scholarly journals Parliament2: Fast Structural Variant Calling Using Optimized Combinations of Callers

2018 ◽  
Author(s):  
Samantha Zarate ◽  
Andrew Carroll ◽  
Olga Krashenina ◽  
Fritz J Sedlazeck ◽  
Goo Jun ◽  
...  
Keyword(s):  
Variant Calling ◽  
Structural Variant ◽  
New Methods ◽  
Local Environments ◽  
Resource Requirements ◽  
The Individual

AbstractHere we present Parliament2 – a structural variant caller which combines multiple best-in-class structural variant callers to create a highly accurate callset. This captures more events than the individual callers achieve independently. Parliament2 uses a call-overlap-genotype approach that is highly extensible to new methods and presents users the choice to run some or all of Breakdancer, Breakseq, CNVnator, Delly, Lumpy, and Manta to run. Parliament2 applies an additional parallelization framework to speed certain callers and executes these in parallel, taking advantage of the different resource requirements to complete structural variant calling much faster than running the programs individually. Parliament2 is available as a Docker container, which pre-installs all required dependencies. This allows users to run any caller with easy installation and execution. This Docker container can easily be deployed in cloud or local environments and is available as an app on DNAnexus.

scholarly journals Analyzing Low-Level mtDNA Heteroplasmy—Pitfalls and Challenges from Bench to Benchmarking

2021 ◽  
Vol 22 (2) ◽  
pp. 935
Author(s):  
Federica Fazzini ◽  
Liane Fendt ◽  
Sebastian Schönherr ◽  
Lukas Forer ◽  
Bernd Schöpf ◽  
...  
Keyword(s):  
Variant Calling ◽  
Illumina Miseq ◽  
Bioinformatic Analysis ◽  
Low Level ◽  
Sequencing Technologies ◽  
Laboratory Setup ◽  
Dna Mixture ◽  
The Individual ◽  
Highly Sensitive Detection ◽  
Sensitivity Specificity

Massive parallel sequencing technologies are promising a highly sensitive detection of low-level mutations, especially in mitochondrial DNA (mtDNA) studies. However, processes from DNA extraction and library construction to bioinformatic analysis include several varying tasks. Further, there is no validated recommendation for the comprehensive procedure. In this study, we examined potential pitfalls on the sequencing results based on two-person mtDNA mixtures. Therefore, we compared three DNA polymerases, six different variant callers in five mixtures between 50% and 0.5% variant allele frequencies generated with two different amplification protocols. In total, 48 samples were sequenced on Illumina MiSeq. Low-level variant calling at the 1% variant level and below was performed by comparing trimming and PCR duplicate removal as well as six different variant callers. The results indicate that sensitivity, specificity, and precision highly depend on the investigated polymerase but also vary based on the analysis tools. Our data highlight the advantage of prior standardization and validation of the individual laboratory setup with a DNA mixture model. Finally, we provide an artificial heteroplasmy benchmark dataset that can help improve somatic variant callers or pipelines, which may be of great interest for research related to cancer and aging.

The Use of Jigs in Aeroplane Manufacture

1918 ◽  
Vol 22 (86) ◽  
pp. 39-48
Author(s):  
R. Borlase Matthews
Keyword(s):  
Metal Working ◽  
High Class ◽  
New Methods ◽  
The Individual ◽  
Building Operation ◽  
New Industry

A new industry calls for new methods—autrea jours, autres mceurs—and the aeroplane industry is therefore not exceptional in demanding many departures from recognised woodworking practice. In the first place the number of machines required to–day is so large that their construction should be described as a manufacturing rather than a building operation. That is to say, they should preferably be almost entirely put together by the aid of accurate machinery instead of being dependent to such an extent upon the skill of the individual workman, in trying and fitting one part to another until the whole is built up. In this connection it may be remarked that the design of the metal fittings for aeroplanes is not such as to call for any radical departure from previous high class small metal working practice. It is the woodworking side of the business which presents the new scope for initiative. It is this latter aspect, therefore, which will be considered here.

scholarly journals Can the Optical Fluctuations of 3C 273 be Random?

