. 231-238
Author(s):  
Neha M. Jain ◽  
Alison Culley ◽  
Christine M. Micheel ◽  
Travis J. Osterman ◽  
Mia A. Levy
Keyword(s):  
Clinical Trial ◽  
Next Generation Sequencing ◽  
False Positive ◽  
False Positives ◽  
Genomic Profile ◽  
Next Generation ◽  
Oncology Patients ◽  
Initial Trial ◽  
Individual Trial ◽  
Generation Sequencing

PURPOSE Tumor next-generation sequencing reports typically generate trial recommendations for patients based on their diagnosis and genomic profile. However, these require additional refinement and prescreening, which can add to physician burden. We wanted to use human prescreening efforts to efficiently refine these trial options and also elucidate the high-value parameters that have a major impact on efficient trial matching. METHODS Clinical trial recommendations were generated based on diagnosis and biomarker criteria using an informatics platform and were further refined by manual prescreening. The refined results were then compared with the initial trial recommendations and the reasons for false-positive matches were evaluated. RESULTS Manual prescreening significantly reduced the number of false positives from the informatics generated trial recommendations, as expected. We found that trial-specific criteria, especially recruiting status for individual trial arms, were a high value parameter and led to the largest number of automated false-positive matches. CONCLUSION Reflex clinical trial matching approaches that refine trial recommendations based on the clinical details as well as trial-specific criteria have the potential to help alleviate physician burden for selecting the most appropriate trial for their patient. Investing in publicly available resources that capture the recruiting status of a trial at the cohort or arm level would, therefore, allow us to make meaningful contributions to increase the clinical trial enrollments by eliminating false positives.

scholarly journals Next-generation sequencing indicates false-positive MRD results and better predicts prognosis after SCT in patients with childhood ALL

2017 ◽  
Vol 52 (7) ◽  
pp. 962-968 ◽  
Author(s):  
M Kotrova ◽  
V H J van der Velden ◽  
J J M van Dongen ◽  
R Formankova ◽  
P Sedlacek ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Next Generation ◽  
Childhood All ◽  
Generation Sequencing

A novel approach to improve detection of somatic DNA variants in solid tumors by next-generation sequencing from FFPE samples.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e22177-e22177 ◽  
Author(s):  
Nitin Udar ◽  
Robert Haigis ◽  
Thomas Gros ◽  
Agda Karina Lucio-Eterovic ◽  
Qingxiu Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Deep Sequencing ◽  
False Positive ◽  
Limit Of Detection ◽  
Low Frequency ◽  
Sample Type ◽  
Next Generation ◽  
Novel Approach ◽  
Ffpe Samples ◽  
Generation Sequencing

e22177 Background: Low frequency variant detection by sequencing is a highly desired goal for therapy selection in cancer especially the detection of actionable targets. The lower limit of detection using Sanger sequening is ~20% minor allele frequency (MAF). Deep sequencing of target genes using next generation sequencing (NGS) is gaining popularity. Formalin Fixed Paraffin Embedded (FFPE) tissue is the most common sample type in solid tumor histopathology. However, because the fixation process fragments DNA and damages it at varying frequencies, downstream processes can potentially misclassify modified bases and generate artifacts. We have developed a protocol that addresses both of these issues in a multiplex assay that involves deep sequencing using NGS of targets implicated in lung, gastric, colon, melanoma and ovarian cancers. Methods: The sample set includes 168 FFPE samples and 82 non FFPE samples. TruSeq Custom Amplicon technology was used to generate libraries for targets across 26 genes. Deep sequencing was done on a NGS platform (Illumina-MiSeq). Results: The DNA quality test, which surveys multiple genomic targets by qPCR, was an accurate determinant of DNA amplifiability and yielded a 99% sample success rate. A sensitivity of <5% MAF was achieved by sequencing at a depth of 1,000X for all targets. In order to differentiate true low frequency variants from fixation and other artifacts, our novel approach investigates each of the two DNA strands independently. The information is bioinformatically combined to distinguish true variants from artifacts. Testing of the FFPE samples with a 5% MAF cut off using the two strand approach reduced the potential false positive rate by ~ 40% when compared to information from only one strand of DNA. A comparative analysis of matched FF and FFPE sample showed that a high percentage of false positive calls were present even in the fresh frozen samples at this high level of sensitivity, if only using information from one strand. Conclusions: This protocol, efficiently and accurately detect low frequency variants by NGS in DNA extracted from FFPE tissues.

scholarly journals rmvPFBAM: Removing Primers from BAM Files Based on Amplicon-Based Next-Generation Sequencing and Cloud Computing When Analyzing Personal Genome Data

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Yanjun Ma
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Large Scale ◽  
Genomic Data ◽  
Next Generation Sequencing Data ◽  
Personal Genome ◽  
Next Generation ◽  
Sequencing Data ◽  
Personal Genomic ◽  
Generation Sequencing

Personal genomic data constitute one important part of personal health data. However, due to the large amount of personal genomic data obtained by the next-generation sequencing technology, special tools are needed to analyze these data. In this article, we will explore a tool analyzing cloud-based large-scale genome sequencing data. Analyzing and identifying genomic variations from amplicon-based next-generation sequencing data are necessary for the clinical diagnosis and treatment of cancer patients. When processing the amplicon-based next-generation sequencing data, one essential step is removing primer sequences from the reads to avoid detecting false-positive mutations introduced by nonspecific primer binding and primer extension reactions. At present, the removing primer tools usually discard primer sequences from the FASTQ file instead of BAM file, but this method could cause some downstream analysis problems. Only one tool (BAMClipper) removes primer sequences from BAM files, but it only modified the CIGAR value of the BAM file, and false-positive mutations falling in the primer region could still be detected based on its processed BAM file. So, we developed one cutting primer tool (rmvPFBAM) removing primer sequences from the BAM file, and the mutations detected based on the processed BAM file by rmvPFBAM are highly credible. Besides that, rmvPFBAM runs faster than other tools, such as cutPrimers and BAMClipper.

scholarly journals Psychology and Law, Meet Open Science

2021 ◽  
Author(s):  
Bradley David McAuliff ◽  
Melanie B. Fessinger ◽  
Anthony Perillo ◽  
Jennifer Torkildson Perillo
Keyword(s):  
Open Access ◽  
False Positive ◽  
Psychological Research ◽  
Open Science ◽  
Open Access Publishing ◽  
Next Generation ◽  
Research Practices ◽  
Questionable Research Practices ◽  
Psychology And Law ◽  
Open Materials

As the field of psychology and law begins to embrace more transparent and accessible science, many questions arise about what open science actually is and how to do it. In this chapter, we contextualize this reform by examining fundamental concerns about psychological research—irreproducibility and replication failures, false-positive errors, and questionable research practices—that threaten its validity and credibility. Next, we turn to psychology’s response by reviewing the concept of open science and explaining how to implement specific practices—preregistration, registered reports, open materials/data/code, and open access publishing—designed to make research more transparent and accessible. We conclude by weighing the implications of open science for the field of psychology and law, specifically with respect to how we conduct and evaluate research, as well as how we train the next generation of psychological scientists and share scientific findings in applied settings.

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