Search

Your search keyword '"Bjerregaard, P"' showing total 650 results
Start Over Author "Bjerregaard, P" Search Limiters Full Text
650 results on '"Bjerregaard, P"'

1. Application of Soft Actor-Critic Algorithms in Optimizing Wastewater Treatment with Time Delays Integration

Author

Mohammadi, Esmaeel, Ortiz-Arroyo, Daniel, Hansen, Aviaja Anna, Stokholm-Bjerregaard, Mikkel, Gros, Sebastien, Anand, Akhil S, and Durdevic, Petar

Subjects
Electrical Engineering and Systems Science - Systems and Control, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Wastewater treatment plants face unique challenges for process control due to their complex dynamics, slow time constants, and stochastic delays in observations and actions. These characteristics make conventional control methods, such as Proportional-Integral-Derivative controllers, suboptimal for achieving efficient phosphorus removal, a critical component of wastewater treatment to ensure environmental sustainability. This study addresses these challenges using a novel deep reinforcement learning approach based on the Soft Actor-Critic algorithm, integrated with a custom simulator designed to model the delayed feedback inherent in wastewater treatment plants. The simulator incorporates Long Short-Term Memory networks for accurate multi-step state predictions, enabling realistic training scenarios. To account for the stochastic nature of delays, agents were trained under three delay scenarios: no delay, constant delay, and random delay. The results demonstrate that incorporating random delays into the reinforcement learning framework significantly improves phosphorus removal efficiency while reducing operational costs. Specifically, the delay-aware agent achieved 36% reduction in phosphorus emissions, 55% higher reward, 77% lower target deviation from the regulatory limit, and 9% lower total costs than traditional control methods in the simulated environment. These findings underscore the potential of reinforcement learning to overcome the limitations of conventional control strategies in wastewater treatment, providing an adaptive and cost-effective solution for phosphorus removal.

Published
2024

2. A two-dimensional gallium phosphide optomechanical crystal in the resolved-sideband regime

Author

Tamaki, Sho, Kristensen, Mads Bjerregaard, Martel, Théo, Braive, Rémy, and Schliesser, Albert

Subjects
Quantum Physics, Physics - Optics
Abstract

Faithful quantum state transfer between telecom photons and microwave frequency mechanical oscillations necessitate a fast conversion rate and low thermal noise. Two-dimensional (2D) optomechanical crystals (OMCs) are favorable candidates that satisfy those requirements. 2D OMCs enable sufficiently high mechanical frequency (1$\sim$10 GHz) to make the resolved-sideband regime achievable, a prerequisite for many quantum protocols. It also supports higher thermal conductance than 1D structures, mitigating the parasitic laser absorption heating. Furthermore, gallium phosphide (GaP) is a promising material choice thanks to its large electronic bandgap of 2.26 eV, which suppresses two-photon absorption, and high refractive index $n$ = 3.05 at the telecom C-band, leading to a high-$Q$ optical mode. Here, we fabricate and characterize a 2D OMC made of GaP. We realize a high optical $Q$-factor of $7.9\times 10^{4}$, corresponding to a linewidth $\kappa/2\pi$ = 2.5 GHz at the telecom frequency 195.6 THz. This optical mode couples to several mechanical modes, whose frequencies all exceed the cavity linewidth. The most strongly coupled mode oscillates at 7.7 GHz, more than 3 times the optical linewidth, while achieving a substantial vacuum optomechanical coupling rate $g_{\mathrm{0}}/2\pi$ = 450 kHz. This makes the platform a promising candidate for a long-lived, deterministic quantum memory for telecom photons at low temperatures.

Published
2024

3. Attenuation-adjusted deep learning of pore defects in 2D radiographs of additive manufacturing powders

Author

Bjerregaard, Andreas, Schumacher, David, and Sporring, Jon

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing, 68U10 (Primary) 68T45, 68T07, 94A08 (Secondary), I.4.6, I.4.1, J.2, I.2.10, I.5.4
Abstract

The presence of gas pores in metal feedstock powder for additive manufacturing greatly affects the final AM product. Since current porosity analysis often involves lengthy X-ray computed tomography (XCT) scans with a full rotation around the sample, motivation exists to explore methods that allow for high throughput -- possibly enabling in-line porosity analysis during manufacturing. Through labelling pore pixels on single 2D radiographs of powders, this work seeks to simulate such future efficient setups. High segmentation accuracy is achieved by combining a model of X-ray attenuation through particles with a variant of the widely applied UNet architecture; notably, F1-score increases by $11.4\%$ compared to the baseline UNet. The proposed pore segmentation is enabled by: 1) pretraining on synthetic data, 2) making tight particle cutouts, and 3) subtracting an ideal particle without pores generated from a distance map inspired by Lambert-Beers law. This paper explores four image processing methods, where the fastest (yet still unoptimized) segments a particle in mean $0.014s$ time with F1-score $0.78$, and the most accurate in $0.291s$ with F1-score $0.87$. Due to their scalable nature, these strategies can be involved in making high throughput porosity analysis of metal feedstock powder for additive manufacturing., Comment: Implementation on https://github.com/yhsure/porosity

Published
2024

4. Time Series Dataset for Modeling and Forecasting of $N_2O$ in Wastewater Treatment

Author

Hansen, Laura Debel, Rani, Anju, Stokholm-Bjerregaard, Mikkel Algren, Stentoft, Peter Alexander, Arroyo, Daniel Ortiz, and Durdevic, Petar

Subjects
Electrical Engineering and Systems Science - Systems and Control
Abstract

In this paper, we present two years of high-resolution nitrous oxide ($N_2O$) measurements for time series modeling and forecasting in wastewater treatment plants (WWTP). The dataset comprises frequent, real-time measurements from a full-scale WWTP, with a sample interval of 2 minutes, making it ideal for developing models for real-time operation and control. This comprehensive bio-chemical dataset includes detailed influent and effluent parameters, operational conditions, and environmental factors. Unlike existing datasets, it addresses the unique challenges of modeling $N_2O$, a potent greenhouse gas, providing a valuable resource for researchers to enhance predictive accuracy and control strategies in wastewater treatment processes. Additionally, this dataset significantly contributes to the fields of machine learning and deep learning time series forecasting by serving as a benchmark that mirrors the complexities of real-world processes, thus facilitating advancements in these domains. We provide a detailed description of the dataset along with a statistical analysis to highlight its characteristics, such as nonstationarity, nonnormality, seasonality, heteroscedasticity, structural breaks, asymmetric distributions, and intermittency, which are common in many real-world time series datasets and pose challenges for forecasting models., Comment: 10 pages, 4 figures. This publication accompanies the Mendeley dataset available at this URL (version 1): https://data.mendeley.com/datasets/xmbxhscgpr/1

Published
2024

5. Wastewater Treatment Plant Data for Nutrient Removal System

Author

Mohammadi, Esmaeel, Rani, Anju, Stokholm-Bjerregaard, Mikkel, Ortiz-Arroyo, Daniel, and Durdevic, Petar

Subjects
Electrical Engineering and Systems Science - Systems and Control, Computer Science - Computational Engineering, Finance, and Science, Electrical Engineering and Systems Science - Signal Processing
Abstract

This paper introduces the Agtrup (BlueKolding) dataset, collected from Denmark's Agtrup wastewater treatment plant, specifically designed to enhance phosphorus removal via chemical and biological methods. This rich dataset is assembled through a high-frequency Supervisory Control and Data Acquisition (SCADA) system data collection process, which captures a wide range of variables related to the operational dynamics of nutrient removal. It comprises time-series data featuring measurements sampled to a frequency of two minutes across various control, process, and environmental variables. The comprehensive dataset aims to foster significant advancements in wastewater management by supporting the development of sophisticated predictive models and optimizing operational strategies. By providing detailed insights into the interactions and efficiencies of chemical and biological phosphorus removal processes, the dataset serves as a vital resource for environmental researchers and engineers focused on improving the sustainability and effectiveness of wastewater treatment operations. The ultimate goal of this dataset is to facilitate the creation of digital twins and the application of machine learning techniques, such as deep reinforcement learning, to predict and enhance system performance under varying operational conditions., Comment: Data Paper

Published
2024

6. Digital Evolution: Novo Nordisk's Shift to Ontology-Based Data Management

Author

Tan, Shawn Zheng Kai, Baksi, Shounak, Bjerregaard, Thomas Gade, Elangovan, Preethi, Gopalakrishnan, Thrishna Kuttikattu, Hric, Darko, Joumaa, Joffrey, Li, Beidi, Rabbani, Kashif, Venkatesan, Santhosh Kannan, Valdez, Joshua Daniel, and Kuriakose, Saritha Vettikunnel

