cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking
Creators: name: Langdon, Erin M.
name: Forest, M. Gregory
name: Crutchley, John M.
name: Holt, Liam J.
name: McLaughlin, Grace A.
name: Gladfelter, Amy S.
name: Newby, Jay M.
Publisher: name: American Society for Cell Biology (ASCB)
Year: 2020

description: The spatial structure and physical properties of the cytosol are not well understood. Measurements of the material state of the cytosol are challenging due to its spatial and temporal heterogeneity. Recent development of genetically encoded multimeric nanoparticles (GEMs) has opened up study of the cytosol at the length scales of multiprotein complexes (20-60 nm). We developed an image analysis pipeline for 3D imaging of GEMs in the context of large, multinucleate fungi where there is evidence of functional compartmentalization of the cytosol for both the nuclear division cycle and branching. We applied a neural network to track particles in 3D and then created quantitative visualizations of spatially varying diffusivity. Using this pipeline to analyze spatial diffusivity patterns, we found that there is substantial variability in the properties of the cytosol. We detected zones where GEMs display especially low diffusivity at hyphal tips and near some nuclei, showing that the physical state of the cytosol varies spatially within a single cell. Additionally, we observed significant cell-to-cell variability in the average diffusivity of GEMs. Thus, the physical properties of the cytosol vary substantially in time and space and can be a source of heterogeneity within individual cells and across populations.
Head and Neck Tumor Segmentation for MRI-Guided Applications Challenge
Creators: name: Wahid, Kareem
name: Naser, Mohamed
name: Dede, Cem
name: Attia, Serageldin
name: El-Habashy, Dina
name: Rooney, Michael
name: Mohamed, Abdallah
name: Fuller, Clifton D.
Publisher: name: Zenodo
Year: 2024
Subjects: Segmentation
MRI
head and neck cancer
radiotherapy
MICCAI 2024 challenges

description: Radiation therapy (RT) is a cornerstone of cancer treatment for a wide variety of malignancies. Chief among the beneficiaries of RT as a treatment modality is head and neck cancer (HNC). Recent years have seen an increasing interest in MRI-guided RT planning. As opposed to more traditional CT-based RT planning, MRI-guided approaches afford superior soft tissue contrast and resolution, allow for functional imaging through special multiparametric sequences (e.g., diffusion-weighted imaging [DWI]), and permit daily adaptive RT through intra-therapy imaging using MRI-Linac devices. Subsequently, improved treatment planning through MRI-guided adaptive RT approaches would maximize tumor destruction while minimizing side effects. Given the great potential for MRI-guided adaptive RT planning, it is anticipated that these technologies will transform clinical practice paradigms for HNC.  The extensive data volume for MRI-guided HNC RT planning makes manual tumor segmentation by physicians — the current clinical standard — often impractical due to time constraints. This is compounded by the fact that HNC tumors are among the most challenging structures for clinicians to segment. Artificial intelligence (AI) approaches that leverage RT data to improve patient treatment have been an exceptional area of interest for the research community in recent years. The use of deep learning in particular has made significant strides in HNC tumor auto-segmentation. These innovations have largely been driven by MICCAI public data challenges such as the HECKTOR Challenge, and the SegRap Challenge. However, to-date, there exist no large publicly available AI-ready adaptive RT HNC datasets for public distribution. It stands to reason that community-driven AI innovations would be a remarkable asset to developing technologies for the clinical translation of MRI-guided RT.  In this proposal, we describe a data science challenge focused on the segmentation of HNC tumors for MRI-guided adaptive RT applications. The challenge will be composed of 2 tasks focused on automated segmentation of tumor volumes on 1. pre-RT multiparametric MRI images and 2. mid-RT multiparametric MRI images. Our challenge is particularly unique as it seeks to ascertain whether incorporating prior timepoint data into auto-segmentation algorithms leads to enhanced performance for RT applications.
Additional file 2: of Characteristics of morbidity and mortality conferences associated with the implementation of patient safety improvement initiatives, an observational study
Creators: name: François, Patrice
name: Prate, Frédéric
name: Vidal-Trecan, Gwenaëlle
name: Jean-François Quaranta
name: Labarere, José
name: Sellier, Elodie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Document analysis. (DOCX 22 kb)
Tenaspis angularis
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Tenaspis
Tenaspis angularis

