Article
Geography
Jiangfeng She, Bo Chen, Junzhong Tan, Qiang Zhao, Rongcun Ge
Summary: This study proposes a novel method for simplifying 3D building models by considering both the model mesh and building structure. The experimental results show that the proposed method achieves a high simplification rate while maintaining the simplification quality, and the simplified building model is consistent with the original model in spatial analysis.
TRANSACTIONS IN GIS
(2022)
Article
Biochemistry & Molecular Biology
Ya Cui, Fanglue Peng, Dan Wang, Yumei Li, Jason Sheng Li, Lei Li, Wei Li
Summary: Genome-wide association studies have identified numerous non-coding SNPs associated with human traits and diseases, with functional interpretation remaining a challenge. The concept of 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) has been established to interpret a portion of GWAS SNPs. The 3'aQTL-atlas provides a comprehensive database of nearly 1.49 million SNPs associated with APA across 49 human tissues, aiming to explain genetic basis of APA and APA-linked susceptibility genes in human traits and diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Y. H. Yang
Summary: The emergence of multi-sample multi-condition single-cell multi-cohort studies allows researchers to investigate different cell states. The algorithm scMerge2 enables integration and analysis of large-scale single-cell datasets, revealing accurate signatures of disease progression and removing dataset variability in various single-cell profiling technologies.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Mohammad Hossein Nadian, Sepideh Farmani, Ali Ghazizadeh
Summary: A new software called MATres was developed for accurate targeting and designing of skull implants for brain stimulation and electrophysiological recording. The software showed promising results in both human and macaque studies.
JOURNAL OF NEUROSCIENCE METHODS
(2023)
Article
Cardiac & Cardiovascular Systems
Monika Mohenska, Nathalia M. Tan, Alex Tokolyi, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Karel van Duijvenboden, Hieu T. Nim, Yuan M. M. Ji, Natalie Charitakis, Denis Bienroth, Francesca Bolk, Celine Vivien, Anja S. Knaupp, David R. Powell, David A. Elliott, Enzo R. Porrello, Susan K. Nilsson, Gonzalo del Monte-Nieto, Nadia A. Rosenthal, Fernando J. Rossello, Jose M. Polo, Mirana Ramialison
Summary: Researchers combined transcriptomics with 3D modelling to investigate spatial gene expression in the mammalian heart by dissecting and sequencing 18 anatomical sections of the adult mouse heart. They identified known and novel genes with complex spatial expression in heart sub-compartments, and created 3D-cardiomics for easy exploration of these data in a 3D model of the heart.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2022)
Article
Multidisciplinary Sciences
Boram Lee, Ju-Hyun Lee, Dai Hyun Kim, Eun Sil Kim, Bo Kyoung Seo, Im Joo Rhyu, Woong Sun
Summary: Transparency is crucial for studying and understanding the structure and function of biological specimens. This study improved the recipe for adjusting the refractive index of media and achieved a single-step procedure. It can be used for ECM-rich tissues and can be combined with other methods to further enhance transparency.
SCIENTIFIC REPORTS
(2022)
Article
Materials Science, Multidisciplinary
Yuwei Qu, Zhichao Song, Jun Zhang
Summary: Highly sensitive and long-term stable ethanol gas sensors based on 3D urchin-like ZnO micro/nanospheres are synthesized. The sensors exhibit a high sensitivity of 15.0, fast response and recovery times of 14 seconds and 7 seconds respectively when detecting 200 ppm ethanol gas at 280 degrees C. After 450 days of storage, the sensors still maintain a sensitivity of 5.9 towards 200 ppm ethanol gas at the same operating temperature.
Article
Cell Biology
Michael H. Nichols, Victor G. Corces
Summary: Chromatin is organized in the nucleus via CTCF loops and compartmental domains, with distinct paradigms of compartmental domain formation identified in different cell types in human tissues. The forces driving compartmental domain formation in human cells are conserved, with diverse compartmentalization patterns attributed to differences in chromatin features. This study offers mechanistic insights into the fundamental forces driving the 3D organization of the genome, extending findings to suggest similar principles at work beyond humans.
