Overestimation of tumor mutational burden (TMB) using algorithms compared to germline subtraction.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 2621-2621
Author(s):  
Kaushal Parikh ◽  
Robert Huether ◽  
Kevin White ◽  
Derick Hoskinson ◽  
Haidong Dong ◽  
...  
Keyword(s):  
Germline Variation ◽  
Tumor Mutational Burden ◽  
Level 3 ◽  
Somatic Alterations ◽  
Level 1 ◽  
The Difference ◽  
Clinical Trial Results ◽  
Population Databases ◽  
Allelic Fraction ◽  
Level 2

2621 Background: TMB is an emerging predictor of survival with immunotherapy. TMB is determined by taking the difference between somatic and germline datasets when tumor-normal pairs are available. In the case of commonly utilized tumor-only sequencing, additional steps are needed to estimate the somatic alterations. Computational tools have been developed that determine germline contribution based on sample copy state, purity estimates and occurrence of the variant in population databases. Given the potential bias of population datasets, we hypothesized that tumor-only filtering approaches may overestimate the actual TMB. Methods: We assessed the TMB from 50 tumors in 10 diseases including all missense, indels, and frameshift variants with an allelic fraction (AF) ≥5% and Coverage ≥100X within the tumor. Tumor-only TMB was evaluated against the gold standard of matched germline subtracted TMB at three levels. Level 1 removed all the tumor-only variants with AF in the non-TCGA ExAC database ≥1%. Level 2 removed all variants observed in population databases simulating a naive approach of removing germline variation. Level 3 used an internal tumor-only pipeline for calculating TMB. Results: There were significantly higher estimates of TMB with Level 1, Level 2 and Level 3 tumor-only filtering approaches than that determined by germline subtraction, resulting in significant bias. Whereas there was no correlation between TMB estimates and tumor-germline TMB for Level 1 filtering, there were improvements in correlations for Level 2 and Level 3. Conclusions: The tumor-only approaches that filter variants in population databases overestimate TMB compared to that determined by germline subtraction. Despite improved correlations with more stringent filtering approaches, these falsely elevated estimates may result in the inappropriate categorization of tumor specimens and negatively impact clinical trial results and patient outcomes. [Table: see text]

scholarly journals MATHEMATICAL JUSTIFICATION OF SENIOR HIGH SCHOOL STUDENTS IN STATISTICS

MATHEdunesa ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 297-304
Author(s):  
Masyita Putri Firdausy ◽  
Abdul Haris Rosyidi
Keyword(s):  
High School ◽  
High School Students ◽  
School Students ◽  
Mathematical Concepts ◽  
Level 3 ◽  
Level 1 ◽  
The Difference ◽  
The Right ◽  
Mathematical Justification ◽  
Level 2

Justification is the process of justifying a claim that is supported with evidence. Justification is the center of mathematics. Justification plays an important role in learning because it can help students improve understanding of mathematical concepts. By using a qualitative approach, this study aims to analyze the mathematical justification of high school students in solving problems on statistical topics. This research was conducted on 122 high school students by giving justification test questions on the topic of statistics resulted in 17% (21 students) included in the level justification level 3, 16% (19 students) included in level 2, 47% (47 students) included in level 1, and 20% (25 students) the rest are included in level 0. Further analysis was carried out to see the mathematical justification process by each level. The mathematical justification process consists of three stages, 1) the process of recognition; 2) the development process (building-with), and 3) understanding (awareness) process. Level 3 and level 2 students can recognize the problem and determine the right strategy to solve the problem, level 3 and level 2 students are also able to execute the strategy and interpret the results of the calculations they have done. The difference in level 3 and level 2 students lies in the understanding the concepts they have. Level 1 students can recognize problems and determine solution strategies. Although level 1 students can recognize and do calculations well, level 1 students fail in interpreting the results of calculations performed. While students who are level 0 are not able to recognize the problem, so level 0 students do not carry out the justification process.

scholarly journals An Internet Investigation of Mental Health Status of 1144 Different Status Identities in South China during Outbreak of COVID-19