description: Tenaspis angularis (Gorham, 1880)
USA; MEXICO: CS
= Hyas angularis Gorham, 1880
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
An unexpected, pH-sensitive step of the enterovirus D68 lifecycle
Creators: name: Aponte-Diaz, David
name: Vogt, Matthew R.
name: Cameron, Craig E.
Publisher: name: American Society for Microbiology
Year: 2023

description: Enterovirus D68 (EV-D68) contributes significantly to pathogen-induced respiratory illnesses and severe neurological disorders like acute flaccid myelitis. We lack EV-D68 preventive measures, and knowledge of its molecular and cellular biology is incomplete. Multiple studies have highlighted the role of membrane compartments and autophagy during picornavirus multiplication. Galitska et al. found that EV-D68 also exploits cellular autophagic compartments and relies on autophagic machinery as pro-viral factors (G. Galitska, A. Jassey, M. A. Wagner, N. Pollack, et al., mBio e02141-23, 2023, https://doi.org/10.1128/mbio.02141-23). Surprisingly, failure of the autophagic compartment to acidify early during EV-D68 infection causes a delay in RNA synthesis that has not been reported for other enteroviruses. This delay appears to reflect the inability of viral proteins 2B and 3A to engage membranes stably, leading to their degradation in the cytoplasm. Observations like this underscore the importance of studying individual members of the virus genus. It will be interesting to understand how this phenomenon connects to EV-D68 pathogenesis, if at all.
Additional file 4: of Characteristics of morbidity and mortality conferences associated with the implementation of patient safety improvement initiatives, an observational study
Creators: name: François, Patrice
name: Prate, Frédéric
name: Vidal-Trecan, Gwenaëlle
name: Jean-François Quaranta
name: Labarere, José
name: Sellier, Elodie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Observation of MMC meeting. (DOCX 23 kb)
Additional file 1: Table S1. of The association of cardiovascular risk factors with saturated fatty acids and fatty acid desaturase indices in erythrocyte in middle-aged Korean adults
Creators: name: Kim, Seung
name: Jeon, So
name: Lee, Seung-Min
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Hematology

description: Fatty acid compositions in the male and female subjects in the study. (DOCX 16Â kb)
Partial demixing of RNA-protein complexes leads to intradroplet patterning in phase-separated biological condensates
Creators: name: Zhao, Jia
name: Gladfelter, Amy S.
name: Forest, M. Gregory
name: McLaughlin, Grace
name: Newby, Jay
name: Gasior, Kelsey
Publisher: name: American Physical Society (APS)
Year: 2019

description: An emerging mechanism for intracellular organization is liquid-liquid phase separation (LLPS). Found in both the nucleus and the cytoplasm, liquidlike droplets condense to create compartments that are thought to promote and inhibit specific biochemistry. In this work, a multiphase, Cahn-Hilliard diffuse interface model is used to examine RNA-protein interactions driving LLPS. We create a bivalent system that allows for two different species of protein-RNA complexes and model the competition that arises for a shared binding partner, free protein. With this system we demonstrate that the binding and unbinding of distinct RNA-protein complexes leads to diverse spatial pattern formation and dynamics within droplets. Both the initial formation and transient behavior of spatial patterning are subject to the exchange of free proteins between RNA-protein complexes. This study illustrates that spatiotemporal heterogeneity can emerge within phase-separated biological condensates with simple binding reactions and competition. Intradroplet patterning may influence droplet composition and, subsequently, cellular organization on a larger scale.
MOESM1 of Herbicide-resistant cotton (Gossypium hirsutum) plants: an alternative way of manual weed removal
Creators: name: Latif, Ayesha
name: Rao, Abdul
name: Khan, Muhammad
name: Shahid, Naila
name: Bajwa, Kamran
name: Ashraf, Muhammad
name: Abbas, Malik
name: Azam, Muhammad
name: Shahid, Ahmad
name: Nasir, Idrees
name: Tayyab Husnain
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Additional file 1. Transformation efficieny and Molecular analysis of putative transgenic crop.
An immersed interface method for discrete surfaces
Creators: name: Griffith, Boyce E
name: Bhalla, Amneet Pal Singh
name: Craven, Brent A
name: Kolahdouz, Ebrahim M
Publisher: name: Elsevier
Year: 2019

