Review
Medicine, Research & Experimental
Mark Chandy, Detlef Obal, Joseph C. Wu
Summary: Induced pluripotent stem cells (iPSCs) are a powerful modeling system to investigate the effects of environmental exposure on the cardiovascular system. They can elucidate the impacts of environmental factors and genetic polymorphisms on cardiovascular diseases.
EMBO MOLECULAR MEDICINE
(2022)
Article
Computer Science, Artificial Intelligence
Chunzhi Gu, Xuequan Lu, Chao Zhang
Summary: This paper proposes a probability-based approach for color transfer and treats it as a parameter estimation problem. By utilizing Gaussian Mixture Model and Expectation-Maximization algorithm for optimization, multiple high-quality color transfer results can be generated.
PATTERN RECOGNITION
(2022)
Review
Biochemistry & Molecular Biology
Ma'mon M. Hatmal, Mohammad A. I. Al-Hatamleh, Amin N. Olaimat, Walhan Alshaer, Hanan Hasan, Khaled A. Albakri, Enas Alkhafaji, Nada N. Issa, Murad A. Al-Holy, Salim M. Abderrahman, Atiyeh M. Abdallah, Rohimah Mohamud
Summary: Human breast milk contains not only nutritional components but also abundant microRNAs, which can impact epigenetic mechanisms and regulate immune and physiological functions. Studying the microRNA composition of human breast milk is important for improving nutrition during pregnancy and infancy and preventing future diseases.
Article
Multidisciplinary Sciences
Kyle N. Klein, Peiyao A. Zhao, Xiaowen Lyu, Takayo Sasaki, Daniel A. Bartlett, Amar M. Singh, Ipek Tasan, Meng Zhang, Lotte P. Watts, Shin-ichiro Hiraga, Toyoaki Natsume, Xuemeng Zhou, Timour Baslan, Danny Leung, Masato T. Kanemaki, Anne D. Donaldson, Huimin Zhao, Stephen Dalton, Victor G. Corces, David M. Gilbert
Summary: Loss of RIF1 disrupts the temporal order of DNA replication, leading to changes in chromatin modifications and genome architecture. Depletion of RIF1 causes increased heterogeneity between individual cells, resulting in replication-dependent disruption of histone modifications and alterations in genome architecture. These effects are magnified with successive cycles of altered replication timing.
Article
Multidisciplinary Sciences
Nicolas Altemose, Glennis A. Logsdon, Andrey Bzikadze, Pragya Sidhwani, Sasha A. Langley, Gina Caldas, Savannah J. Hoyt, Lev Uralsky, Fedor D. Ryabov, Colin J. Shew, Michael E. G. Sauria, Matthew Borchers, Ariel Gershman, Alla Mikheenko, Valery A. Shepelev, Tatiana Dvorkina, Olga Kunyavskaya, Mitchell R. Vollger, Arang Rhie, Ann M. McCartney, Mobin Asri, Ryan Lorig-Roach, Kishwar Shafin, Julian K. Lucas, Sergey Aganezov, Daniel Olson, Leonardo Gomes de Lima, Tamara Potapova, Gabrielle A. Hartley, Marina Haukness, Peter Kerpedjiev, Fedor Gusev, Kristof Tigyi, Shelise Brooks, Alice Young, Sergey Nurk, Sergey Koren, Sofie R. Salama, Benedict Paten, Evgeny Rogaev, Aaron Streets, Gary H. Karpen, Abby F. Dernburg, Beth A. Sullivan, Aaron F. Straight, Travis J. Wheeler, Jennifer L. Gerton, Evan E. Eichler, Adam M. Phillippy, Winston Timp, Megan Y. Dennis, Rachel J. O'Neill, Justin M. Zook, Michael C. Schatz, Pavel A. Pevzner, Mark Diekhans, Charles H. Langley, Ivan A. Alexandrov, Karen H. Miga
Summary: Current human genome assemblies have neglected repetitive sequences near centromeres, hindering our understanding of their organization and evolution. A new approach has allowed researchers to comprehensively study these sequences, revealing their structural rearrangements and variations.