1972 ◽  
Vol 44 ◽  
pp. 179-187
Author(s):  
James Terrell ◽  
Kenneth H. Olsen
Keyword(s):  
Power Spectrum ◽  
Spectrum Analysis ◽  
Periodic Variation ◽  
Power Spectrum Analysis ◽  
Effective Length ◽  
New Methods ◽  
The Individual ◽  
Random Fluctuations ◽  
Optical Brightness ◽  
Computer Generation

The fluctuations in optical brightness of the quasi-stellar object 3C 273 have been investigated to determine whether the suggested periodicity of ∼ 10 yr is supported by the observational data extending over 80 yr. New methods of obtaining information from the power spectrum have been used, and moments and trends have also been investigated. No statistically-supportable evidence has been found in the power spectrum for such a non-random variation. The moments and trends are consistent with random fluctuations. If the observed fluctuations are of shot-noise character, due to random outbursts of light, the individual pulses must occur at the rate of 15 ± 5 per year and have an average effective length of 3.2 ± 1 yr. These conclusions were verified by computer-generation and power-spectrum analysis of such random signals. Thus any periodic variation in the brightness of 3C 273, if present, is completely obscured by random fluctuations. The power spectrum, moments, and trend are all consistent with random but long-lasting outbursts of light.

scholarly journals Control of THz Surface Plasmons by Geometric Phases

2021 ◽  
Vol 8 ◽  
Author(s):  
Shulin Hu ◽  
Peng Wang ◽  
Cai Zhou ◽  
Min Hu ◽  
Yuli Xiong ◽  
...  
Keyword(s):  
Surface Plasmons ◽  
Photonic Devices ◽  
Geometric Phases ◽  
New Methods ◽  
Wide Range ◽  
On Chip ◽  
The Individual ◽  
Meta Atom ◽  
Topological Charges ◽  
Tunable Emission

Surface plasmons (SPs) are expected to have a wide range of applications in many fields, so they have recently attracted much attention. However, most of the previous studies achieved the manipulation of SPs through designing the structure of the individual meta-atom. When developing the next generation of integrated photonic devices and components, it is essential to seek out new methods of software control, which enable more diverse modulation and higher efficiency. Here, the tunable emission of SPs with metasurfaces is systematically studied. SPs are a source of on-chip plasmonic vortices (PVs). To verify the controllability of the directional excitation of SPs, we designed beam deflectors with different angles of surface waves (SWs). Furthermore, PVs with different topological charges were generated by arranging spatially varied microslits. The proposed control strategy provides a common platform for various promising applications, such as on-chip generation of the propagation control of SPs and PVs.

scholarly journals Research troikas: a plan for fostering psychiatric research in a region

1992 ◽  
Vol 16 (10) ◽  
pp. 605-607 ◽  
Author(s):  
Andrew Sims
Keyword(s):  
Medical Profession ◽  
Clinical Care ◽  
Alternative Therapies ◽  
Practitioner Research ◽  
Psychiatric Research ◽  
Treatment Service ◽  
New Methods ◽  
Brain Dead ◽  
The Individual ◽  
Methods Of Treatment

Without research psychiatry is brain dead! Perhaps the most significant discriminator between medical practice and the ‘alternative therapies’ is the responsibility, often honoured, of the medical profession to evaluate and hence vindicate its treatment methods. For the individual practitioner, research helps to maintain the highest standards of involvement in clinical care. In psychiatry many new methods of treatment and innovatory types of treatment service have been introduced over recent years. Their continued and extended use should not be justified by the zeal of their advocates but by demonstration of their efficacy.