Article
Ecology
Sara Rolfe, Steve Pieper, Arthur Porto, Kelly Diamond, Julie Winchester, Shan Shan, Henry Kirveslahti, Doug Boyer, Adam Summers, A. Murat Maga
Summary: Large-scale digitization projects are generating high-resolution microCT scans of vertebrates, which are shared with the community using open licenses. A new application, SlicerMorph, provides biologists with a platform to conveniently handle 3D images and data, facilitating landmark analysis and morphometric research.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Dapeng Wang, Vinod Kumar, Katie L. Burnham, Alexander J. Mentzer, Brian D. Marsden, Julian C. Knight
Summary: The COvid-19 Multi-omics Blood ATlas (COMBAT) project has developed a database, COMBATdb, for exploring multi-modal datasets related to COVID-19 and other infectious diseases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Anatomy & Morphology
Johannes A. Smit, Karl Jacobs, Babette Bais, Berrie Meijer, Marjolein N. Seinen, Karel de Bree, Tyas Veldhuis, Jaco Hagoort, Kees H. de Jong, Corstiaan C. Breugem, Roelof-Jan Oostra, Bernadette S. de Bakker
Summary: This study provides a comprehensive overview of the development of cranial nerves, including morphologic changes and relative growth, in human embryos. Three-dimensional reconstructions and volume measurements were used for analysis.
Article
Multidisciplinary Sciences
Chin-Fu Liu, Johnny Hsu, Xin Xu, Ganghyun Kim, Shannon M. M. Sheppard, Erin L. L. Meier, Michael I. I. Miller, Argye E. E. Hillis, Andreia V. V. Faria
Summary: The locus and extent of brain damage in vascular insult can be quickly and easily quantified with vascular atlases. However, there is a lack of readily available digital MRI arterial atlas for automated data analyses. In this study, we created a digital arterial territory atlas based on lesion distributions in 1,298 patients with acute stroke. This atlas provides a valuable resource for large-scale, reproducible processing and analysis of brain MRIs in patients with stroke and other conditions.
Article
Neurosciences
Yuguo Yu, Adil Akif, Peter Herman, Miao Cao, Douglas L. Rothman, Richard E. Carson, Divyansh Agarwal, Alan C. Evans, Fahmeed Hyder
Summary: This study establishes a digital 3D atlas of cortical energy based on the energetic costs of different cortical regions. The atlas is validated using glucose oxidation measurements and reveals heterogeneous activity rates across cortical regions. The distribution of synaptic connections plays a crucial role in cortical energetics. Additionally, some cortical areas act as hubs with higher metabolic rates and synaptic density. The open-source BrainEnergyAtlas provides a granular framework for exploring design principles in energy-constrained human cortical circuits.
Article
Biochemistry & Molecular Biology
Alberto Giubilini, Massimo Messori, Federica Bondioli, Paolo Minetola, Luca Iuliano, Gustav Nystro''m, Katharina Maniura-Weber, Markus Rottmar, Gilberto Siqueira
Summary: While biomaterials are crucial for tissue repair, the removal of non-bio-based and non-bioresorbable scaffolds often leads to negative consequences for patients and the healthcare system. The use of new biopolymers in tissue regeneration is limited due to mechanical and biological challenges. However, incorporating reinforcing agents into biopolymers can enhance their properties. This study focused on developing a bio-based and bioresorbable composite material by combining PHBH with CNCs, demonstrating its printability and cytocompatibility, and showing the influence of CNC content on the functional properties of the scaffolds. Tailoring the properties of PHBH with CNCs expands its potential for tissue engineering applications.
Article
Multidisciplinary Sciences
Hyosung An, John W. Smith, Bingqiang Ji, Stephen Cotty, Shan Zhou, Lehan Yao, Falon C. Kalutantirige, Wenxiang Chen, Zihao Ou, Xiao Su, Jie Feng, Qian Chen
Summary: This study explores the three-dimensional nanomorphology of crumpled polyamide membranes and establishes quantitative links between morphology and performance, using electron tomography, reaction-diffusion theory, machine learning, and liquid-phase atomic force microscopy.
Letter
Public, Environmental & Occupational Health
Bernadette S. de Bakker, Aleena Babar, Kees C. N. Tol
JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE
(2022)
Editorial Material
Anatomy & Morphology
Bjarke Jensen, Gustav J. Strijkers, Steffen E. Petersen, Mary N. Sheppard, Roelof-Jan Oostra, Vincent M. Christoffels
JOURNAL OF ANATOMY
(2022)
Article
Anatomy & Morphology
J. van Schuppen, A. E. van der Hulst, I. M. Kuipers, B. Straver, S. M. Boekholdt, R. N. Planken, R. J. Oostra
Summary: By presenting a case of dual drainage of the right upper lobe of the lung and discussing anomalous pulmonary venous return, this study provides insights into the minority of cases where the anomalous pulmonary veins cross the midline. Understanding embryonic development and anatomical variations leads to better interpretation of imaging, accurate description of morphology, and more precise planning of interventions for patients with complex vascular anatomy.