2020 ◽  
Author(s):  
Qianyi Luo ◽  
Shaomin Deng ◽  
Kai Wu ◽  
Zhiyao Wu ◽  
Weiyang Mai ◽  
...  
Keyword(s):  
Mental Health ◽  
Health Status ◽  
South China ◽  
Online Survey ◽  
Mental Health Status ◽  
Level 3 ◽  
Different Populations ◽  
Level 1 ◽  
The Difference ◽  
Level 2

Abstract Background At the end of 2019, the Coronavirus disease 2019 (COVID-19), with highly infectious, transmits rapidly. So it has caused people panic to a certain degree. Methods This cross-sectional study performed via an online survey run from January 30 to March 30, 2020. 1144 people in South China (287 of level 1 population, 121 of level 2 population, 160 of level 3 population, 576 of level 4 population ) were investigated. GAD-7 scale, PHQ-9 scale, and PSS-10 scale were used to evaluate the mental health status of different populations. Results Among 1144 subjects, the average GAD-7 score was 4(1,8), the average PHQ-9 score was 4(1,9), and the average PSS-10 score was 16(11,19). There were statistically significant differences in the scores of GAD-7 (H = 15.235, P <0.01), PHQ-9 (H = 9.265, P = 0.026), and PSS-10 (H = 8.435, P = 0.049) among different levels of population. In the score of GAD-7: The anxiety degree of the level 1 population is higher than that of the level 2 population and the level 4 population. The difference between the two pairs is statistically significant (Z = -2.932, -4.012, -2.949, P <0.005). There are significant differences in items of“becoming easily annoyed or irritable”, "seemingly terrible things will happen"(Z = -3.399 ~ -2.055, P <0.005); Score of PHQ-9: The depression degree of the level 1 population and the level 2 population is higher than that of the level 4 population, and the difference between the two pairs is statistically significant (Z = -3.38, -2.682, P <0.005). There are significant differences in items of "difficult to fall asleep or not awake", "feeling depressed" and other related items (Z = -2.885 ~ -2.003, P <0.005); Score of PSS-10: The stress degree of the level 3 population is higher than that of the level 1 population and the level 4 population (Z = -3.693 ~ -2.702, P <0.005). There are significant differences in items of "feel confident", "life are as expected", "the ability to control anger", "the things are all under control" and other related items (Z = -4.782 ~ -2.102, P <0.005). Conclusion There are differences in the effects of COVID-19 on the mental health of people with different identities. Appropriate psychological interventions should be provided for different populations in combination with their mental health status.

EVALUASI PELATIHAN DI PT. PUPUK KUJANG CIKAMPEK

2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Lania Muharsih ◽  
Ratih Saraswati
Keyword(s):  
Training Evaluation ◽  
Work Productivity ◽  
Learning Behavior ◽  
Level 3 ◽  
Level 1 ◽  
Four Levels ◽  
A Company ◽  
Level 2 ◽  
Evaluation Sheet ◽  
Assessment Factor

This study aims to determine the training evaluation at PT. Kujang Fertilizer. PT. Pupuk Kujang is a company engaged in the field of petrochemicals. Evaluation sheet of PT. Fertilizer Kujang is made based on Kirkpatrick's theory which consists of four levels of evaluation, namely reaction, learning, behavior, and results. At level 1, namely reaction, in the evaluation sheet is in accordance with the theory of Kirkpatrick, at level 2 that is learning should be held pretest and posttest but only made scale. At level 3, behavior, according to theory, but on assessment factor number 3, quantity and work productivity should not need to be included because they are included in level 4. At level 4, that is the result, here is still lacking to get a picture of the results of the training that has been carried out because only based on answers from superiors without evidence of any documents.   Keywords: Training Evaluation, Kirkpatrick Theory.    Penelitian ini bertujuan mengetahui evaluasi training di PT. Pupuk Kujang. PT. Pupuk Kujang merupakan perusahaan yang bergerak di bidang petrokimia. Lembar evaluasi PT. Pupuk Kujang dibuat berdasarkan teori Kirkpatrick yang terdiri dari empat level evaluasi, yaitu reaksi, learning, behavior, dan hasil. Pada level 1 yaitu reaksi, di lembar evaluasi tersebut sudah sesuai dengan teori dari Kirkpatrick, pada level 2 yaitu learning seharusnya diadakan pretest dan posttest namun hanya dibuatkan skala. Pada level 3 yaitu behavior, sudah sesuai teori namun pada faktor penilaian nomor 3 kuantitas dan produktivitas kerja semestinya tidak perlu dimasukkan karena sudah termasuk ke dalam level 4. Pada level 4 yaitu hasil, disini masih sangat kurang untuk mendapatkan gambaran hasil dari pelatihan yang sudah dilaksanakan karena hanya berdasarkan dari jawaban atasan tanpa bukti dokumen apapun.   Kata kunci: Evaluasi Pelatihan, Teori Kirkpatrick.