description: Fluid-structure systems occur in a range of scientific and engineering applications. The immersed boundary (IB) method is a widely recognized and effective modeling paradigm for simulating fluid-structure interaction (FSI) in such systems, but a difficulty of the IB formulation of these problems is that the pressure and viscous stress are generally discontinuous at fluid-solid interfaces. The conventional IB method regularizes these discontinuities, which typically yields low-order accuracy at these interfaces. The immersed interface method (IIM) is an IB-like approach to FSI that sharply imposes stress jump conditions, enabling higher-order accuracy, but prior applications of the IIM have been largely restricted to numerical methods that rely on smooth representations of the interface geometry. This paper introduces an immersed interface formulation that uses only a C 0 representation of the immersed interface, such as those provided by standard nodal Lagrangian finite element methods. Verification examples for models with prescribed interface motion demonstrate that the method sharply resolves stress discontinuities along immersed boundaries while avoiding the need for analytic information about the interface geometry. Our results also demonstrate that only the lowest-order jump conditions for the pressure and velocity gradient are required to realize global second-order accuracy. Specifically, we demonstrate second-order global convergence rates along with nearly second-order local convergence in the Eulerian velocity field, and between first- and second-order global convergence rates along with approximately first-order local convergence for the Eulerian pressure field. We also demonstrate approximately second-order local convergence in the interfacial displacement and velocity along with first-order local convergence in the fluid traction along the interface. As a demonstration of the method's ability to tackle more complex geometries, the present approach is also used to simulate flow in a patient-averaged anatomical model of the inferior vena cava, which is the large vein that carries deoxygenated blood from the lower extremities back to the heart. Comparisons of the general hemodynamics and wall shear stress obtained by the present IIM and a body-fitted discretization approach show that the present method yields results that are in good agreement with those obtained by the body-fitted approach.
Additional file 1 of Gene set analysis using sufficient dimension reduction
Creators: name: Huey-Miin Hsueh
name: Chen-An Tsai
Publisher: name: Figshare
Year: 2016
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology

description: The effect of slice numbers on SDR method. (PDF 126 kb)
Tenaspis chamelensis Zaragoza-Caballero, Lopez-Perez and Rodriguez-Miron 2021
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Tenaspis
Tenaspis chamelensis

description: Tenaspis chamelensis Zaragoza-Caballero, López-Pérez and Rodríguez-Mirón 2021
MEXICO: JC Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Magnetic liposome design for drug release systems responsive to super-low frequency alternating current magnetic field (AC MF)
Creators: name: Klyachko, Natalia L
name: Vishwasrao, Hemant M
name: Kabanov, Alexander V
name: Vlasova, Kseniya Yu
name: Golovin, Yuri I
name: Le-Deygen, Irina M
name: Kireev, Igor I
name: Ramsey, Jacob D
name: Rudakovskaya, Polina G
name: Sokolsky-Papkov, Marina
name: Piroyan, Alexander
Publisher: name: Elsevier
Year: 2019