Subjects
Computer Science - Databases
Abstract

Biomedical data is growing exponentially, and managing it is increasingly challenging. While Findable, Accessible, Interoperable and Reusable (FAIR) data principles provide guidance, their adoption has proven difficult, especially in larger enterprises like pharmaceutical companies. In this manuscript, we describe how we leverage an Ontology-Based Data Management (OBDM) strategy for digital transformation in Novo Nordisk Research & Early Development. Here, we include both our technical blueprint and our approach for organizational change management. We further discuss how such an OBDM ecosystem plays a pivotal role in the organizations digital aspirations for data federation and discovery fuelled by artificial intelligence. Our aim for this paper is to share the lessons learned in order to foster dialogue with parties navigating similar waters while collectively advancing the efforts in the fields of data management, semantics and data driven drug discovery., Comment: 14 pages, 2 figures

Published
2024

7. Improved Long Short-Term Memory-based Wastewater Treatment Simulators for Deep Reinforcement Learning

Author

Mohammadi, Esmaeel, Ortiz-Arroyo, Daniel, Stokholm-Bjerregaard, Mikkel, Hansen, Aviaja Anna, and Durdevic, Petar

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Electrical Engineering and Systems Science - Systems and Control
Abstract

Even though Deep Reinforcement Learning (DRL) showed outstanding results in the fields of Robotics and Games, it is still challenging to implement it in the optimization of industrial processes like wastewater treatment. One of the challenges is the lack of a simulation environment that will represent the actual plant as accurately as possible to train DRL policies. Stochasticity and non-linearity of wastewater treatment data lead to unstable and incorrect predictions of models over long time horizons. One possible reason for the models' incorrect simulation behavior can be related to the issue of compounding error, which is the accumulation of errors throughout the simulation. The compounding error occurs because the model utilizes its predictions as inputs at each time step. The error between the actual data and the prediction accumulates as the simulation continues. We implemented two methods to improve the trained models for wastewater treatment data, which resulted in more accurate simulators: 1- Using the model's prediction data as input in the training step as a tool of correction, and 2- Change in the loss function to consider the long-term predicted shape (dynamics). The experimental results showed that implementing these methods can improve the behavior of simulators in terms of Dynamic Time Warping throughout a year up to 98% compared to the base model. These improvements demonstrate significant promise in creating simulators for biological processes that do not need pre-existing knowledge of the process but instead depend exclusively on time series data obtained from the system.

Published
2024

8. Interlaboratory study of the operational stability of automated sorption balances

Author

Zelinka, Samuel L., Glass, Samuel V., Lazarcik, Eleanor Q. D., Thybring, Emil E., Altgen, Michael, Rautkari, Lauri, Curling, Simon, Cao, Jinzhen, Wang, Yujiao, Künniger, Tina, Nyström, Gustav, Dreimol, Christopher Hubert, Burgert, Ingo, Uyup, Mohd Khairun Anwar, Khadiran, Tumirah, Roper, Mark G., Broom, Darren P., Schwarzkopf, Matthew, Yudhanto, Arief, Subah, Mohammad, Lubineau, Gilles, Fredriksson, Maria, Strojecki, Marcin, Olek, Wiesław, Majka, Jerzy, Pedersen, Nanna Bjerregaard, Burnett, Daniel J., Garcia, Armando R., Verdonck, Els, Dreisbach, Frieder, Waguespack, Louis, Schott, Jennifer, Esteban, Luis G., Garcia-Iruela, Alberto, Colinart, Thibaut, Rémond, Romain, Mazian, Brahim, Perre, Patrick, Emmerich, Lukas, and Li, Ling

Published
2024
Full Text
View/download PDF

9. Deep Learning Based Simulators for the Phosphorus Removal Process Control in Wastewater Treatment via Deep Reinforcement Learning Algorithms

Author

Mohammadi, Esmaeel, Stokholm-Bjerregaard, Mikkel, Hansen, Aviaja Anna, Nielsen, Per Halkjær, Ortiz-Arroyo, Daniel, and Durdevic, Petar

Subjects
Electrical Engineering and Systems Science - Systems and Control, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Phosphorus removal is vital in wastewater treatment to reduce reliance on limited resources. Deep reinforcement learning (DRL) is a machine learning technique that can optimize complex and nonlinear systems, including the processes in wastewater treatment plants, by learning control policies through trial and error. However, applying DRL to chemical and biological processes is challenging due to the need for accurate simulators. This study trained six models to identify the phosphorus removal process and used them to create a simulator for the DRL environment. Although the models achieved high accuracy (>97%), uncertainty and incorrect prediction behavior limited their performance as simulators over longer horizons. Compounding errors in the models' predictions were identified as one of the causes of this problem. This approach for improving process control involves creating simulation environments for DRL algorithms, using data from supervisory control and data acquisition (SCADA) systems with a sufficient historical horizon without complex system modeling or parameter estimation., Comment: Journal Paper

Published
2024
Full Text
View/download PDF

10. Association between COVID-19 and the incidence of type 1 diabetes in Portugal – a registry study

Author

Bjerregaard-Andersen, Morten, Da Silva, Jessica, Diogo, Rui, Claro, Ana Raquel, Ferro, Inês, Romana, Andreia, Rocha, Patrícia, Sá, Beatriz, Lobarinhas, Goreti, Rolim, Sara, Juhl, Claus Bogh, Højlund, Kurt, Fernandes, Isabel, Antunes, Sónia, Félix Calha, Maria Manuela, Gama, Guida, Amálio, Sofia, Figueiras, Mariana, Silva, Teresa, Rosado, Margarida, Ferrão, Estela, Arez, Luísa, Baptista, Ana, Martins Ferreira, Adriana, Alba, Diana, Godinho, Carlos, Leite, Ana Luísa, Afonso Lopes, Maria de Lurdes, Sampaio, Maria Lurdes, Serra-Caetano, Joana, and Carvalho, Eugenia

Published
2024
Full Text
View/download PDF

12. A Long-lived and Efficient Optomechanical Memory for Light

Author

Kristensen, Mads Bjerregaard, Kralj, Nenad, Langman, Eric, and Schliesser, Albert

Subjects
Quantum Physics
Abstract

We demonstrate a memory for light based on optomechanically induced transparency. We achieve a long storage time by leveraging the ultra-low dissipation of a soft-clamped mechanical membrane resonator, which oscillates at MHz frequencies. At room temperature, we demonstrate a lifetime $T_1 \approx 23\,\mathrm{ms}$ and a retrieval efficiency $\eta \approx 40\%$ for classical coherent pulses. We anticipate storage of quantum light to be possible at moderate cryogenic conditions ($T\approx 10\,\mathrm{K}$). Such systems could find applications in emerging quantum networks, where they can serve as long-lived optical quantum memories by storing optical information in a phononic mode.

Published
2023

13. A galaxy group candidate at z~3.7 in the COSMOS field

Author

Sillassen, Nikolaj Bjerregaard, Jin, Shuowen, Magdis, Georgios E., Daddi, Emanuele, Weaver, John R., Gobat, Raphael, Kokorev, Vasily, Valentino, Francesco, Finoguenov, Alexis, Shuntov, Marko, Gómez-Guijarro, Carlos, Coogan, Rosemary, Greve, Thomas R., Toft, Sune, and Sese, David B.