scholarly journals An Atmospheric Visibility Grading Method Based on Ensemble Learning and Stochastic Weight Average

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 869
Author(s):  
Xiuguo Zou ◽  
Jiahong Wu ◽  
Zhibin Cao ◽  
Yan Qian ◽  
Shixiu Zhang ◽  
...  
Keyword(s):  
Ensemble Learning ◽  
Traffic Accidents ◽  
Feature Sets ◽  
Atmospheric Visibility ◽  
Average Accuracy ◽  
Level 3 ◽  
Visual Characteristics ◽  
Level 1 ◽  
Grading Model ◽  
Level 2

In order to adequately characterize the visual characteristics of atmospheric visibility and overcome the disadvantages of the traditional atmospheric visibility measurement method with significant dependence on preset reference objects, high cost, and complicated steps, this paper proposed an ensemble learning method for atmospheric visibility grading based on deep neural network and stochastic weight averaging. An experiment was conducted using the scene of an expressway, and three visibility levels were set, i.e., Level 1, Level 2, and Level 3. Firstly, the EfficientNet was transferred to extract the abstract features of the images. Then, training and grading were performed on the feature sets through the SoftMax regression model. Subsequently, the feature sets were ensembled using the method of stochastic weight averaging to obtain the atmospheric visibility grading model. The obtained datasets were input into the grading model and tested. The grading model classified the results into three categories, with the grading accuracy being 95.00%, 89.45%, and 90.91%, respectively, and the average accuracy of 91.79%. The results obtained by the proposed method were compared with those obtained by the existing methods, and the proposed method showed better performance than those of other methods. This method can be used to classify the atmospheric visibility of traffic and reduce the incidence of traffic accidents caused by atmospheric visibility.

The Magical Number Two, Plus or Minus One: Some Limits on our Capacity for Processing Musical Information

2002 ◽  
Vol 6 (2) ◽  
pp. 185-219 ◽  
Author(s):  
Adam Ockelford
Keyword(s):  
Cognitive Processing ◽  
General Principle ◽  
Empirical Work ◽  
Theoretical Framework ◽  
Musical Structure ◽  
Magical Number ◽  
Level 3 ◽  
Level 1 ◽  
Level 2

Like all fields of human artistic endeavour, music is constrained by our cognitive processing requirements and limitations (Swain, 1986; Lerdahl, 1988; Huron, 2001). This articleconsiders particular forms of constraint pertaining to the relationships that the structure-seeking mind (subconsciously) fabricates between perceived musical events. It is proposed that 2±1 may be a universal limitation pertaining to the level of relationships so ideated. That is, in terms of Lewin'S (1987) theoretical framework in which “intervals” can be intuited between the “elements” of musical “spaces”, it is posited that the cognition of musical structure occurs either through intervals (level 1), through intervals between these (level 2), or — in some circumstances — through intervals between these(level 3). This proposition is explored through the psychomusicological model developed by Ockelford (1991, 1993, 1999), which too analyses musical structure in terms of the relationships that may be cognised between its discrete perceptual components. In particular, the model identifies a type of cognitive link through which events (at any level) arefelt to imply others the same or similar — through so-called “zygonic” relationships. This theory suggests a further general principle: that the highest level of relationship inoperation at any given point must be zygonic if the music is to be structurally coherent. Evidence for this, and for the limit on the level of relationships of 2±1, is offeredthrough a series of musical examples, which illustrate a variety of musical organisation in action. Finally, empirical work is suggested to explore further the theoretical ideas that arepresented here.

