bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB-187: Enhanced mapping of N6-methyladenosine (m6A) RNA modification sites with m6A-eCLIP
Authors: Rabano Ines , Shishkin Alexander A. , Shen Kylie , Foster Heather M. , Chu Peter , Van Nostrand Eric L. , Yeo Gene W. 
Published: September 2020

Abstract
N6-methyladenosine (m6A) is the most prevalent epitranscriptomic RNA modification found in eukaryotes and has been shown to regulate many stages of RNA biology including splicing, secondary/tertiary structure, localization, stability, and translation. Adenosine modifications are actively added, recognized, and removed by a series of “writer”, “reader”, and “eraser” proteins, making m6A a dynamic and reversible system for regulating RNAs. Further, there are now clear links between m6A writer, reader, and eraser proteins as well as m6A state of specific mRNAs to cancer pathogenesis, indicating that both global and specific dysregulation of m6A can have targeted effects that lead to disease. Thus, there is a need for methods to robustly profile m6A-modification states in both cell lines as well as tissues, and in normal as well as diseased or modified states. Advancements in high-throughput sequencing have led to the development of methods to map m6A transcriptome-wide, but there remains a need for improved methods that are scalable across conditions and treatments and with low abundance samples, such as blood or patient tissue. To address this need, we adapted enhanced crosslinking and immunoprecipitation (eCLIP) to create an optimized protocol for profiling m6A modification sites with 20-50-fold less starting RNA material (m6A-eCLIP). Using m6A-eCLIP, we recover traditional m6A motif enrichment and positioning enrichment at stop codons, validating the accuracy of the approach. Further, the improved handling and efficiency enabled us to profile m6A status across cell types and tissues, showing that m6A-eCLIP can be a robust method that is widely applicable for epitranscriptomic profiling across a range of conditions.
Citation Format: Ines Rabano, Alexander A. Shishkin, Kylie Shen, Heather M. Foster, Peter Chu, Eric L. Van Nostrand, Gene W. Yeo. Enhanced mapping of N6-methyladenosine (m6A) RNA modification sites with m6A-eCLIP [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-187.
Abstract LB-279: Multi-grain rice diet decreases risk of breast cancer in Korean women: Results from the Health Examinees study
Authors: Shin Woo-Kyoung , Lee Hwi-Won , Shin Aesun , Lee Jong-koo , Kang Daehee 
Published: September 2020

Abstract
Background: Several studies have examined associations between breast cancer risk and individual foods and nutrients. Most studies have evaluated risks associated with individual foods and nutrients, rather than measures of whole-diet. The objective of this study was to investigate the association between dietary patterns and the risk for breast cancer. Methods: A total of 93,306 women aged 40-69 years were enrolled in the prospective cohort study in the Health Examinees-Gem (HEXA-G) study between 2004 and 2013. Information on cancer diagnosis in the eligible cohort was retrieved from the Korea Central Cancer Registry through 31 December 2014. Dietary patterns were identified using factor analysis of data from a 106-item validated food frequency questionnaire. We conducted a multivariable Cox regression model to obtain the hazard ratio (HR) and 95% confidence interval (CI) for the risk of breast cancer according to the dietary pattern scores. Results: A total of 359 incident cases of breast cancer occurred over an average follow-up period of 6.3 years. Using a factor analysis, we identified three major dietary patterns, which explained 23.9% of the total variance, based on the daily total food intake (g/day) from 37 food groups: the Vegetables and seaweed pattern (greater intake of yellow-green and other vegetables, seaweed, lean fish, and shellfish), the Flour and meat pattern (greater intake of bread, pizza and hamburger, red meat, and poultry), the White rice and salt fermented fish pattern (greater intake of white rice and salt fermented fish). We found that the women who had higher white rice and salt fermented fish pattern scores tend to have higher risk of breast cancer. Multivariate HR (95% CI) comparing the highest with the lowest quintiles of White rice and salt fermented fish pattern scores was 1.35 (1.00, 1.84) (p for trend = 0.0384). Other two dietary patterns, the Vegetables and seaweed pattern and the Flour and meat pattern, showed no significant association with the breast cancer risk for women. Conclusion: The White rice and salt fermented fish pattern was associated with a increased risk of breast cancer, but further investigation involving subgroup analysis is warranted.
Citation Format: Woo-Kyoung Shin, Hwi-Won Lee, Aesun Shin, Jong-koo Lee, Daehee Kang. Multi-grain rice diet decreases risk of breast cancer in Korean women: Results from the Health Examinees study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-279.
Abstract LB-310: Whole-exome sequencing reveals genetic underpinnings of salivary adenoid cystic carcinoma and tongue carcinoma in Chinese population
Authors: Li Ning , Wang Shuhang , Yu Yue , Fang Yuan , Huang Huiyao , Wu Dawei , Fang Hong , Sun Chao , Yu Anqi , Fan Qi , Cheng Shi-Yuan 
Published: September 2020