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We report a galaxy group candidate HPC1001 at $z\approx3.7$ in the COSMOS field. This structure was selected as a high galaxy overdensity at $z>3$ in the COSMOS2020 catalog. It contains ten candidate members, of which eight are assembled in a $10''\times10''$ area with the highest sky density among known protoclusters and groups at $z>3$. Four out of ten sources were also detected at 1.2$~$mm with Atacama Large Millimeter Array continuum observations. Photometric redshifts, measured by four independent methods, fall within a narrow range of $3.5

Published
2022
Full Text
View/download PDF

14. Detection of Furigana Text in Images

Author

Bjerregaard, Nikolaj Kjøller, Cheplygina, Veronika, and Heinrich, Stefan

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Furigana are pronunciation notes used in Japanese writing. Being able to detect these can help improve optical character recognition (OCR) performance or make more accurate digital copies of Japanese written media by correctly displaying furigana. This project focuses on detecting furigana in Japanese books and comics. While there has been research into the detection of Japanese text in general, there are currently no proposed methods for detecting furigana. We construct a new dataset containing Japanese written media and annotations of furigana. We propose an evaluation metric for such data which is similar to the evaluation protocols used in object detection except that it allows groups of objects to be labeled by one annotation. We propose a method for detection of furigana that is based on mathematical morphology and connected component analysis. We evaluate the detections of the dataset and compare different methods for text extraction. We also evaluate different types of images such as books and comics individually and discuss the challenges of each type of image. The proposed method reaches an F1-score of 76\% on the dataset. The method performs well on regular books, but less so on comics, and books of irregular format. Finally, we show that the proposed method can improve the performance of OCR by 5\% on the manga109 dataset. Source code is available via \texttt{\url{https://github.com/nikolajkb/FuriganaDetection}}, Comment: This project was originally submitted by NKB in fulfillment of the 30 ECTS MSc thesis at the IT University of Copenhagen

Published
2022

15. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

Author

Ramdas, Shweta, Judd, Jonathan, Graham, Sarah E, Kanoni, Stavroula, Wang, Yuxuan, Surakka, Ida, Wenz, Brandon, Clarke, Shoa L, Chesi, Alessandra, Wells, Andrew, Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W, Locke, Adam E, Marouli, Eirini, Zajac, Greg JM, Wu, Kuan-Han H, Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T, Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F, Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M, Rasheed, Humaira, Havulinna, Aki S, Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A, Lingren, Todd, Feng, QiPing, Kullo, Iftikhar J, Narita, Akira, Takayama, Jun, Martin, Hilary C, Hunt, Karen A, Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E, Campbell, Archie, Lin, Kuang, Millwood, Iona Y, Rasheed, Asif, Hindy, George, Faul, Jessica D, Zhao, Wei, Weir, David R, Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R, Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M, Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian’an, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achilleas, Hottenga, Jouke Jan, Wood, Andrew R, Ji, Yingji, Gao, Zishan, Haworth, Simon, Mitchell, Ruth E, Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A, Yao, Jie, Manichaikul, Ani, Lee, Wen-Jane, Hsiung, Chao Agnes, Warren, Helen R, Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L, Goel, Anuj, and Sabater-Lleal, Maria

Subjects
Human Genome, Biotechnology, Genetics, 2.1 Biological and endogenous factors, Aetiology, Chromatin, Genome-Wide Association Study, Genomics, Humans, Lipids, Polymorphism, Single Nucleotide, Million Veterans Program, Global Lipids Genetics Consortium, complex traits, fine-mapping, functional genomics, lipid biology, post-GWAS, regulatory mechanism, variant prioritization, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.

Published
2022

21. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

Author

Okholm, Trine Line Hauge, Sathe, Shashank, Park, Samuel S, Kamstrup, Andreas Bjerregaard, Rasmussen, Asta Mannstaedt, Shankar, Archana, Chua, Zong Ming, Fristrup, Niels, Nielsen, Morten Muhlig, Vang, Søren, Dyrskjøt, Lars, Aigner, Stefan, Damgaard, Christian Kroun, Yeo, Gene W, and Pedersen, Jakob Skou

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer Genomics, Cancer, Urologic Diseases, Human Genome, 2.1 Biological and endogenous factors, Binding Sites, Carcinogenesis, Carrier Proteins, Exons, Gene Expression Regulation, Neoplastic, Hep G2 Cells, Humans, Introns, K562 Cells, Neoplasms, RNA, RNA, Circular, RNA-Binding Proteins, Trans-Activators, Transcriptome, Urinary Bladder Neoplasms, Circular RNAs, RNA-binding proteins, RBP sponges, circCDYL, Bladder cancer, Tumorigenesis, Clinical Sciences
Abstract

BackgroundCircular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts.MethodsWe conduct an extensive screen of circRNA-RBP interactions in the ENCODE cell lines HepG2 and K562. We profile circRNAs in deep-sequenced total RNA samples and analyze circRNA-RBP interactions using a large set of eCLIP data with binding sites of 150 RBPs. We validate interactions for select circRNAs and RBPs by performing RNA immunoprecipitation and functionally characterize our most interesting candidates by conducting knockdown studies followed by RNA-Seq.ResultsWe generate a comprehensive catalog of circRNA-RBP interactions in HepG2 and K562 cells. We show that KHSRP binding sites are enriched in flanking introns of circRNAs and that KHSRP depletion affects circRNA biogenesis. We identify circRNAs that are highly covered by RBP binding sites and experimentally validate individual circRNA-RBP interactions. We show that circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, is almost completely covered with GRWD1 binding sites in HepG2 cells, and that circCDYL depletion counteracts the effect of GRWD1 depletion. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g., TP53. Finally, we show that elevated levels of circCDYL are associated with overall survival of bladder cancer patients.ConclusionsOur study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis.

Published
2020

22. Nut Consumption and Renal Function Among Women With a History of Gestational Diabetes

Author

Ajjarapu, Aparna S, Hinkle, Stefanie N, Wu, Jing, Li, Mengying, Rawal, Shristi, Francis, Ellen C, Chen, Liwei, Pitsava, Georgia, Bjerregaard, Anne A, Grunnet, Louise G, Vaag, Allan, Zhu, Yeyi, Ma, Ronald CW, Damm, Peter, Mills, James L, Olsen, Sjurdur F, and Zhang, Cuilin

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Nutrition and Dietetics, Nutrition, Diabetes, Kidney Disease, Prevention, Clinical Research, Renal and urogenital, Metabolic and endocrine, Adult, Cohort Studies, Denmark, Diabetes, Gestational, Diet, Female, Glomerular Filtration Rate, Humans, Kidney, Kidney Diseases, Longitudinal Studies, Middle Aged, Nuts, Pregnancy, Clinical Sciences, Urology & Nephrology, Clinical sciences, Nutrition and dietetics
Abstract

ObjectiveNut intake has been associated with reduced cardiometabolic risk, but few studies have examined its association with renal function. We examined associations between nut intake and renal function among women with previous gestational diabetes mellitus (GDM), a population with an increased risk for renal dysfunction.Design and methodsThis study included 607 women with a history of GDM who participated in the Diabetes & Women's Health Study (2012-2014) follow-up clinical examination in Denmark. At the clinic, biospecimens were collected, and habitual intake of nuts (9 types) in the past year was assessed using a food frequency questionnaire. A total of 330 women free of major chronic diseases were included in the analysis. Total nut intake was classified as none (≤1 serving/month), monthly (2-3 servings/month), weekly (1-6 servings/week), and daily (≥1 serving/day). One serving was defined as 28 g. Renal function markers included estimated glomerular rate (eGFR) and urinary albumin-to-creatinine ratio (UACR), calculated based on plasma creatinine (mg/dL), and urinary albumin (mg/L), and creatinine (mg/dL) measurements, respectively. We estimated percent differences with 95% confidence intervals for each outcome by nut intake, adjusted for current body mass index, age, physical activity, energy intake, alcohol consumption, and vegetables intake.ResultsWe observed a nonlinear association between total nut intake and UACR with lowest UACR values among women with weekly intake. Compared to women with weekly intake (n = 222), the adjusted UACR values were higher by 86% [95% confidence interval: 15%, 202%], 24% [-1%, 54%], and 117% [22%, 288%] among women with no (n = 13), monthly (n = 86), and daily (n = 9) intake, respectively. Compared to weekly consumers, daily nut consumers also had 9% [0%, 19%] significantly higher eGFR values, but eGFR values were similar among women with no and monthly intake.ConclusionModerate nut consumption may be beneficial to kidney health among women with prior GDM.