Systems biology markup language: Level 2 and beyond

2003 ◽  
Vol 31 (6) ◽  
pp. 1472-1473 ◽  
Author(s):  
A. Finney ◽  
M. Hucka
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Chemical Species ◽  
Biochemical Networks ◽  
Markup Language ◽  
Exchange Format ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Level 1 ◽  
Level 2

The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks. We continue developing SBML collaboratively with the modelling community to meet their evolving needs. The recently introduced SBML Level 2 includes several enhancements to the original Level 1, and features under development for SBML Level 3 include model composition, multistate chemical species and diagrams.

Knowledge Acquired from Learning: New Evidence of Hierarchical Conceptualization

1994 ◽  
Vol 79 (2) ◽  
pp. 975-993 ◽  
Author(s):  
Alberto Montare
Keyword(s):  
Sex Differences ◽  
Knowledge Acquisition ◽  
Reversal Learning ◽  
Concept Formation ◽  
Learning Task ◽  
Learning Rates ◽  
Level 3 ◽  
Level 1 ◽  
New Evidence ◽  
Level 2

Following successful inductive acquisition of procedural cognition of a discrimination-reversal learning task, 50 female and 50 male undergraduates articulated declarative cognizance of knowledge acquired from learning. Tests of four hypotheses showed that (1) increasingly higher levels of declarative cognizance were associated with faster learning rates, (2) six new cases of cognition-without-cognizance were observed, (3) students presumably using secondary signalization learned faster than those presumably using primary signalization, and (4) no sex differences in learning rates or declarative cognizance were observed. The notion that explicit levels of declarative cognizance may represent implicit hierarchical conceptualization comprised of four systems of knowledge acquisition led to the conclusions that primary signalization may account for inductive senscept formation at Level 1 and for inductive percept formation at Level 2, whereas emergent secondary signalization may account for inductive precept formation at Level 3 and for inductive concept formation at Level 4.

scholarly journals Assessing a Prototype Database for Comprehensive Global Aquatic Land Cover Mapping

2021 ◽  
Vol 13 (19) ◽  
pp. 4012
Author(s):  
Panpan Xu ◽  
Nandin-Erdene Tsendbazar ◽  
Martin Herold ◽  
Jan G. P. W. Clevers
Keyword(s):  
Land Cover ◽  
Life Form ◽  
Land Cover Mapping ◽  
Commission Errors ◽  
Multiple User ◽  
Level 3 ◽  
Level 1 ◽  
Level 2 ◽  
Global Datasets ◽  
Flooded Areas

The monitoring of Global Aquatic Land Cover (GALC) plays an essential role in protecting and restoring water-related ecosystems. Although many GALC datasets have been created before, a uniform and comprehensive GALC dataset is lacking to meet multiple user needs. This study aims to assess the effectiveness of using existing global datasets to develop a comprehensive and user-oriented GALC database and identify the gaps of current datasets in GALC mapping. Eight global datasets were reframed to construct a three-level (i.e., from general to detailed) prototype database for 2015, conforming with the United Nations Land Cover Classification System (LCCS)-based GALC characterization framework. An independent validation was done, and the overall results show some limitations of current datasets in comprehensive GALC mapping. The Level-1 map had considerable commission errors in delineating the general GALC distribution. The Level-2 maps were good at characterizing permanently flooded areas and natural aquatic types, while accuracies were poor in the mapping of temporarily flooded and waterlogged areas as well as artificial aquatic types; vegetated aquatic areas were also underestimated. The Level-3 maps were not sufficient in characterizing the detailed life form types (e.g., trees, shrubs) for aquatic land cover. However, the prototype GALC database is flexible to derive user-specific maps and has important values to aquatic ecosystem management. With the evolving earth observation opportunities, limitations in the current GALC characterization can be addressed in the future.