Abstract
Background: Salivary adenoid cystic carcinoma (ACC) and oral tongue squamous cell carcinoma (OTSCC) are rare malignancies with low incidence and dismal prognosis. The molecular underpinnings of these remain poorly understood, particularly in Asian population. Methods: Through a whole-exome sequencing analysis of 13 OTSCC and 30 ACC patients, a systematic overview of the mutational features in single-nucleotide variations, copy number variations and chromosomal variations were illustrated. Results: In addition to the well-characterized alterations previously reported in Caucasian patients, such as TP53 mutations (11/13, 84.6%) in OTSCC and MYB-NFIB fusion in ACC (11/30, 36.7%), we also observed several novel genetic changes, including FOXP1-TEX261 fusion (1/13, 7.7%) and MYB-FMO5 fusion (1/30, 3.3%) in OTSCC and ACC respectively, which might play a role in facilitating tumor progression. The data exhibited promising translational value as numerous actionable genes were identified with mutations. 76.9% OTSCC and 20% salivary ACC harbored at least one alteration in actionable genes, mutations in CDKN2A (4/13, 30.8%), NTRK3 (3/13, 23.1%) in OTSCC and FGFR2 (2/30, 6.7%), BRAF (2/30, 6.7%) in salivary gland ACC, suggesting targeted immunotherapy might be an effective intervention. Instead of MYB-independent NFIB fusions previously reported in ACC, only NFIB-independent MYB fusions were found in our cohort, indicating that alterations in NFIB rather than MYB might be essential to ACC tumorigenesis. Conclusions: This study reveals the genetic underpinnings of two rare malignancies in Chinese population, illustrating consistent mutational features with published literature as well as demonstrating several distinct genetic alterations, warranting further investigations.
Citation Format: Ning Li, Shuhang Wang, Yue Yu, Yuan Fang, Huiyao Huang, Dawei Wu, Hong Fang, Chao Sun, Anqi Yu, Qi Fan, Shi-Yuan Cheng. Whole-exome sequencing reveals genetic underpinnings of salivary adenoid cystic carcinoma and tongue carcinoma in Chinese population [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-310.
Abstract LB-315: Oncology research applications on an electrical impedance based, high accuracy sequencing platform
Authors: Paliwal Saurabh , Fallahi Mohammad , Nabi Ali , Clark Tyson A. , Dong Bin , Bagchi Srijeeta , Jouzi Maryam , Ritchie Hannah , Bonar Lydia , Thomas Anthony , Tangprasertchai Narin , Barmi Meysam R. , Gomes Xavier , Sankar Subra , Esfandyarpour Hesaam 
Published: September 2020