Published
2020

24. A prospective study of artificially sweetened beverage intake and cardiometabolic health among women at high risk

Author

Hinkle, Stefanie N, Rawal, Shristi, Bjerregaard, Anne Ahrendt, Halldorsson, Thor I, Li, Mengying, Ley, Sylvia H, Wu, Jing, Zhu, Yeyi, Chen, Liwei, Liu, Aiyi, Grunnet, Louise Groth, Rahman, Mohammad L, Kampmann, Freja Bach, Mills, James L, Olsen, Sjurdur F, and Zhang, Cuilin

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Nutrition and Dietetics, Diabetes, Prevention, Clinical Research, Obesity, Nutrition, Reproductive health and childbirth, Metabolic and endocrine, Good Health and Well Being, Adult, Beverages, Body Mass Index, Cardiovascular Diseases, Cohort Studies, Denmark, Diabetes Mellitus, Type 2, Diabetes, Gestational, Female, Follow-Up Studies, Glycated Hemoglobin, Humans, Metabolic Diseases, Pregnancy, Prospective Studies, Risk Factors, Sweetening Agents, Women's Health, artificially sweetened beverages, nonnutritive sweeteners, soda, diet, obesity, diabetes, cardiometabolic health, gestational diabetes, Engineering, Medical and Health Sciences, Nutrition & Dietetics, Clinical sciences, Nutrition and dietetics
Abstract

BackgroundArtificially sweetened beverages (ASBs) are commonly consumed and recommended for individuals at high risk for cardiometabolic diseases; however, the health effects of ASBs remain contradictory. Given that cross-sectional analyses are subject to reverse causation, prospective studies with long-term follow-up are needed to evaluate associations between ASBs and cardiometabolic health, especially among high-risk individuals.ObjectiveThe aim of this study was to examine associations of ASB intake and cardiometabolic health among high-risk women with prior gestational diabetes mellitus (GDM).MethodsWe included 607 women with GDM from the Danish National Birth Cohort (DNBC; 1996-2002) who completed a clinical exam 9-16 y after the DNBC pregnancy for the Diabetes & Women's Health (DWH) Study (2012-2014). We assessed ASB intake using FFQs completed during the DNBC pregnancy and at the DWH Study clinical exam. We examined cardiometabolic outcomes at the DWH clinical exam. We estimated percentage differences in continuous cardiometabolic markers and RRs for clinical endpoints in association with ASB intake both during pregnancy and at follow-up adjusted for prepregnancy BMI, diet, and lifestyle factors. Sensitivity analyses to account for reverse causation were performed.ResultsIn pregnancy and at follow-up, 30.4% and 36.4% of women regularly (≥2 servings/wk) consumed ASB, respectively. Consumption of ASBs, both during pregnancy and at follow-up, was associated with higher glycated hemoglobin (HbA1c), insulin, HOMA-IR, triglycerides, liver fat, and adiposity and with lower HDL at follow-up. After adjustment for covariates, particularly prepregnancy BMI, the majority of associations between ASB intake in pregnancy and outcomes at follow-up became null with the exception of HbA1c. ASB intake at follow-up (≥1 serving/d compared with

Published
2019

28. Quadriceps Activation After Anterior Cruciate Ligament Reconstruction: The Early Bird Gets the Worm!

Author

MOIROUX–SAHRAOUI, Ayrton, FORELLI, Florian, MAZEAS, Jean, RAMBAUD, Alexandre JM, BJERREGAARD, Andreas, and RIERA, Jérôme

Subjects
EXERCISE physiology, ANTERIOR cruciate ligament surgery, EXERCISE therapy, CENTRAL nervous system, MUSCLE weakness, TRANSCUTANEOUS electrical nerve stimulation, ELECTRIC stimulation, QUADRICEPS muscle
Abstract

Arthrogenic Muscle Inhibition (AMI) is a phenomenon observed in individuals with joint injury or pathology, characterized by a reflexive inhibition of surrounding musculature, altered neuromuscular control, and compromised functional performance. After anterior cruciate ligament reconstruction (ACLR) one of the most obvious consequences of AMI is the lack of quadriceps activation and strength. Understanding the underlying mechanisms of AMI is crucial for developing effective therapeutic interventions. The surgical procedure needed to reconstruct the ACL has biochemical et physiological consequences such as inflammation, pain, and altered proprioception. These alterations contribute to the development of AMI. Therapeutic interventions aimed at addressing AMI encompass a multidimensional approach targeting pain reduction, inflammation management, proprioceptive training, and quadriceps activation. Early management focusing on pain modulation through modalities like ice, compression, and pharmacological agents help mitigate the inflammatory response and alleviate pain, thereby reducing the reflexive inhibition of quadriceps. Quadriceps activation techniques such as neuromuscular electrical stimulation (NMES) and biofeedback training aid in overcoming muscle inhibition and restoring muscle strength. NMES elicits muscle contractions through electrical stimulation, bypassing the inhibitory mechanisms associated with AMI, thus facilitating muscle activation and strength gains. Comprehensive rehabilitation programs tailored to individual needs and stage of recovery are essential for optimizing outcomes in AMI. The objective of this clinical viewpoint is to delineate the significance of adopting a multimodal approach for the effective management of AMI, emphasizing the integration of pain modulation, proprioceptive training, muscle activation techniques, and manual therapy interventions. Highlighting the critical role of early intervention and targeted rehabilitation programs, this article aims to underscore their importance in restoring optimal function and mitigating long-term complications associated with AMI. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

29. Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

Author

Griswold, Max G, Fullman, Nancy, Hawley, Caitlin, Arian, Nicholas, Zimsen, Stephanie RM, Tymeson, Hayley D, Venkateswaran, Vidhya, Tapp, Austin Douglas, Forouzanfar, Mohammad H, Salama, Joseph S, Abate, Kalkidan Hassen, Abate, Degu, Abay, Solomon M, Abbafati, Cristiana, Abdulkader, Rizwan Suliankatchi, Abebe, Zegeye, Aboyans, Victor, Abrar, Mohammed Mehdi, Acharya, Pawan, Adetokunboh, Olatunji O, Adhikari, Tara Ballav, Adsuar, Jose C, Afarideh, Mohsen, Agardh, Emilie Elisabet, Agarwal, Gina, Aghayan, Sargis Aghasi, Agrawal, Sutapa, Ahmed, Muktar Beshir, Akibu, Mohammed, Akinyemiju, Tomi, Akseer, Nadia, Asfoor, Deena H Al, Al-Aly, Ziyad, Alahdab, Fares, Alam, Khurshid, Albujeer, Ammar, Alene, Kefyalew Addis, Ali, Raghib, Ali, Syed Danish, Alijanzadeh, Mehran, Aljunid, Syed Mohamed, Alkerwi, Ala'a, Allebeck, Peter, Alvis-Guzman, Nelson, Amare, Azmeraw T, Aminde, Leopold N, Ammar, Walid, Amoako, Yaw Ampem, Amul, Gianna Gayle Herrera, Andrei, Catalina Liliana, Angus, Colin, Ansha, Mustafa Geleto, Antonio, Carl Abelardo T, Aremu, Olatunde, Ärnlöv, Johan, Artaman, Al, Aryal, Krishna K, Assadi, Reza, Ausloos, Marcel, Avila-Burgos, Leticia, Avokpaho, Euripide F, Awasthi, Ashish, Ayele, Henok Tadesse, Ayer, Rakesh, Ayuk, Tambe B, Azzopardi, Peter S, Badali, Hamid, Badawi, Alaa, Banach, Maciej, Barker-Collo, Suzanne Lyn, Barrero, Lope H, Basaleem, Huda, Baye, Estifanos, Bazargan-Hejazi, Shahrzad, Bedi, Neeraj, Béjot, Yannick, Belachew, Abate Bekele, Belay, Saba Abraham, Bennett, Derrick A, Bensenor, Isabela M, Bernabe, Eduardo, Bernstein, Robert S, Beyene, Addisu Shunu, Beyranvand, Tina, Bhaumik, Soumyadeeep, Bhutta, Zulfiqar A, Biadgo, Belete, Bijani, Ali, Bililign, Nigus, Birlik, Sait Mentes, Birungi, Charles, Bizuneh, Hailemichael, Bjerregaard, Peter, Bjørge, Tone, Borges, Guilherme, Bosetti, Cristina, Boufous, Soufiane, Bragazzi, Nicola Luigi, Brenner, Hermann, and Butt, Zahid A