description: HYPOTHESIS: Magnetic liposomes are shown to release the entrapped dye once modulated by low frequency AC MF. The mechanism and effectiveness of MF application should depend on lipid composition, magnetic nanoparticles (MNPs) properties, temperature and field parameters. EXPERIMENTS: The study was performed using liposomes of various lipid composition and embedded hydrophobic MNPs. The liposomes structural changes were studied by the transmission electron microscopy (TEM) and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and the leakage was monitored by the fluorescent dye release. FINDINGS: Magnetic liposomes exposure to the AC MF resulted in the clustering of the MNPs in the membranes and disruption of the lipid packaging. Addition of cholesterol diminished the dye release from the saturated lipid-based liposomes. Replacement of the saturated lipid for unsaturated one also decreased the dye release. The dye release depended on the strength, but not the frequency of the field. Thus, the oscillating motion of MNPs in AC MF ruptures the gel phase membranes of saturated lipids. As the temperature increases the disruption also increases. In the liquid crystalline membranes formed by unsaturated lipids the deformations and defects created by mechanical motion of the MNPs are more likely to heal and results in decreased release.
Additional file 3: of Characteristics of morbidity and mortality conferences associated with the implementation of patient safety improvement initiatives, an observational study
Creators: name: François, Patrice
name: Prate, Frédéric
name: Vidal-Trecan, Gwenaëlle
name: Jean-François Quaranta
name: Labarere, José
name: Sellier, Elodie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Observation d'une réunion. (DOC 81 kb)
Additional file 1: Table S1. of Regulatory dissection of the CBX5 and hnRNPA1 bi-directional promoter in human breast cancer cells reveals novel transcript variants differentially associated with HP1Îą down-regulation in metastatic cells
Creators: name: Vad-Nielsen, Johan
name: Jakobsen, Kristine
name: Daugaard, Tina Fuglsang
name: Thomsen, Rune
name: BrĂźgmann, Anja
name: Boe SĂ¸Rensen
name: Nielsen, Anders
Publisher: name: Figshare
Year: 2016
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Plant Biology
subject: Computational Biology

description: Sequences for primers used in RT-qPCR. (DOCX 17 kb)
Overcoming anti-PEG antibody mediated accelerated blood clearance of PEGylated liposomes by pre-infusion with high molecular weight free PEG
Creators: name: Jennette, J Charles
name: DeWalle, Alexander C
name: Montgomery, Stephanie A
name: Piscitelli, Joseph A
name: Lai, Samuel K
name: Zamboni, William C
name: Harris, Taylor N
name: Price, Lauren S L
name: Saw, Ran Sing
name: Ciociola, Elizabeth C
name: Forest, M Gregory
name: Chan, Andy K P
name: Hu, Peiqi
name: Wessler, Timothy
name: Herity, Leah B
name: Cao, Yanguang
name: McSweeney, Morgan D
Publisher: name: Elsevier
Year: 2019

description: Antibodies that specifically bind polyethylene glycol (PEG), i.e. anti-PEG antibodies (APA), are associated with reduced efficacy and increased risk of serious adverse events for several PEGylated therapeutics. Here, we explored the concept of using free PEG molecules to saturate circulating APA. Surprisingly, we found that 40 kDa free PEG effectively restored the prolonged circulation of PEGylated liposomes in the presence of high titers of pre-existing APA for at least 48 hours in mice. In contrast, lower molecular weight free PEG (≤ 10 kDa) failed to restore circulation beyond a few hours. These in vivo results were consistent with estimates from a minimal physiologically based pharmacokinetic model. Importantly, the infusion of free PEG appeared to be safe in mice previously sensitized by injection of PEGylated liposomes, and free PEG did not elicit excess APA production even in mice with pre-existing adaptive immunity against PEG. Our results support further investigation of high molecular weight free PEG as a potential method to control and overcome high titers of APA, restoring the prolonged circulation of PEGylated liposomes and possibly other PEGylated therapeutics.
Performance-based earthquake engineering with the first-order reliability method
Creators: name: Koduru, Smitha Devi
Publisher: name: University of British Columbia
Year: 2008