Article
Multidisciplinary Sciences
Silvio Zaina, Manel Esteller, Isabel Goncalves, Gertrud Lund
Summary: Accelerated epigenetic ageing has been detected in peripheral blood cells of atherosclerotic patients, but evidence in the vascular wall is lacking. This study investigates the trends of epigenetic ageing in the atheroma and finds dynamic DNA methylation age mosaicism that is related to atherosclerosis, changes from acceleration to deceleration with chronological ageing, and is consistent in both human aorta and carotid atheroma.
Review
Biotechnology & Applied Microbiology
Marta Pogribna, George Hammons
Summary: This review summarizes the current evidence of alterations in cytosine DNA methylation and histone modifications in response to nanomaterials and nanoparticles exposures, highlighting existing knowledge gaps regarding the role of epigenetic alterations in their toxicity. Additionally, it discusses the potential role of epigenetic changes as translational biomarkers for detecting adverse effects of nanomaterials and nanoparticles.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Article
Psychiatry
Yukihiro Takemura, Takaki Tanifuji, Satoshi Okazaki, Yutaka Shinko, Ikuo Otsuka, Tadasu Horai, Toshiyuki Shirai, Katsuro Aso, Noriya Yamamoto, Akitoyo Hishimoto
Summary: The use of methamphetamine accelerates biological aging and induces specific changes in DNA methylation-based age-predictive factors.
PSYCHIATRY RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Lars Fuhrmann, Saskia Lindner, Alexander-Thomas Hauser, Clemens Hoese, Oliver Kretz, Clemens D. Cohen, Maja T. Lindenmeyer, Wolfgang Sippl, Manfred Jung, Tobias B. Huber, Nicola Wanner
Summary: Research suggests that low nephron numbers at birth may increase the risk of chronic kidney disease or hypertension later in life. Environmental stressors such as maternal malnutrition, medication, and smoking can affect renal size at birth. The study also found that using metanephric organ cultures can simulate single-variable environmental conditions, aiding in studying the role of epigenetic modifiers in renal development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ariel Gershman, Michael E. G. Sauria, Xavi Guitart, Mitchell R. Vollger, Paul W. Hook, Savannah J. Hoyt, Miten Jain, Alaina Shumate, Roham Razaghi, Sergey Koren, Nicolas Altemose, Gina Caldas, Glennis A. Logsdon, Arang Rhie, Evan E. Eichler, Michael C. Schatz, Rachel J. O'Neill, Adam M. Phillippy, Karen H. Miga, Winston Timp
Summary: This study presents a high-resolution epigenetic analysis of the telomere-to-telomere human reference genome, revealing important insights into gene activity, clinical regulation, and providing a framework for investigating elusive regions of the genome.
Article
Engineering, Civil
Xiaoxu Chen, Chengyuan Zhang, Zhanhong Cheng, Yuang Hou, Lijun Sun
Summary: Car-following models are essential for microscopic traffic simulation. This study presents a data-driven model based on a Bayesian Gaussian mixture model for probabilistic forecasting of human car-following behaviors. The model captures the temporal dynamics of human car-following behaviors and provides accurate predictions with quantified uncertainty. The results suggest that this model is promising for modeling and forecasting car-following behaviors.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2023)
Article
Biochemistry & Molecular Biology
Filomena Mazzeo, Rosaria Meccariello, Ezia Guatteo
Summary: The use and abuse of opioids have negative health effects, including addiction and overdose. Understanding how opioids affect the dopamine circuit in the brain can provide insights into addiction processes and help develop effective therapies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Automation & Control Systems
Xiangrui Zhang, Chunyue Song, Jun Zhao, Xiaogang Deng
Summary: This article proposes a robust domain adaptation method to mitigate the negative effect of sensor degradation on soft sensor modeling. By decomposing industrial data into Gaussian domains, a domain discrepancy indicator is designed for domain adaptation and process mode recognition. Furthermore, a domain mapping is applied to correct the drifted online input data, enhancing the robustness of the soft sensor.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2022)
Article
Chemistry, Multidisciplinary
Jose F. Rodrigues, Sebastien Bailly, Jean-Louis Pepin, Lorraine Goeuriot, Gabriel Spadon, Sihem Amer-Yahia
Summary: This research introduces an unsupervised machine-learning methodology that translates CPAP therapy adherence data into discrete numbers corresponding to 30-day patterns and captures the dynamic nature of CPAP through time series summaries. The method allows for more precise evaluation of therapy adherence and early identification of treatment issues.