Abstract
Next Generation Sequencing (NGS) technologies have revolutionized basic biological and clinical research, especially in oncology. NGS cancer assays are used to determine cancer predisposition, identify tumor mutations, monitor treatment response and develop personalized therapies. Here, GenapSys presents a scalable, low cost, and high accuracy sequencing platform based on electrical impedance detection. We demonstrate that a single run with a 16M sensor chip generates up to 2 Gb of data, with greater than 99% raw accuracy and an average read length of about 150 bp. We highlight its applications for oncology research, using diverse cancer panels on reference and clinical samples. We tested hybrid-capture and multiplex PCR-based cancer panels on a range of DNA sources, including oncology reference standards derived from cell line DNA, cfDNA standards, as well as clinical samples: FFPE, fresh frozen tumor tissue, and blood. For hybrid-capture libraries, we used the IDT xGen Pan Cancer 1.5 and Exome Research panels. We detected low frequency mutations in the range of 1%-24.5% across multiple reference standards with the cancer panel, and observed high correlation in allele frequency with expected values (R2 &gt; 0.99). Similar results were obtained with an amplicon panel, the Ion AmpliSeq Cancer Hotspot Panel v2. Whole exome sequencing and pan cancer sequencing of clinical FFPE, fresh frozen and blood samples showed high concordance (F1-score &gt; 95%) of SNV mutation calling with commonly used NGS technology. Thus, we demonstrate that the GenapSys Sequencing Platform is an accurate, scalable, and low cost solution for oncology research on a wide range of sample types and NGS assays.
Citation Format: Saurabh Paliwal, Mohammad Fallahi, Ali Nabi, Tyson A. Clark, Bin Dong, Srijeeta Bagchi, Maryam Jouzi, Hannah Ritchie, Lydia Bonar, Anthony Thomas, Narin Tangprasertchai, Meysam R. Barmi, Xavier Gomes, Subra Sankar, Hesaam Esfandyarpour. Oncology research applications on an electrical impedance based, high accuracy sequencing platform [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-315.
Dynamic real-time capacity constrained routing algorithm for evacuation planning problem
Authors: Abusalama Jawad , Razali Sazalinsyah , Choo Yun-Huoy , Momani Lina , Alkharabsheh Abdelrahman 
Published: September 2020

<span>Usually, disasters occurred over a relatively short time in anytime and anywhere. Most occupancies haven’t absolute knowledge about the prevention or safety consciousness to deal with disasters. During disaster occurred, evacuation processes are conducted to save people life, and if there is no appropriate evacuation plan, the situation will become worse. Thus, finding optimal planning to evacuate the occupancy people is critical in many cases i.e. emergency evacuation. In this paper, a Dynamic Real-Time Capacity Constrained Routing (DRTCCR) Algorithm has been proposed and analyzed. Such algorithm will investigate the capacity constraints of the evacuation network in real-time by modelling the capacities at the time of series to improve current solutions of the evacuation planning problem. Such algorithm will produce an optimal solution for evacuation planning problem. Performance evaluation on many network models illustrates that the DRTCCR algorithm improves the previous evacuation planning by reducing the evacuation time as well as the computational cost. In addition, DRTCCR algorithm has the ability to recalculate and find out the optimal path dynamically in real-time irrespective the number of trapped people as well as the transportation network size. Analytical experiments have been done and illustrate the efficiency of the proposed algorithm.</span>
Naïve Bayes and linear discriminate analysis based diagnostic analytic of harmonic source identification
Authors: Jopri M. H , Ghani MR Ab , Abdullah A.R , Sutikno Tole , Manap M , Too J. 
Published: September 2020

<span>The diagnostic analytic type of harmonic source is a vital research due to diagnose and identify type of harmonic source that exist in the power system. This paper presents a comparison of machine learning (ML) algorithm namely as the Naïve Bayes (NB) and linear discriminate analysis (LDA) in identifying and diagnosing the harmonic sources. The MLs inputs are the voltage and current feature sets that estimated from the time-frequency representation (TFR) of S-transform analysis. Four specific cases of harmonic source location are considered in this research, whereas harmonic voltage (H<sub>V</sub>) and harmonic current (H<sub>C</sub>) source type-load are used in the diagnosing process. The sufficiency of the proposed methodology is tested and verified on the IEEE 4-bust test feeder, and to prevent overfitting, the K-fold cross-validation technique is implemented for performance evaluation. To identify the best ML, the performance measurement consist of the accuracy, precision, geometric mean, F-measure, sensitivity, and specificity are conducted.</span>
<p><strong>Comparative assessment of pollen micromorphology of <em>Salvia assurgens</em> (Lamiaceae), an endemic sage from Mexico</strong></p>
Authors: BEDOLLA-GARCÍA BRENDA Y. , CASTRO-MORALES MAYRA , CULTID-MEDINA CARLOS A. 
Published: September 2020