description: Performance-based earthquake engineering is an emerging field of study that complements the prescriptive methods that the design codes provide to ensure adequate seismic performance of structures. Accounting for uncertainties in the performance assessments forms an important component in this area. In this context, the present study focuses on two broad themes; first, treatment of uncertainties and the application of the first-order reliability method (FORM) in finite-element reliability analysis, and second, the seismic risk assessment of reinforced concrete structures for performance states such as, collapse and monetary loss. In the first area, the uncertainties arising from inherent randomness (“aleatory uncertainty”) and due to the lack of knowledge (“epistemic uncertainty”) are identified. A framework for the separation of these uncertainties is proposed. Following this, the applicability of FORM to the linear and nonlinear finite-element structural models under static and dynamic loading is investigated. The case studies indicate that FORM is applicable for linear and nonlinear static problems. Strategies are proposed to circumvent and remedy potential challenges to FORM. In the case of dynamic problems, the application of FORM is studied with an emphasis on cumulative response measures. The limit-state surface is shown to have a closed and nonlinear geometric shape. Solution methods are proposed to obtain probability bounds based on the FORM results. In the application-oriented second area of research, at first, the probability of collapse of a reinforced concrete frame is assessed with nonlinear static analysis. By modelling the post-failure behaviour of individual structural members, the global response of the structure is estimated beyond the component failures. The final application is the probabilistic assessment of monetary loss for a high-rise shear wall building due to the seismic hazard in the Cascadia subduction zone. A 3-dimensional finite-element model of the structure with nonlinear material models is subjected to stochastic ground motions in the reliability analysis. The parameters for the stochastic ground motion model are developed for Vancouver, Canada. Monetary losses due to the damage of structural and non-structural components are included.
Additional file 5: Figure S1. of Identification of genomic variants putatively targeted by selection during dog domestication
Creators: name: Cagan, Alex
name: Blass, Torsten
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: PCA plot of samples included in this study. PCA of genome-wide polymorphism data from 67 dogs and 7 wolves. The percentage of the total variance explained by the first and second principal component are labeled on the X and Y axis, respectively. PC1 clearly separates dogs from wolves while PC2 primarily separates dogs by geographic origin. (DOCX 144 kb)
A role for the neuropeptide somatostatin in the neurobiology of behaviors associated with substances abuse and affective disorders
Creators: name: Robinson, Stacey L
name: Thiele, Todd E
Publisher: name: Elsevier
Year: 2020

description: In recent years, neuropeptides which display potent regulatory control of stress-related behaviors have been extensively demonstrated to play a critical role in regulating behaviors associated with substance abuse and affective disorders. Somatostatin (SST) is one neuropeptide known to significantly contribute to emotionality and stress behaviors. However, the role of SST in regulating behavior has received relatively little attention relative to other stress-involved peptides, such as neuropeptide Y or corticotrophin releasing factor. This review characterizes our current understanding of the role of SST and SST-expressing cells in general in modulating several behaviors intrinsically linked to substance abuse and affective disorders, specifically: anxiety and fear; stress and depression; feeding and drinking; and circadian rhythms. We further summarize evidence of a direct role for the SST system, and specifically somatostatin receptors 2 and 4, in substance abuse disorders. This article is part of the special issue on 'Neuropeptides'.
Tenaspis gonzalenzis Zaragoza-Caballero 1995
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Tenaspis
Tenaspis gonzalenzis

description: Tenaspis gonzalenzis Zaragoza-Caballero, 1995
MEXICO: CS, VE Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Immersed Methods for Fluid-Structure Interaction
Creators: name: Griffith, Boyce E
name: Patankar, Neelesh A
Publisher: name: Annual Reviews
Year: 2019

description: Fluid-structure interaction is ubiquitous in nature and occurs at all biological scales. Immersed methods provide mathematical and computational frameworks for modeling fluid-structure systems. These methods, which typically use an Eulerian description of the fluid and a Lagrangian description of the structure, can treat thin immersed boundaries and volumetric bodies, and they can model structures that are flexible or rigid or that move with prescribed deformational kinematics. Immersed formulations do not require body-fitted discretizations and thereby avoid the frequent grid regeneration that can otherwise be required for models involving large deformations and displacements. This article reviews immersed methods for both elastic structures and structures with prescribed kinematics. It considers formulations using integral operators to connect the Eulerian and Lagrangian frames and methods that directly apply jump conditions along fluid-structure interfaces. Benchmark problems demonstrate the effectiveness of these methods, and selected applications at Reynolds numbers up to approximately 20,000 highlight their impact in biological and biomedical modeling and simulation.
A sharp interface Lagrangian-Eulerian method for rigid-body fluid-structure interaction
Creators: name: Scotten, L.N.
name: Griffith, B.E.
name: Craven, B.A.
name: Kolahdouz, E.M.
name: Bhalla, A.P.S.
Publisher: name: Elsevier
Year: 2021