Subjects
Epidemiology, Public Health, Health Sciences, Substance Misuse, Alcoholism, Alcohol Use and Health, Women's Health, Prevention, Aging, Behavioral and Social Science, 2.4 Surveillance and distribution, Oral and gastrointestinal, Stroke, Cancer, Good Health and Well Being, Adolescent, Adult, Age Distribution, Aged, Aged, 80 and over, Alcohol Drinking, Cause of Death, Commerce, Female, Global Burden of Disease, Global Health, Humans, Male, Middle Aged, Observational Studies as Topic, Population Surveillance, Prevalence, Prospective Studies, Quality-Adjusted Life Years, Retrospective Studies, Risk Assessment, Risk Factors, Sex Distribution, Young Adult, GBD 2016 Alcohol Collaborators, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundAlcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions. With our comprehensive approach to health accounting within the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (DALYs) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older.MethodsUsing 694 data sources of individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use, we produced estimates of the prevalence of current drinking, abstention, the distribution of alcohol consumption among current drinkers in standard drinks daily (defined as 10 g of pure ethyl alcohol), and alcohol-attributable deaths and DALYs. We made several methodological improvements compared with previous estimates: first, we adjusted alcohol sales estimates to take into account tourist and unrecorded consumption; second, we did a new meta-analysis of relative risks for 23 health outcomes associated with alcohol use; and third, we developed a new method to quantify the level of alcohol consumption that minimises the overall risk to individual health.FindingsGlobally, alcohol use was the seventh leading risk factor for both deaths and DALYs in 2016, accounting for 2·2% (95% uncertainty interval [UI] 1·5-3·0) of age-standardised female deaths and 6·8% (5·8-8·0) of age-standardised male deaths. Among the population aged 15-49 years, alcohol use was the leading risk factor globally in 2016, with 3·8% (95% UI 3·2-4·3) of female deaths and 12·2% (10·8-13·6) of male deaths attributable to alcohol use. For the population aged 15-49 years, female attributable DALYs were 2·3% (95% UI 2·0-2·6) and male attributable DALYs were 8·9% (7·8-9·9). The three leading causes of attributable deaths in this age group were tuberculosis (1·4% [95% UI 1·0-1·7] of total deaths), road injuries (1·2% [0·7-1·9]), and self-harm (1·1% [0·6-1·5]). For populations aged 50 years and older, cancers accounted for a large proportion of total alcohol-attributable deaths in 2016, constituting 27·1% (95% UI 21·2-33·3) of total alcohol-attributable female deaths and 18·9% (15·3-22·6) of male deaths. The level of alcohol consumption that minimised harm across health outcomes was zero (95% UI 0·0-0·8) standard drinks per week.InterpretationAlcohol use is a leading risk factor for global disease burden and causes substantial health loss. We found that the risk of all-cause mortality, and of cancers specifically, rises with increasing levels of consumption, and the level of consumption that minimises health loss is zero. These results suggest that alcohol control policies might need to be revised worldwide, refocusing on efforts to lower overall population-level consumption.FundingBill & Melinda Gates Foundation.

Published
2018

30. Dicloxacillin induces CYP2C19, CYP2C9 and CYP3A4 in vivo and in vitro

Author

Stage, Tore Bjerregaard, Graff, Magnus, Wong, Susan, Rasmussen, Louise Ladebo, Nielsen, Flemming, Pottegård, Anton, Brøsen, Kim, Kroetz, Deanna L, Khojasteh, S Cyrus, and Damkier, Per

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Clinical Research, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Adult, Anti-Bacterial Agents, Area Under Curve, Chromatography, Liquid, Cross-Over Studies, Cytochrome P-450 CYP2C19, Cytochrome P-450 CYP2C9, Cytochrome P-450 CYP3A, Cytochrome P-450 Enzyme System, Dicloxacillin, Drug Interactions, Enzyme Induction, Female, Hepatocytes, Humans, Male, Mass Spectrometry, Young Adult, Pharmacology & Pharmacy, Pharmacology and pharmaceutical sciences
Abstract

AimThe aim of this study was to study potential cytochrome P450 (CYP) induction by dicloxacillin.MethodsWe performed an open-label, randomized, two-phase, five-drug clinical pharmacokinetic cocktail crossover study in 12 healthy men with and without pretreatment with 1 g dicloxacillin three times daily for 10 days. Plasma and urine were collected over 24 h and the concentration of all five drugs and their primary metabolites was determined using a liquid chromatography coupled to triple quadrupole mass spectrometry method. Cryopreserved primary human hepatocytes were exposed to dicloxacillin for 48 h and changes in gene expression and the activity of CYP3A4, CYP2C9, CYP2B6 and CYP1A2 were investigated. The activation of nuclear receptors by dicloxacillin was assessed using luciferase assays.ResultsA total of 10 days of treatment with dicloxacillin resulted in a clinically and statistically significant reduction in the area under the plasma concentration-time curve from 0 to 24 h for omeprazole (CYP2C19) {geometric mean ratio [GMR] [95% confidence interval (CI)]: 0.33 [0.24, 0.45]}, tolbutamide (CYP2C9) [GMR (95% CI): 0.73 (0.65, 0.81)] and midazolam (CYP3A4) [GMR (95% CI): 0.54 (0.41, 0.72)]. Additionally, other relevant pharmacokinetic parameters were affected, indicating the induction of CYP2C- and CYP3A4-mediated metabolism by dicloxacillin. Investigations in primary hepatocytes showed a statistically significant dose-dependent increase in CYP expression and activity by dicloxacillin, caused by activation of the pregnane X receptor.ConclusionsDicloxacillin is an inducer of CYP2C- and CYP3A-mediated drug metabolism, and we recommend caution when prescribing dicloxacillin to users of drugs with a narrow therapeutic window.

Published
2018

32. Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma

Author

Holm, Jeppe Sejerø, Funt, Samuel A., Borch, Annie, Munk, Kamilla Kjærgaard, Bjerregaard, Anne-Mette, Reading, James L., Maher, Colleen, Regazzi, Ashley, Wong, Phillip, Al-Ahmadie, Hikmat, Iyer, Gopa, Tamhane, Tripti, Bentzen, Amalie Kai, Herschend, Nana Overgaard, De Wolf, Susan, Snyder, Alexandra, Merghoub, Taha, Wolchok, Jedd D., Nielsen, Morten, Rosenberg, Jonathan E., Bajorin, Dean F., and Hadrup, Sine Reker