APPLIED SCIENCES-BASEL
(2022)
Review
Pharmacology & Pharmacy
Chenglong Cheng, Yajie Wu, Yurong Huang, Qiuyun Xue, Yuting Wang, Faxue Liao, Xiaomei Wang, Chenggui Miao
Summary: Osteoarthritis is a leading cause of disability and pain worldwide, and abnormal autophagy has been closely associated with this degenerative disease. Drugs targeting autophagy have shown significant potential in hindering the progression of osteoarthritis. The occurrence and development of autophagy in osteoarthritis are regulated by various factors, and it has greatly influenced the pathological mechanism of the disease. However, further research is needed to determine how autophagy affects the pathology of osteoarthritis and its application in treatment and diagnosis.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Jorn Loetsch, Sebastian Malkusch, Alfred Ultsch
Summary: Optimal distribution-preserving class-proportional downsampling yields data subsets that reflect the structure of the entire data better than those obtained with the standard method. By using distributional similarity as the only selection criterion, the proposed method does not in any way affect the results of a later planned analysis.
Article
Chemistry, Multidisciplinary
Joern Loetsch, Constantin A. Hintschich, Petros Petridis, Juergen Pade, Thomas Hummel
Summary: The study found that patients with nasal polyposis are a well-predisposed group for reliable self-assessment, but the correlation between self-ratings and actual olfactory test results was weak mainly due to group differences in olfactory diagnoses. While olfactory self-ratings weakly correlated with quality of life scores, they were informative in assigning categorical olfactory diagnoses.
APPLIED SCIENCES-BASEL
(2021)
Article
Cell Biology
Sebastian Malkusch, Johanna Rahm, Marina S. Dietz, Mike Heilemann, Jean-Baptiste Sibarita, Jorn Lotsch
Summary: This study proposes a method that analyzes the differences in receptor mobility between internalin B-treated and -untreated cells. By using hidden Markov modeling and explainable artificial intelligence, the key differences in MET under different treatment conditions are learned from single-particle tracking data, allowing for inference of cellular information.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Biochemistry & Molecular Biology
Teemu Miettinen, Anni I. Nieminen, Pekka Mantyselka, Eija Kalso, Jorn Lotsch
Summary: Recent scientific evidence suggests that metabolomic changes are associated with chronic pain phenotypes. However, problems such as sleep disorders or obesity may complicate the metabolome pattern. In this study, common metabolomics markers at the interface of persistent pain, sleep, and obesity were identified. Two independent lines of data analysis were used to investigate the complex phenotype. The findings suggest that metabolomic changes associated with co-occurring problems may play a role in the development of severe pain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Alfred Ultsch, Joern Loetsch
Summary: In bioinformatics data processing, data transformations are commonly used for data projection and clustering. However, the commonly used Euclidean distance metric is not scale invariant and may be inappropriate for complex variables, leading to negative impacts on cluster analysis results. This study proposes the EDO transformation as a better alternative to traditional z-standardization, and demonstrates its effectiveness through simulations and real data applications.