description: This paper introduces a sharp interface method to simulate fluid-structure interaction (FSI) involving rigid bodies immersed in viscous incompressible fluids. The capabilities of this methodology are benchmarked using a range of test cases and demonstrated using large-scale models of biomedical FSI. The numerical approach developed herein, which we refer to as an immersed Lagrangian-Eulerian (ILE) method, integrates aspects of partitioned and immersed FSI formulations by solving separate momentum equations for the fluid and solid subdomains, as in a partitioned formulation, while also using non-conforming discretizations of the dynamic fluid and structure regions, as in an immersed formulation. A simple Dirichlet-Neumann coupling scheme is used, in which the motion of the immersed solid is driven by fluid traction forces evaluated along the fluid-structure interface, and the motion of the fluid along that interface is constrained to match the solid velocity and thereby satisfy the no-slip condition. To develop a practical numerical method, we adopt a penalty approach that approximately imposes the no-slip condition along the fluid-structure interface. In the coupling strategy, a separate discretization of the fluid-structure interface is tethered to the volumetric solid mesh via stiff spring-like penalty forces. Our fluid-structure coupling scheme relies on an immersed interface method (IIM) for discrete geometries, which enables the accurate determination of both velocities and stresses along complex internal interfaces. Numerical methods for FSI can suffer from instabilities related to the added mass effect, but the computational tests indicate that the methodology introduced here remains stable for selected test cases across a range of solid-fluid density ratios, including extremely small, nearly equal, equal, and large density ratios. Biomedical FSI demonstration cases include results obtained using this method to simulate the dynamics of a bileaflet mechanical heart valve in a pulse duplicator, and to model transport of blood clots in a patient-averaged anatomical model of the inferior vena cava.
Additional file 3: Table S3. of Compassionate use of orphan drugs
Creators: name: Hyry, Hanna
name: Manuel, Jeremy
name: Cox, Timothy
name: Roos, Jonathan
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Compassionate use programmes notified to EMA by Member States arranged by year. A table of compassionate use programmes notified to EMA by Member States, obtained from EMA via a freedom of information request. (DOCX 175 kb)
A hybrid semi-Lagrangian cut cell method for advection-diffusion problems with Robin boundary conditions in moving domains
Creators: name: Griffith, Boyce E
name: Barrett, Aaron
name: Fogelson, Aaron L
Publisher: name: Elsevier
Year: 2021

description: We present a new discretization approach to advection-diffusion problems with Robin boundary conditions on complex, time-dependent domains. The method is based on second order cut cell finite volume methods introduced by Bochkov et al. [8] to discretize the Laplace operator and Robin boundary condition. To overcome the small cell problem, we use a splitting scheme along with a semi-Lagrangian method to treat advection. We demonstrate second order accuracy in the L 1, L 2, and L âˆž norms for both analytic test problems and numerical convergence studies. We also demonstrate the ability of the scheme to convert one chemical species to another across a moving boundary.
Microphotus LeConte 1866
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Microphotus

description: Genus Microphotus LeConte, 1866.
NAR: BC, SO, CH; MTZ: SC
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 1: of Characteristics of morbidity and mortality conferences associated with the implementation of patient safety improvement initiatives, an observational study
Creators: name: François, Patrice
name: Prate, Frédéric
name: Vidal-Trecan, Gwenaëlle
name: Jean-François Quaranta
name: Labarere, José
name: Sellier, Elodie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Analyse documentaire. (DOC 105 kb)
Poly(2-oxazoline)-magnetite NanoFerrogels: Magnetic field responsive theranostic platform for cancer drug delivery and imaging
Creators: name: Sokolsky-Papkov, Marina
name: Seo, Youngee
name: Wan, Xiaomeng
name: Ghazanfari, Lida
name: Kabanov, Alexander V
name: Vishwasrao, Hemant M
name: Master, Alyssa
Publisher: name: Elsevier
Year: 2021