Published
2022
Full Text
View/download PDF

35. Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Author

Kanoni, Stavroula, Graham, Sarah E., Wang, Yuxuan, Surakka, Ida, Ramdas, Shweta, Zhu, Xiang, Clarke, Shoa L., Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W., Locke, Adam E., Marouli, Eirini, Zajac, Greg J. M., Wu, Kuan-Han H., Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T., Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F., Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M., Rasheed, Humaira, Havulinna, Aki S., Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A., Lingren, Todd, Feng, QiPing, Kullo, Iftikhar J., Narita, Akira, Takayama, Jun, Martin, Hilary C., Hunt, Karen A., Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E., Campbell, Archie, Lin, Kuang, Millwood, Iona Y., Rasheed, Asif, Hindy, George, Faul, Jessica D., Zhao, Wei, Weir, David R., Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R., Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M., Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian’an, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achilleas, Hottenga, Jouke Jan, Wood, Andrew R., Ji, Yingji, Gao, Zishan, Haworth, Simon, Yousri, Noha A., Mitchell, Ruth E., Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A., Yao, Jie, Manichaikul, Ani, Hwu, Chii-Min, Hung, Yi-Jen, Warren, Helen R., Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L., Goel, Anuj, Sabater-Lleal, Maria, Noordam, Raymond, Mauro, Pala, Matteo, Floris, McDaid, Aaron F., Marques-Vidal, Pedro, Wielscher, Matthias, Trompet, Stella, Sattar, Naveed, Møllehave, Line T., Munz, Matthias, Zeng, Lingyao, Huang, Jianfeng, Yang, Bin, Poveda, Alaitz, Kurbasic, Azra, Lamina, Claudia, Forer, Lukas, Scholz, Markus, Galesloot, Tessel E., Bradfield, Jonathan P., Ruotsalainen, Sanni E., Daw, EWarwick, Zmuda, Joseph M., Mitchell, Jonathan S., Fuchsberger, Christian, Christensen, Henry, Brody, Jennifer A., Vazquez-Moreno, Miguel, Feitosa, Mary F., Wojczynski, Mary K., Wang, Zhe, Preuss, Michael H., Mangino, Massimo, Christofidou, Paraskevi, Verweij, Niek, Benjamins, Jan W., Engmann, Jorgen, Tsao, Noah L., Verma, Anurag, Slieker, Roderick C., Lo, Ken Sin, Zilhao, Nuno R., Le, Phuong, Kleber, Marcus E., Delgado, Graciela E., Huo, Shaofeng, Ikeda, Daisuke D., Iha, Hiroyuki, Yang, Jian, Liu, Jun, Demirkan, Ayşe, Leonard, Hampton L., Marten, Jonathan, Frank, Mirjam, Schmidt, Börge, Smyth, Laura J., Cañadas-Garre, Marisa, Wang, Chaolong, Nakatochi, Masahiro, Wong, Andrew, Hutri-Kähönen, Nina, Sim, Xueling, Xia, Rui, Huerta-Chagoya, Alicia, Fernandez-Lopez, Juan Carlos, Lyssenko, Valeriya, Nongmaithem, Suraj S., Bayyana, Swati, Stringham, Heather M., Irvin, Marguerite R., Oldmeadow, Christopher, Kim, Han-Na, Ryu, Seungho, Timmers, Paul R. H. J., Arbeeva, Liubov, Dorajoo, Rajkumar, Lange, Leslie A., Prasad, Gauri, Lorés-Motta, Laura, Pauper, Marc, Long, Jirong, Li, Xiaohui, Theusch, Elizabeth, Takeuchi, Fumihiko, Spracklen, Cassandra N., Loukola, Anu, Bollepalli, Sailalitha, Warner, Sophie C., Wang, Ya Xing, Wei, Wen B., Nutile, Teresa, Ruggiero, Daniela, Sung, Yun Ju, Chen, Shufeng, Liu, Fangchao, Yang, Jingyun, Kentistou, Katherine A., Banas, Bernhard, Nardone, Giuseppe Giovanni, Meidtner, Karina, Bielak, Lawrence F., Smith, Jennifer A., Hebbar, Prashantha, Farmaki, Aliki-Eleni, Hofer, Edith, Lin, Maoxuan, Concas, Maria Pina, Vaccargiu, Simona, van der Most, Peter J., Pitkänen, Niina, Cade, Brian E., van der Laan, Sander W., Chitrala, Kumaraswamy Naidu, Weiss, Stefan, Bentley, Amy R., Doumatey, Ayo P., Adeyemo, Adebowale A., Lee, Jong Young, Petersen, Eva R. B., Nielsen, Aneta A., Choi, Hyeok Sun, Nethander, Maria, Freitag-Wolf, Sandra, Southam, Lorraine, Rayner, Nigel W., Wang, Carol A., Lin, Shih-Yi, Wang, Jun-Sing, Couture, Christian, Lyytikäinen, Leo-Pekka, Nikus, Kjell, Cuellar-Partida, Gabriel, Vestergaard, Henrik, Hidalgo, Bertha, Giannakopoulou, Olga, Cai, Qiuyin, Obura, Morgan O., van Setten, Jessica, Li, Xiaoyin, Liang, Jingjing, Tang, Hua, Terzikhan, Natalie, Shin, Jae Hun, Jackson, Rebecca D., Reiner, Alexander P., Martin, Lisa Warsinger, Chen, Zhengming, Li, Liming, Kawaguchi, Takahisa, Thiery, Joachim, Bis, Joshua C., Launer, Lenore J., Li, Huaixing, Nalls, Mike A., Raitakari, Olli T., Ichihara, Sahoko, Wild, Sarah H., Nelson, Christopher P., Campbell, Harry, Jäger, Susanne, Nabika, Toru, Al-Mulla, Fahd, Niinikoski, Harri, Braund, Peter S., Kolcic, Ivana, Kovacs, Peter, Giardoglou, Tota, Katsuya, Tomohiro, de Kleijn, Dominique, de Borst, Gert J., Kim, Eung Kweon, Adams, Hieab H. H., Ikram, M. Arfan, Zhu, Xiaofeng, Asselbergs, Folkert W., Kraaijeveld, Adriaan O., Beulens, Joline W. J., Shu, Xiao-Ou, Rallidis, Loukianos S., Pedersen, Oluf, Hansen, Torben, Mitchell, Paul, Hewitt, Alex W., Kähönen, Mika, Pérusse, Louis, Bouchard, Claude, Tönjes, Anke, Chen, Yii-Der Ida, Pennell, Craig E., Mori, Trevor A., Lieb, Wolfgang, Franke, Andre, Ohlsson, Claes, Mellström, Dan, Cho, Yoon Shin, Lee, Hyejin, Yuan, Jian-Min, Koh, Woon-Puay, Rhee, Sang Youl, Woo, Jeong-Taek, Heid, Iris M., Stark, Klaus J., Zimmermann, Martina E., Völzke, Henry, Homuth, Georg, Evans, Michele K., Zonderman, Alan B., Polasek, Ozren, Pasterkamp, Gerard, Hoefer, Imo E., Redline, Susan, Pahkala, Katja, Oldehinkel, Albertine J., Snieder, Harold, Biino, Ginevra, Schmidt, Reinhold, Schmidt, Helena, Bandinelli, Stefania, Dedoussis, George, Thanaraj, Thangavel Alphonse, Kardia, Sharon L. R., Peyser, Patricia A., Kato, Norihiro, Schulze, Matthias B., Girotto, Giorgia, Böger, Carsten A., Jung, Bettina, Joshi, Peter K., Bennett, David A., De Jager, Philip L., Lu, Xiangfeng, Mamakou, Vasiliki, Brown, Morris, Caulfield, Mark J., Munroe, Patricia B., Guo, Xiuqing, Ciullo, Marina, Jonas, Jost B., Samani, Nilesh J., Kaprio, Jaakko, Pajukanta, Päivi, Tusié-Luna, Teresa, Aguilar-Salinas, Carlos A., Adair, Linda S., Bechayda, Sonny Augustin, de Silva, H. Janaka, Wickremasinghe, Ananda R., Krauss, Ronald M., Wu, Jer-Yuarn, Zheng, Wei, Hollander, Anneke Iden, Bharadwaj, Dwaipayan, Correa, Adolfo, Wilson, James G., Lind, Lars, Heng, Chew-Kiat, Nelson, Amanda E., Golightly, Yvonne M., Wilson, James F., Penninx, Brenda, Kim, Hyung-Lae, Attia, John, Scott, Rodney J., Rao, D. C., Arnett, Donna K., Hunt, Steven C., Walker, Mark, Koistinen, Heikki A., Chandak, Giriraj R., Mercader, Josep M., Costanzo, Maria C., Jang, Dongkeun, Burtt, Noël P., Villalpando, Clicerio Gonzalez, Orozco, Lorena, Fornage, Myriam, Tai, EShyong, van Dam, Rob M., Lehtimäki, Terho, Chaturvedi, Nish, Yokota, Mitsuhiro, Liu, Jianjun, Reilly, Dermot F., McKnight, Amy Jayne, Kee, Frank, Jöckel, Karl-Heinz, McCarthy, Mark I., Palmer, Colin N. A., Vitart, Veronique, Hayward, Caroline, Simonsick, Eleanor, van Duijn, Cornelia M., Jin, Zi-Bing, Qu, Jia, Hishigaki, Haretsugu, Lin, Xu, März, Winfried, Gudnason, Vilmundur, Tardif, Jean-Claude, Lettre, Guillaume, Hart, Leen M.‘t, Elders, Petra J. M., Damrauer, Scott M., Kumari, Meena, Kivimaki, Mika, van der Harst, Pim, Spector, Tim D., Loos, Ruth J. F., Province, Michael A., Parra, Esteban J., Cruz, Miguel, Psaty, Bruce M., Brandslund, Ivan, Pramstaller, Peter P., Rotimi, Charles N., Christensen, Kaare, Ripatti, Samuli, Widén, Elisabeth, Hakonarson, Hakon, Grant, Struan F. A., Kiemeney, Lambertus A. L. M., de Graaf, Jacqueline, Loeffler, Markus, Kronenberg, Florian, Gu, Dongfeng, Erdmann, Jeanette, Schunkert, Heribert, Franks, Paul W., Linneberg, Allan, Jukema, J. Wouter, Khera, Amit V., Männikkö, Minna, Jarvelin, Marjo-Riitta, Kutalik, Zoltan, Francesco, Cucca, Mook-Kanamori, Dennis O., van Dijk, Ko Willems, Watkins, Hugh, Strachan, David P., Grarup, Niels, Sever, Peter, Poulter, Neil, Chuang, Lee-Ming, Rotter, Jerome I., Dantoft, Thomas M., Karpe, Fredrik, Neville, Matt J., Timpson, Nicholas J., Cheng, Ching-Yu, Wong, Tien-Yin, Khor, Chiea Chuen, Li, Hengtong, Sabanayagam, Charumathi, Peters, Annette, Gieger, Christian, Hattersley, Andrew T., Pedersen, Nancy L., Magnusson, Patrik K. E., Boomsma, Dorret I., Willemsen, Allegonda H. M., Cupples, LAdrienne, van Meurs, Joyce B. J., Ghanbari, Mohsen, Gordon-Larsen, Penny, Huang, Wei, Kim, Young Jin, Tabara, Yasuharu, Wareham, Nicholas J., Langenberg, Claudia, Zeggini, Eleftheria, Kuusisto, Johanna, Laakso, Markku, Ingelsson, Erik, Abecasis, Goncalo, Chambers, John C., Kooner, Jaspal S., de Vries, Paul S., Morrison, Alanna C., Hazelhurst, Scott, Ramsay, Michèle, North, Kari E., Daviglus, Martha, Kraft, Peter, Martin, Nicholas G., Whitfield, John B., Abbas, Shahid, Saleheen, Danish, Walters, Robin G., Holmes, Michael V., Black, Corri, Smith, Blair H., Baras, Aris, Justice, Anne E., Buring, Julie E., Ridker, Paul M., Chasman, Daniel I., Kooperberg, Charles, Tamiya, Gen, Yamamoto, Masayuki, van Heel, David A., Trembath, Richard C., Wei, Wei-Qi, Jarvik, Gail P., Namjou, Bahram, Hayes, M. Geoffrey, Ritchie, Marylyn D., Jousilahti, Pekka, Salomaa, Veikko, Hveem, Kristian, Åsvold, Bjørn Olav, Kubo, Michiaki, Kamatani, Yoichiro, Okada, Yukinori, Murakami, Yoshinori, Kim, Bong-Jo, Thorsteinsdottir, Unnur, Stefansson, Kari, Zhang, Jifeng, Chen, YEugene, Ho, Yuk-Lam, Lynch, Julie A., Rader, Daniel J., Tsao, Philip S., Chang, Kyong-Mi, Cho, Kelly, O’Donnell, Christopher J., Gaziano, John M., Wilson, Peter W. F., Frayling, Timothy M., Hirschhorn, Joel N., Kathiresan, Sekar, Mohlke, Karen L., Sun, Yan V., Morris, Andrew P., Boehnke, Michael, Brown, Christopher D., Natarajan, Pradeep, Deloukas, Panos, Willer, Cristen J., Assimes, Themistocles L., and Peloso, Gina M.