Dyadic Designs in Lifespan Developmental Methodology

2019 ◽  
Author(s):  
Jeremy B. Yorgason ◽  
Melanie S. Hill ◽  
Mallory Millett
Keyword(s):  
Repeated Measures ◽  
Structural Equation ◽  
Equation Modeling ◽  
Daily Diaries ◽  
Intensive Longitudinal Data ◽  
New Methods ◽  
Actor Partner Interdependence Model ◽  
Parents And Children ◽  
Research Questions ◽  
The Individual

The study of development across the lifespan has traditionally focused on the individual. However, dyadic designs within lifespan developmental methodology allow researchers to better understand individuals in a larger context that includes various familial relationships (husbands and wives, parents and children, and caregivers and patients). Dyadic designs involve data that are not independent, and thus outcome measures from dyad members need to be modeled as correlated. Typically, non-independent outcomes are appropriately modeled using multilevel or structural equation modeling approaches. Many dyadic researchers use the actor-partner interdependence model as a basic analysis framework, while new and exciting approaches are coming forth in the literature. Dyadic designs can be extended and applied in various ways, including with intensive longitudinal data (e.g., daily diaries), grid sequence analysis, repeated measures actor/partner interdependence models, and vector field diagrams. As researchers continue to use and expand upon dyadic designs, new methods for addressing dyadic research questions will be developed.

Information Quantitative Analysis on Psychological Research

2014 ◽  
Vol 610 ◽  
pp. 680-685
Author(s):  
Cong Jing Ren ◽  
Yang Liu
Keyword(s):  
Quantitative Analysis ◽  
Power Analysis ◽  
Statistical Power ◽  
Information Science ◽  
Psychological Research ◽  
Statistical Manual ◽  
Diagnostic And Statistical Manual ◽  
New Methods ◽  
Fast Development ◽  
The Individual

With the fast development of the theories and techniques in information science in recent years, a variety of new methods have been used to help scholars in other fields manage the corresponding knowledge. This paper applied the research methods of information science to psychology to analyze the literature in psychology cited by ISI Web of Knowledge, then got a better understanding of psychology science. In order to understand the dynamics of psychology science, we conducted a quantitative analysis based on 8137 articles cited by SCI or SSCI, and used CiteSpace II to visualize the trends and patterns in the scientific literatures. In the end, the authors drew the following conclusions: (1) among all the individual authors, Cohen J and Seligman MEP share the highest citation times; (2) publications like Positive Psychology - An Introduction, Diagnostic and Statistical Manual of Mental Disorders (DSM), Statistical Power Analysis for the Behavioral Sciences have ranked first in the cited papers; (3) community psychology, clinical psychology, behavior, personality, model, self-are the hot areas and the frontier fields in psychology research.

Bringing Back the Person into Behavioural Personality Science Using Big Data

2020 ◽  
Vol 34 (5) ◽  
pp. 670-686
Author(s):  
Karl–Heinz Renner ◽  
Stephanie Klee ◽  
Timo von Oertzen
Keyword(s):  
Big Data ◽  
Literature Review ◽  
New Technologies ◽  
Research Topics ◽  
Personality Psychology ◽  
Individual Person ◽  
New Methods ◽  
Data Collection And Analysis ◽  
History Of ◽  
The Individual

Behaviour and the individual person are important but widely neglected topics of personality psychology. We argue that new technologies to collect and new methods to analyse Big (Behavioural) Data have the potential to bring back both more behaviour and the individual person into personality science. The call for studying the individual person in the history of personality science, the related idiographic/nomothetic divide, as well as attempts to reconcile these two approaches are briefly reviewed. Furthermore, different meanings of the term idiographic and some unique selling points that emphasize the importance of idiographic research are highlighted. A nonexhaustive literature review shows that a wealth of behaviours are considered in extant personality studies using such Big Data but only in a nomothetic way. Against this background, we demonstrate the potential of Big Data collection and analysis with regard to four idiographic research topics: (i) unique manifestations of common traits and the resurgence of personal dispositions, (ii) idiographic prediction, (iii) intraindividual consistency versus variability of behaviour and (iv) intraindividual personality trait change through intervention. Methodological, ethical and legal pitfalls of doing Big Data research with individual persons as well as potential countermeasures are considered.

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