SURGICAL AND RADIOLOGIC ANATOMY
(2022)
Article
Acoustics
Y. Dawood, C. Honhoff, A-S van der Post, S. D. Roosendaal, B. F. Coolen, G. J. Strijkers, E. Pajkrt, B. S. De Bakker
Summary: This study aimed to compare the application of micro-CT and HF-MRI in postmortem whole-body fetal imaging. The results showed that micro-CT outperformed HF-MRI in both quantitative and qualitative outcomes, suggesting it as the preferred imaging modality for early gestation and an indispensable tool in postmortem imaging services.
ULTRASOUND IN OBSTETRICS & GYNECOLOGY
(2022)
Article
Anatomy & Morphology
Johannes A. Smit, Karl Jacobs, Babette Bais, Berrie Meijer, Marjolein N. Seinen, Karel de Bree, Tyas Veldhuis, Jaco Hagoort, Kees H. de Jong, Corstiaan C. Breugem, Roelof-Jan Oostra, Bernadette S. de Bakker
Summary: This study provides a comprehensive overview of the development of cranial nerves, including morphologic changes and relative growth, in human embryos. Three-dimensional reconstructions and volume measurements were used for analysis.
Review
Medicine, Legal
Anika Veenstra, Wim Kerkhoff, Roelof-Jan Oostra, Ignasi Galtes
Summary: Compared to cranial gunshot trauma, diagnosing and interpreting gunshot trauma in long bones presents challenges and controversies. This study reviews published literature on fracture patterns resulting from gunshot trauma in human long bones, providing practical guidance for forensic anthropologists. Different types of fractures, both direct and indirect, have been observed in various parts of the long bones. Some fractures are associated with specific contexts or mechanisms, aiding forensic reconstruction. Future research should focus on medical data and utilize bone surrogates and computer modeling for detailed and realistic reconstructions of gunshot trauma.
FORENSIC SCIENCE MEDICINE AND PATHOLOGY
(2022)
Review
Anesthesiology
Kristin Keunen, Nicolaas H. Sperna Weiland, Bernadette S. Bakker, Linda S. Vries, Markus F. Stevens
Summary: Neonatal surgery and anesthesia pose risks to the developing brain due to immature regulatory mechanisms and immune response. Brain injury during this period can have long-term consequences on cognitive, learning, and behavioral functions. This review provides a summary of early brain development, discusses brain injury and neurodevelopmental outcomes after neonatal surgery, and proposes a new disease model that includes inflammation, vascular immaturity, and neurotoxicity as mechanisms of injury.
PEDIATRIC ANESTHESIA
(2022)
Review
Cell Biology
Yousif Dawood, Marieke F. J. Buijtendijk, Harsha Shah, Johannes A. Smit, Karl Jacobs, Jaco Hagoort, Roelof-Jan Oostra, Tom Bourne, Maurice J. B. van den Hoff, Bernadette S. de Bakker
Summary: Due to advancements in ultrasound techniques, the focus of antenatal ultrasound screening is shifting towards the first trimester of pregnancy. However, the early first trimester remains a challenging area due to limitations in scanning techniques. It is important to obtain images of early anatomical development to enhance our understanding in this field. New imaging techniques can provide better images for studying early embryonic development and also be used in training and education.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Correction
Medicine, Legal
Anika Veenstra, Wim Kerkhoff, Roelof-Jan Oostra, Ignasi Galtes
FORENSIC SCIENCE MEDICINE AND PATHOLOGY
(2022)
Review
Developmental Biology
Roelof-Jan Oostra, Annelieke N. Schepens-Franke, Giovanni Magno, Alberto Zanatta, Lucas L. Boer
Summary: Conjoined triplets are rare human malformations, and the number and mutual position of hearts are crucial for correct diagnoses.
BIRTH DEFECTS RESEARCH
(2022)
Article
Pediatrics
Daniel Docter, Yousif Dawood, Karl Jacobs, Jaco Hagoort, Roelof-Jan Oostra, Maurice J. B. van den Hoff, Owen J. Arthurs, Bernadette S. de Bakker
Summary: In recent years, fetal postmortem micro-CT imaging has gained popularity as a substitute for autopsy, especially in early gestation fetuses. This article provides an overview of the latest research in this field, including the use of contrast-enhanced micro-CT, endovascular staining, and placental studies.