BMC BIOINFORMATICS
(2022)
Article
Medicine, General & Internal
Joern Loetsch, Anne Huster, Thomas Hummel
Summary: This study expanded the clinical diagnostic repertoire of olfaction by including additional tests, revealing the importance of odor dilution sorting tasks in cluster assignment. These findings provide a new direction for future olfaction research.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Behavioral Sciences
Brandon Gunasekera, Cathy Davies, Grace Blest-Hopley, Mattia Veronese, Nick F. Ramsey, Matthijs G. Bossong, Joaquim Radua, Sagnik Bhattacharyya
Summary: This study investigated the acute spatial effect of THC on regional brain activation or blood flow in human subjects. The researchers also explored the relationship between the neuromodulatory effects of THC and the expression of CB1R and CB2R receptors. The findings suggest that THC has neuromodulatory effects in brain regions involved in cognitive tasks and processes, with stronger effects observed in regions with higher levels of CB1R expression.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2022)
Review
Pharmacology & Pharmacy
Yazan Noufal, Dario Kringel, Stefan W. Toennes, Rafael Dudziak, Jorn Loetsch
Summary: Prescription of morphine for analgesia has been associated with drug-related deaths at an incidence rate of 0.3% to 4%. The pharmacological properties of morphine make it challenging to determine the causality between morphine administration and patient death, including its slow transfer in the body and the presence of an active metabolite with opioid effects. There is also no defined toxic dose or concentration of morphine. This article summarizes reported deaths related to morphine therapy and analyzes the stability of morphine and its metabolites in postmortem biological samples. It emphasizes the limited validity of inferring the administered dose from postmortem blood concentrations and highlights the need for collaborative assessment among medical experts.
PHARMACOLOGY & THERAPEUTICS
(2023)
Editorial Material
Anesthesiology
Jörn Loetsch, Alfred Ultsch
EUROPEAN JOURNAL OF PAIN
(2023)
Article
Multidisciplinary Sciences
Jörn Loetsch, Alfred Ultsch
Summary: This report proposes a precise method to address the skewed distribution of feature importance, reducing the feature set to the informative minimum. The recursive cABC analysis limits the data projection dimensions while preserving relevant information and guiding feature selection to the most important class-relevant information in machine learning.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Joern Loetsch, Benjamin Mayer, Dario Kringel
Summary: Sex differences in pain perception have been studied extensively, but sex-specific pain pharmacology has not progressed much in precision medicine applications. This study analyzed pain threshold data from male and female volunteers and found that the algorithm could accurately predict a person's sex based on mechanical stimuli, but not thermal stimuli or sensitization responses. This suggests that precision medicine approaches to pain should focus on molecular targets that convert mechanical information into pain signals.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Joern Loetsch, Thomas Hummel, Alfred Ultsch
Summary: This report discusses the random walk component in a clinical olfactory test and explores its characteristics through computer simulations. The results indicate that the starting point and length of the random walk significantly affect the probability of achieving high test scores.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Alfred Ultsch, Joern Loetsch
Summary: Bayesian inference is widely used in science, but its calculation is not robust in regions of low evidence. Researchers propose a robust extension approach that improves class assignment accuracy for extreme values and weak evidence data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Neurosciences
Jorn Loetsch, Alfred Ultsch, Benjamin Mayer, Dario Kringel
Summary: The collection of increasing amounts of data in health care has become relevant for pain therapy and research. This report summarizes the application of artificial intelligence and machine learning methods in pain research and highlights their advantages and limitations.
Article
Biochemistry & Molecular Biology
Joern Loetsch, Laura Mustonen, Hanna Harno, Eija Kalso
Summary: This study identified specific proteins related to persistent postsurgical neuropathic pain (PPSNP) in women who had experienced intercostobrachial nerve injury during breast cancer surgery. These proteins play important roles in immune processes such as cell migration, chemotaxis, and cytokine-signaling. The findings provide insights into the neuroinflammatory processes associated with the development of neuropathic pain after intraoperative nerve lesion.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)