scholarly journals Audit Sistem Pendataan Keluarga Menggunakan Pendekatan Framework COBIT 5 Pada Domain DSS (Studi Kasus: BKKBN Propinsi Jawa Barat)

Teknika ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 78-87
Author(s):  
Angga Maulana Nurhuda ◽  
Ervan Philipus ◽  
Ivan Gunawan
Keyword(s):  
Level 3 ◽  
Level 1 ◽  
Level 2 ◽  
Capability Level

Peran sistem pendataan keluarga dalam rangka mendukung pencapaian program BANGGAKENCANA pada BKKBN Propinsi Jawa Barat adalah untuk menyediakan data dasar sebagai perencanaan strategis, peta kerja, maupun pemetaan mekanisme operasional menjadi krusial untuk menopang keberhasilan program. Untuk memastikan delivery produk, layanan, dan dukungan yang dihasilkan perlu dilakukan evaluasi sehingga dapat menghasilkan tata kelola sistem pendataan keluarga yang lebih optimal. Penelitian ini bertujuan untuk memperoleh ukuran capability level proses TI saat ini kemudian dibandingkan dengan yang diharapkan sehingga dapat diperoleh kesenjangan guna penyusunan rekomendasi yang dapat diimplementasikan pada Siklus Sistem Pendataan Keluarga Tahun 2021 dengan menggunakan kerangka kerja COBIT 5. Data yang diperoleh bersumber dari responden yang berwenang dan kompeten berdasarkan pemetaan diagram RACI pada COBIT 5. Dari hasil penelitian, diketahui bahwa dari 6 proses terpilih pada domain DSS terdapat 4 proses yang mencapai level 1 (performed) dan 2 proses yang berhasil mencapai level 2 (managed process). Tingkat kemampuan manajemen TI yang diharapkan berada pada level 3 sehingga GAP muncul di semua domain yang bermakna saat ini organisasi belum sepenuhnya mengimplementasikan proses yang ditetapkan untuk mencapai tujuan proses. Dari seluruh rangkaian penelitian tersebut dapat disimpulkan bahwa diperoleh nilai level kapabilitas sebesar 1,33 dan terdapat GAP sebesar 1,67 untuk mencapai level yang diharapkan. Dalam penelitian ini disampaikan rekomendasi untuk meningkatkan kapabilitas proses sehingga BKKBN Propinsi Jawa Barat dapat mencapai tingkat kapabilitas yang diharapkan.

scholarly journals IDENTIFIKASI KESALAHAN MATEMATIKA SISWA SMP BERDASARKAN TAHAPAN KASTOLAN

2020 ◽  
Vol 3 (1) ◽  
pp. 77-100
Author(s):  
Antonia Dwi Raharti ◽  
Tri Nova Hasti Yunianta
Keyword(s):  
High School ◽  
High School Students ◽  
Junior High School ◽  
School Students ◽  
Descriptive Research ◽  
Technical Errors ◽  
Level 3 ◽  
Qualitative Descriptive ◽  
Level 1 ◽  
Level 2

The study aims to identify kinds of high school students’ misrepresent in doing their tasks and to provide the appropriate scaffolding as a solution to help the students. This is a qualitative descriptive research. The research subject consists of three junior high school students who have different abilities in Mathematics. They were selected out of 92 students. This research studied the conceptual errors, procedural mistakes, and students’ technical mistakes in working on the problems based on the stages of Kastolan mistakes and the scaffoldings given. Furthermore, the data were collected by using the way of testing, interviewing and documenting techniques. The research data were guarantee validated with the triangulation method. The result of the research showed that there were some errors done by the students in doing the tasks. They were the conceptual errors, procedural mistakes, and technical errors. The scaffoldings given to help the students do the tasks for Level 1 (environmental provisions), Level 2 (explaining, reviewing dan restructuring), and Level 3 (developing conceptual thinking).

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