Published
2022
Full Text
View/download PDF

38. Current-induced runaway vibrations in dehydrogenated graphene nanoribbons

Author

Christensen, Rasmus Bjerregaard, Lü, Jing-Tao, Hedegård, Per, and Brandbyge, Mads

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We employ a semi-classical Langevin approach to study current-induced atomic dynamics in a partially dehydrogenated armchair graphene nanoribbon. All parameters are obtained from density functional theory. The dehydrogenated carbon dimers behave as effective impurities, whose motion decouples from the rest of carbon atoms. The electrical current can couple the dimer motion in a coherent fashion. The coupling, which is mediated by nonconservative and pseudo-magnetic current-induced forces, change the atomic dynamics, and thereby show their signature in this simple system. We study the atomic dynamics and current-induced vibrational instabilities using a simplified eigen-mode analysis.Our study shows that the armchair nanoribbon serves as a possible testbed for probing the current-induced forces., Comment: 6 pages, 2 figures, Beilstein J. Nanotechnology, Thematic Series "Molecular machines and devices"

Published
2015
Full Text
View/download PDF

39. Algebraic structure of the Lorentz and of the Poincar\'e Lie algebras

Author

Bjerregaard, Pablo Alberca, Barquero, Dolores MartÍn, GonzÁlez, CÁndido MartÍn, and Ndoye, Daouda

Subjects
Mathematics - Rings and Algebras
Abstract

We start with the Lorentz algebra $ L=o_{R}(1,3)$ over the reals and find a suitable basis $B$ relative to which the structure constants are integers. Thus we consider the $Z$-algebra $L_{Z}$ which is free as a $Z$-module and its $Z$-basis is $B$. This allows us to define the Lorentz type algebra $L_K:=L_{Z}\otimes_{Z} K$ over any field $K$. In a similar way, we consider Poincar\'e type algebras over any field $K$. In this paper we study the ideal structure of Lorentz and of Poincar\'e type algebras over different fields. It turns out that Lorentz type algebras are simple if and only if the ground field has no square root of $-1$. Thus, they are simple over the reals but not over the complex. Also, if the ground field is of characteristic $2$ then Lorentz and Poincar\'e type algebras are neither simple nor semisimple. We extend the study of simplicity of the Lorentz algebra to the case of a ring of scalars where we have to use the notion of $m$-simplicity (relative to a maximal ideal $m$ of the ground ring of scalars). The Lorentz type algebras over a finite field $F_q$ where $q=p^n$ and $p$ is odd are simple if and only if $n$ is odd and $p$ of the form $p=4k+3$. In case $p=2$ then the Lorentz type algebra are not simple. Once we know the ideal structure of the algebras, we get some information of their automorphism groups. For the Lorentz type algebras (except in the case of characteristic $2$) we describe the affine group scheme of automorphisms and the derivation algebras. For the Poincar\'e algebras we restrict this program to the case of an algebraically closed field of characteristic other than $2$.

Published
2015

40. DLG4-related synaptopathy: a new rare brain disorder

Author

Rodríguez-Palmero, Agustí, Boerrigter, Melissa Maria, Gómez-Andrés, David, Aldinger, Kimberly A., Marcos-Alcalde, Íñigo, Popp, Bernt, Everman, David B., Lovgren, Alysia Kern, Arpin, Stephanie, Bahrambeigi, Vahid, Beunders, Gea, Bisgaard, Anne-Marie, Bjerregaard, V. A., Bruel, Ange-Line, Challman, Thomas D., Cogné, Benjamin, Coubes, Christine, de Man, Stella A., Denommé-Pichon, Anne-Sophie, Dye, Thomas J., Elmslie, Frances, Feuk, Lars, García-Miñaúr, Sixto, Gertler, Tracy, Giorgio, Elisa, Gruchy, Nicolas, Haack, Tobias B., Haldeman-Englert, Chad R., Haukanes, Bjørn Ivar, Hoyer, Juliane, Hurst, Anna C. E., Isidor, Bertrand, Soller, Maria Johansson, Kushary, Sulagna, Kvarnung, Malin, Landau, Yuval E., Leppig, Kathleen A., Lindstrand, Anna, Kleinendorst, Lotte, MacKenzie, Alex, Mandrile, Giorgia, Mendelsohn, Bryce A., Moghadasi, Setareh, Morton, Jenny E., Moutton, Sebastien, Müller, Amelie J., O’Leary, Melanie, Pacio-Míguez, Marta, Palomares-Bralo, Maria, Parikh, Sumit, Pfundt, Rolph, Pode-Shakked, Ben, Rauch, Anita, Repnikova, Elena, Revah-Politi, Anya, Ross, Meredith J., Ruivenkamp, Claudia A. L., Sarrazin, Elisabeth, Savatt, Juliann M., Schlüter, Agatha, Schönewolf-Greulich, Bitten, Shad, Zohra, Shaw-Smith, Charles, Shieh, Joseph T., Shohat, Motti, Spranger, Stephanie, Thiese, Heidi, Mau-Them, Frederic Tran, van Bon, Bregje, van de Burgt, Ineke, van de Laar, Ingrid M. B. H., van Drie, Esmée, van Haelst, Mieke M., van Ravenswaaij-Arts, Conny M., Verdura, Edgard, Vitobello, Antonio, Waldmüller, Stephan, Whiting, Sharon, Zweier, Christiane, Prada, Carlos E., de Vries, Bert B. A., Dobyns, William B., Reiter, Simone F., Gómez-Puertas, Paulino, Pujol, Aurora, and Tümer, Zeynep

Published
2021
Full Text
View/download PDF

41. Inner derivations of exceptional Lie algebras in prime characteristic

Author

Alberca-Bjerregaard, Pablo, Martín-Barquero, Dolores, and Martín-González, Cándido

Subjects
Mathematics - Rings and Algebras
Abstract

It is well-known that every derivation of a semisimple Lie algebra $L$ over an algebraically closed field $F$ with characteristic zero is inner. The aim of this paper is to show what happens if the characteristic of $F$ is prime with $L$ an exceptional Lie algebra. We prove that if $L$ is a Chevalley Lie algebra of type $\{G_2,F_4,E_6,E_7,E_8\}$ over a field of characteristic $p$ then the derivations of $L$ are inner except in the cases $G_2$ with $p=2$, $E_6$ with $p=3$ and $E_7$ with $p=2$.

Published
2014

44. Manufacturing doubt about endocrine disrupter science--A rebuttal of industry-sponsored critical comments on the UNEP/WHO report "State of the Science of Endocrine Disrupting Chemicals 2012".