The present study provides novel information about the pollen of Salvia assurgens. Pollen grains were collected and described based on their observed characters by light microscope and scanning electron microscopy. The species is distinguished from other Mexican salvias by having small pollen grains (14.2 × 18.2 µm), thin primary muri (0.2 µm thick), elongated primary lumina (1.03 µm long) and secondary lumina with relatively few perforations (9, range 5–14). Pollen characters are similar to those of the majority of American salvias. Regarding Mexican sages, there has been little palynological research, and only 23 species of 32 examined have been quantitatively studied. Standardization is needed in different aspects of palynological studies, especially in relation to measurement protocols and data analysis, as well as the increased use of scanning electron microscopy (SEM), since the majority of differences among species are provided by SEM microscope observation.
Response of Global Tropical Cyclone Activity to Increasing CO2: Results from Downscaling CMIP6 Models
Authors: Emanuel Kerry 
Published: September 2020

AbstractGlobal models comprising the sixth-generation Coupled Climate Model Intercomparison Project (CMIP6) are downscaled using a very high-resolution but simplified coupled atmosphere–ocean tropical cyclone model, as a means of estimating the response of global tropical cyclone activity to increasing greenhouse gases. As with a previous downscaling of CMIP5 models, the results show an increase in both the frequency and severity of tropical cyclones, robust across the models downscaled, in response to increasing greenhouse gases. The increase is strongly weighted to the Northern Hemisphere, and especially noteworthy is a large increase in the higher latitudes of the North Atlantic. Changes are insignificant in the South Pacific across metrics. Although the largest increases in track density are far from land, substantial increases in global landfalling power dissipation are indicated. The incidence of rapid intensification increases rapidly with warming, as predicted by existing theory. Measures of robustness across downscaled climate models are presented, and comparisons to tropical cyclones explicitly simulated in climate models are discussed.
Modeling and adaptive robust wavelet control for a liquid container system under slosh and uncertainty
Authors: Al-Mashhadani Mohammad Abdulrahman 
Published: September 2020

Liquid sloshing in moving or stationary containers and flexible uncertainty caused by the slosh are considered to be the most probable causing unexpected coupling effects on the dynamics of many systems such as aerospace, ground vehicles, and high speed industries arms. The coupling of dynamic liquid slosh in a container system with the uncertainty caused by the sensors or dampers is rare documented and this coupling can be considered as a highly nonlinear system. In this paper, an investigation is presented to demonstrate a new approach for enabling the reduction of the liquid slosh and uncertainty by implementing adaptive robust wavelet control technique. Starting by creating the mathematical dynamic model for the nonlinear slosh coupled by uncertainty, adaptive robust control based wavelet transform is applied for calculating optimal motion that minimize residual slosh and uncertainty. Subsequently the adaptive robust control based wavelet network approximation and the appropriate parameter algorithms for the container system with slosh and uncertainty are derived to achieve the feedback linearization, adaptive control, and H∞ tracking performance. The simulation results show that the effects of slosh errors and external uncertainty can be successfully attenuated within a desired attenuation level.
Cultivating change: Engaging residents in research
Authors: Arora Vikram , Bell Paul F , Hagberg Stephen 
Published: September 2020