PEDIATRIC RADIOLOGY
(2023)
Article
Dentistry, Oral Surgery & Medicine
Johannes A. A. Smit, Caroline J. J. Bax, Christl Vermeij-Keers, Bert A. H. Trenning, Bernadette S. S. de Bakker, Corstiaan C. C. Breugem
Summary: This study evaluates the impact of introducing a second-trimester anomaly scan on the prevalence of live births with orofacial clefts in the Netherlands. The results show that the introduction of the scan did not change the overall prevalence of clefts, but there was a decrease in cleft lip with or without alveolus and cleft lip with alveolus and palate, and an increase in cleft palate.
CLEFT PALATE CRANIOFACIAL JOURNAL
(2023)
Article
Genetics & Heredity
Lucas L. Boer, Susanne Gerit Kircher, Helga Rehder, Jana Behunova, Eduard Winter, Helmut Ringl, Anke Scharrer, Elke de Boer, Roelof-Jan Oostra
Summary: The Narrenturm collection in Vienna, Austria, is one of the largest collections of specimens from human origin in Europe, housing over 50,000 objects and approximately 1200 teratological specimens. Despite its significance in dysmorphology research, this collection is not widely known in the scientific community. It contains a wealth of (exceptionally) rare congenital anomalies, serving as a physical repository for human malformation that spans hundreds of years, creating a unique resource for expanding our understanding of developmental conditions, which should be preserved for future generations of scientists.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Article
Medicine, Legal
Parnia Schariatmadary, Maurice C. G. Aalders, Roelof-Jan Oostra, Tristan Krap
Summary: This study found that human bones exhibit luminescent properties during the process of cremation, except for fully carbonized bones, when exposed to a specific light source. The researchers used an alternate light source to visualize and investigate latent details crucial for forensic investigations of burned human remains. The destructive nature of fire causes significant physical and chemical changes to the bone, making the analysis and interpretation of burned remains challenging. A previous observation of a spectral shift in emission bandwidth from green to red with increasing exposure temperature was reproduced in this study using burned human forearms. The quantification of this spectral shift provides evidence for the use of this technique in improving the interpretation of heat-induced changes in bones.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2023)
Article
Developmental Biology
Roelof-Jan Oostra, Ido Solt, Lucas L. Boer
Summary: This article describes a previously misdiagnosed case of symmetric craniorachipagus, which was initially identified as janiceps and as pygopagus. By comparing this case with previous ones, the phenotypic features of craniorachipagus were delineated, and the underreporting of rare conditions like this was discussed. However, further investigations are needed to understand the etiopathogenesis and lethality of this condition.
BIRTH DEFECTS RESEARCH
(2023)
Article
Reproductive Biology
Lei Gong, Siyi Jiang, Jia Tian, Yong Li, Wansu Yu, Lubo Zhang, Daliao Xiao
Summary: Exposure to gestational diabetes mellitus during pregnancy can lead to the development of a neonatal brain hypoxia/ischemia-sensitive phenotype. The PTEN/AKT/mTOR/autophagy signaling pathway plays a role in this process.
REPRODUCTIVE TOXICOLOGY
(2024)
Article
Reproductive Biology
Sudipta Dutta, Kirthiram K. Sivakumar, John W. Erwin, Jone A. Stanley, Joe A. Arosh, Robert J. Taylor, Sakhila K. Banu
Summary: This study found that exposure to hexavalent chromium disrupts follicle development and causes apoptosis by altering epigenetic marks in the ovary.
REPRODUCTIVE TOXICOLOGY
(2024)
Article
Reproductive Biology
Yuxin Li, Xianzhi He, Bin Sun, Nannan Hu, Jiamin Li, Ruolan You, Feiyan Tao, Lei Fang, Yuanyuan Li, Qingfeng Zhai
Summary: This study investigated the toxic effects and mechanism of beta-CYP and EMB on the reproductive system of female rats. The results showed that exposure to these pesticides led to changes in hormone and gene expression in the hypothalamic-pituitary-ovarian axis, as well as alterations in oxidative damage indicators. The findings support the evaluation of the adverse effects of pesticide exposure on reproductive health in greenhouse operations.
REPRODUCTIVE TOXICOLOGY
(2024)
Article
Reproductive Biology
Ran Lee, Won-Young Lee, Hyun-Jung Park
Summary: This study investigates the toxicity of diuron on fetal mouse testes and finds that diuron has a negative impact on the development of fetal Leydig cells, while not affecting germ cells and Sertoli cells.
REPRODUCTIVE TOXICOLOGY
(2024)