Author

Bergman, Åke, Becher, Georg, Blumberg, Bruce, Bjerregaard, Poul, Bornman, Riana, Brandt, Ingvar, Casey, Stephanie C, Frouin, Heloise, Giudice, Linda C, Heindel, Jerrold J, Iguchi, Taisen, Jobling, Susan, Kidd, Karen A, Kortenkamp, Andreas, Lind, P Monica, Muir, Derek, Ochieng, Roseline, Ropstad, Erik, Ross, Peter S, Skakkebaek, Niels Erik, Toppari, Jorma, Vandenberg, Laura N, Woodruff, Tracey J, and Zoeller, R Thomas

Subjects
Animals, Humans, Endocrine Disruptors, EDCs, Endocrine disruption, Endocrine disruptors, Pharmacology and Pharmaceutical Sciences, Toxicology
Abstract

We present a detailed response to the critique of "State of the Science of Endocrine Disrupting Chemicals 2012" (UNEP/WHO, 2013) by financial stakeholders, authored by Lamb et al. (2014). Lamb et al.'s claim that UNEP/WHO (2013) does not provide a balanced perspective on endocrine disruption is based on incomplete and misleading quoting of the report through omission of qualifying statements and inaccurate description of study objectives, results and conclusions. Lamb et al. define extremely narrow standards for synthesizing evidence which are then used to dismiss the UNEP/WHO 2013 report as flawed. We show that Lamb et al. misuse conceptual frameworks for assessing causality, especially the Bradford-Hill criteria, by ignoring the fundamental problems that exist with inferring causality from empirical observations. We conclude that Lamb et al.'s attempt of deconstructing the UNEP/WHO (2013) report is not particularly erudite and that their critique is not intended to be convincing to the scientific community, but to confuse the scientific data. Consequently, it promotes misinterpretation of the UNEP/WHO (2013) report by non-specialists, bureaucrats, politicians and other decision makers not intimately familiar with the topic of endocrine disruption and therefore susceptible to false generalizations of bias and subjectivity.

Published
2015

45. Light emission and finite frequency shot noise in molecular junctions: from tunneling to contact

Author

Lü, Jing-Tao, Christensen, Rasmus Bjerregaard, and Brandbyge, Mads

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Scanning tunneling microscope induced light emission from an atomic or molecular junction has been probed from the tunneling to contact regime in recent experiments. There, the intensity of the light emission shows strong correlation with the current/charge fluctuations at optical frequencies. We show that this is consistent with the established theory in the tunneling regime, by writing the finite-frequency shot noise as a sum of inelastic transitions between different electronic states. Based on this, we develop a practical scheme to perform calculations on realistic structures using Green's functions. The photon emission yields obtained re-produce the essential feature of the experiments., Comment: published version, Phys. Rev. B 88, 045413 (2013)

Published
2013
Full Text
View/download PDF

48. Atlas of Leavitt Path Algebras of small graphs

Author

Bjerregaard, Pablo Alberca, Pino, Gonzalo Aranda, Barquero, Dolores Martín, González, Cándido Martín, and Molina, Mercedes Siles

Subjects
Mathematics - Rings and Algebras
Abstract

The aim of this work is the description of the isomorphism classes of all Leavitt path algebras coming from graphs satisfying Condition (Sing) with up to three vertices. In particular, this classification recovers the one achieved by Abrams et al. in the case of graphs whose Leavitt path algebras are purely infinite simple. The description of the isomorphism classes is given in terms of a series of invariants including the K_0 group, the socle, the number of loops with no exits and the number of hereditary and saturated subsets of the graph.

Published
2011

49. Uncovering the Genetic History of the Present-Day Greenlandic Population

Author

Moltke, Ida, Fumagalli, Matteo, Korneliussen, Thorfinn S, Crawford, Jacob E, Bjerregaard, Peter, Jørgensen, Marit E, Grarup, Niels, Gulløv, Hans Christian, Linneberg, Allan, Pedersen, Oluf, Hansen, Torben, Nielsen, Rasmus, and Albrechtsen, Anders

Subjects
Biological Sciences, Genetics, Human Genome, Adult, DNA, Mitochondrial, Databases, Factual, Evolution, Molecular, Female, Gene Flow, Gene Frequency, Genome, Human, Genotype, Genotyping Techniques, Greenland, Humans, Male, Models, Genetic, Phylogeography, Polymorphism, Single Nucleotide, White People, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Because of past limitations in samples and genotyping technologies, important questions about the history of the present-day Greenlandic population remain unanswered. In an effort to answer these questions and in general investigate the genetic history of the Greenlandic population, we analyzed ∼200,000 SNPs from more than 10% of the adult Greenlandic population (n = 4,674). We found that recent gene flow from Europe has had a substantial impact on the population: more than 80% of the Greenlanders have some European ancestry (on average ∼25% of their genome). However, we also found that the amount of recent European gene flow varies across Greenland and is far smaller in the more historically isolated areas in the north and east and in the small villages in the south. Furthermore, we found that there is substantial population structure in the Inuit genetic component of the Greenlanders and that individuals from the east, west, and north can be distinguished from each other. Moreover, the genetic differences in the Inuit ancestry are consistent with a single colonization wave of the island from north to west to south to east. Although it has been speculated that there has been historical admixture between the Norse Vikings who lived in Greenland for a limited period ∼600-1,000 years ago and the Inuit, we found no evidence supporting this hypothesis. Similarly, we found no evidence supporting a previously hypothesized admixture event between the Inuit in East Greenland and the Dorset people, who lived in Greenland before the Inuit.

Published
2015

50. A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

Author

Moltke, Ida, Grarup, Niels, Jørgensen, Marit E, Bjerregaard, Peter, Treebak, Jonas T, Fumagalli, Matteo, Korneliussen, Thorfinn S, Andersen, Marianne A, Nielsen, Thomas S, Krarup, Nikolaj T, Gjesing, Anette P, Zierath, Juleen R, Linneberg, Allan, Wu, Xueli, Sun, Guangqing, Jin, Xin, Al-Aama, Jumana, Wang, Jun, Borch-Johnsen, Knut, Pedersen, Oluf, Nielsen, Rasmus, Albrechtsen, Anders, and Hansen, Torben

Subjects
Biological Sciences, Genetics, Human Genome, Diabetes, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Adult, Blood Glucose, Codon, Nonsense, Diabetes Mellitus, Type 2, GTPase-Activating Proteins, Gene Frequency, Genetic Variation, Genome-Wide Association Study, Genotype, Greenland, Humans, Insulin, Insulin Resistance, Middle Aged, Muscle, Skeletal, General Science & Technology
Abstract

The Greenlandic population, a small and historically isolated founder population comprising about 57,000 inhabitants, has experienced a dramatic increase in type 2 diabetes (T2D) prevalence during the past 25 years. Motivated by this, we performed association mapping of T2D-related quantitative traits in up to 2,575 Greenlandic individuals without known diabetes. Using array-based genotyping and exome sequencing, we discovered a nonsense p.Arg684Ter variant (in which arginine is replaced by a termination codon) in the gene TBC1D4 with an allele frequency of 17%. Here we show that homozygous carriers of this variant have markedly higher concentrations of plasma glucose (β = 3.8 mmol l(-1), P = 2.5 × 10(-35)) and serum insulin (β = 165 pmol l(-1), P = 1.5 × 10(-20)) 2 hours after an oral glucose load compared with individuals with other genotypes (both non-carriers and heterozygous carriers). Furthermore, homozygous carriers have marginally lower concentrations of fasting plasma glucose (β = -0.18 mmol l(-1), P = 1.1 × 10(-6)) and fasting serum insulin (β = -8.3 pmol l(-1), P = 0.0014), and their T2D risk is markedly increased (odds ratio (OR) = 10.3, P = 1.6 × 10(-24)). Heterozygous carriers have a moderately higher plasma glucose concentration 2 hours after an oral glucose load than non-carriers (β = 0.43 mmol l(-1), P = 5.3 × 10(-5)). Analyses of skeletal muscle biopsies showed lower messenger RNA and protein levels of the long isoform of TBC1D4, and lower muscle protein levels of the glucose transporter GLUT4, with increasing number of p.Arg684Ter alleles. These findings are concomitant with a severely decreased insulin-stimulated glucose uptake in muscle, leading to postprandial hyperglycaemia, impaired glucose tolerance and T2D. The observed effect sizes are several times larger than any previous findings in large-scale genome-wide association studies of these traits and constitute further proof of the value of conducting genetic association studies outside the traditional setting of large homogeneous populations.

Published
2014

Catalog

Books, media, physical & digital resources
See catalog results