Background The American Council of Graduate Medical Education (ACGME) guidelines for scholarly activities by family medicine residents require at least one activity per resident and encourage conference presentations. Meeting these guidelines has traditionally been challenging due to a multitude of factors from lack of time to limited administrative support. Studies have shown that resident participation in research was associated with higher levels of satisfaction with training. We aimed to develop and evaluate the effectiveness of a dedicated research curriculum in achieving ACGME goals for our residents. Methods We performed a need assessment that identified strengths and obstacles related to research which then guided the actions taken to build the curriculum. Revised curricular elements included a research focused lecture series, a restructured journal club, financial support for presentations and project expenses, a specific timeline for project completion, and the development of a regional research day involving multiple family medicine programs. Dedicated research time was built into the resident schedule and presentations at local, regional and national conferences were encouraged and supported. Results Following implementation of the curriculum there was a marked increase in the number of scholarly projects performed by residents. Prior to implementation there had only been one presentation at a national conference in the previous five years. This increased to an average of four presentations per year in the following five year period. On a regional scale, the initial success of the local research day led to a continued expansion and now includes six family medicine programs. Conclusion Implementation of a dedicated multifaceted research curriculum significantly increased the participation of our residents in scholarly activities and led to a near five-fold increase in presentations at regional and national levels. Additionally, resident satisfaction in scholarly activities increased and a far greater number of graduating residents went on to complete fellowships.
Stepping On after Stroke falls-prevention programme for community stroke survivors in Singapore: A feasibility study
Authors: Xu Tianma , Clemson Lindy , O’Loughlin Kate , Lannin Natasha , Dean Catherine M , Koh Gerald 
Published: September 2020

Introduction Intervention studies to date have shown limited evidence of falls reduction in community-dwelling stroke survivors. This study tests the acceptability and feasibility of the Stepping On after Stroke programme in Singapore. Method A pre–post-intervention study design was used over a 6-month period. Falls incidence was the main outcome measure, with the recruitment process and attendance rate recorded to test feasibility. Data analysis from evaluation questionnaires (descriptive statistics) and interviews (content analysis) were applied to determine acceptability. Results Eight stroke participants and seven caregivers completed the programme at two community sites facilitated by two programme leaders. Stroke participants achieved full attendance over the 7-week programme but family caregivers did not (38%). All participants highlighted their acceptability of the group-based falls-prevention programme. Both programme leaders achieved 92% fidelity in session delivery. Four stroke participants fell during the study period. Stroke participants demonstrated clinically meaningful improvements in community participation at 1 month post-intervention. Family caregivers reported no changes in pre–post evaluations. Conclusion The Stepping On after Stroke programme appears feasible and acceptable to therapists and service users in Singapore; however, caregivers’ participation was limited. Findings can be used to further improve the programme and its methodology before testing its effectiveness in a larger-scale trial.
Skeletal Muscle Involvement in Wilson Disease: Clinical and Magnetic Resonance Imaging (MRI) Observations in 2 Families
Authors: Bhoi Sanjeev Kumar , Naik Suprava , Jha Menka , Mishra Biswamohan , Pradhan Nikhilesh 
Published: September 2020

Objective: Skeletal muscle involvement in Wilson disease is rare. Calf muscle pain might be attributed as growing pain in children. We report calf muscle involvement in Wilson disease and describe the magnetic resonance imaging (MRI) findings of leg, differential diagnosis with literature review. Patients and Methods: Our observations describe calf muscle MRI abnormality in 5 cases of Wilson disease from 2 families. The clinical presentations were neurologic in 3, hepatic in 1, and asymptomatic in 1 patient. We systematically describe the clinical characteristics and their calf muscle MRI findings. Results: Three patients had bilateral calf pain and intermittent cramps. The pain was of mild to moderate intensity and managed symptomatically. Serum alkaline phosphatase, creatinine phosphokinase, and needle electromyography were normal. Turbo inversion recovery magnitude sequence MRI of calf muscle revealed hyperintensity in bilateral gastrocnemii muscles. These muscles appear hyperintense in diffusion-weighted imaging. Conclusion: The calf muscle involvement could be attributed to muscle edema due to copper-induced muscle toxicity mediated by inhibition of Na+/K+-ATPase on cellular membranes of fast-twitch gastrocnemii muscles which contain predominant type II myofiber. In Wilson disease patients with calf pain or cramps, muscle MRI may show nonspecific gastrocnemius hyperintensity. Further evaluation may give insight into its pathophysiology.