description: Combining diagnosis and treatment approaches in one entity is the goal of theranostics for cancer therapy. Magnetic nanoparticles have been extensively used as contrast agents for nuclear magnetic resonance imaging as well as drug carriers and remote actuation agents. Poly(2-oxazoline)-based polymeric micelles which have been shown to efficiently solubilize hydrophobic drugs and drug combinations, have high loading capacity (above 40% w/w) for paclitaxel. In this study, we report the development of novel theranostic system, NanoFerrogels, which is designed to capitalize on the magnetic nanoparticle properties as imaging agents and the poly(2-oxazoline)-based micelles as drug loading compartment. We developed six formulations with magnetic nanoparticle content of 0.3~12 % (w/w), with the z-average sizes of 85–130 nm and ξ-potential of 2.7–28.3 mV. The release profiles of paclitaxel from NanoFerrogels were notably dependent on the degree of dopamine grafting on poly(2-oxazoline)-based micelles. Paclitaxel loaded NanoFerrogels showed efficacy against three breast cancer lines which was comparable to free paclitaxel. They also showed improved tumor and lymph node accumulation and signal reduction in vivo (2.7% in tumor; 8.5% in lymph node) compared to clinically approved imaging agent ferumoxytol (FERAHEME®) 24 hours after administration. NanoFerrogels responded to super-low frequency alternating current magnetic field (50 kA m−1, 50 Hz) which accelerated drug release from paclitaxel-loaded NanoFerrogels or caused death of cells loaded with NanoFerrogels. These proof-of-concept experiments demonstrate that NanoFerrogels have potential as remotely actuated theranostic platform for cancer diagnosis and treatment.
A PBPK model recapitulates early kinetics of anti-PEG antibody-mediated clearance of PEG-liposomes
Creators: name: Rath, Marielle K
name: Lai, Samuel K
name: Wessler, Timothy
name: Cao, Yanguang
name: McSweeney, Morgan D
name: Frank, Jonathan E
name: Yuan, Hong
name: Forest, M Gregory
name: Talkington, Anne M
name: Zhang, Tao
name: Li, Zibo
Publisher: name: Elsevier
Year: 2022

description: PEGylation is routinely used to extend the systemic circulation of various protein therapeutics and nanomedicines. Nonetheless, mounting evidence is emerging that individuals exposed to select PEGylated therapeutics can develop antibodies specific to PEG, i.e., anti-PEG antibodies (APA). In turn, APA increase both the risk of hypersensitivity to the drug as well as potential loss of efficacy due to accelerated blood clearance of the drug. Despite the broad implications of APA, the timescales and systemic specificity by which APA can alter the pharmacokinetics and biodistribution of PEGylated drugs remain not well understood. Here, we developed a physiologically based pharmacokinetic (PBPK) model designed to resolve APA's impact on both early- and late-phase pharmacokinetics and biodistribution of intravenously administered PEGylated drugs. Our model accurately recapitulates PK and biodistribution data obtained from PET/CT imaging of radiolabeled PEG-liposomes and PEG-uricase in mice with and without APA, as well as serum levels of PEG-uricase in humans. Our work provides another illustration of the power of high-resolution PBPK models for understanding the pharmacokinetic impacts of anti-drug antibodies and the dynamics with which antibodies can mediate clearance of foreign species.
Additional file 1: of The health beliefs of mothers about preventing cervical cancer and their intention to recommend the Pap test to their daughters: a cross-sectional survey
Creators: name: Kim, Hae
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Survey questionnaire (DOCX 26 kb)
Chemogenetic Inhibition of Corticotropin-Releasing Factor Neurons in the Central Amygdala Alters Binge-Like Ethanol Consumption in Male Mice
Creators: name: Companion, Michel A.
name: Robinson, Stacey L.
name: Marshall, S. Alex
name: Ebert, Suzahn E.
name: Thiele, Todd E.
Publisher: name: American Psychological Association (APA)
Year: 2022

description: Repetitive bouts of binge drinking can lead to neuroplastic events that alter ethanol's pharmacologic effects and perpetuate excessive consumption. The corticotropin-releasing factor (CRF) system is an example of ethanol-induced neuroadaptations that drive excessive ethanol consumption. Our laboratory has previously shown that CRF antagonist, when infused into the central amygdala (CeA), reduces binge-like ethanol consumption. The present study extends this research by assessing the effects of silencing CRF-producing neurons in CeA on binge-like ethanol drinking stemming from "Drinking in the Dark" (DID) procedures. CRF-ires-Cre mice underwent surgery to infuse Gi/o-coupled Designer Receptors Exclusively Activated by Designer Drugs (DREADD) virus or a control virus into either the CeA or basolateral amygdala (BLA). Gi/o-DREADD-induced CRF-neuronal inhibition in the CeA resulted in a 33% decrease in binge-like ethanol consumption. However, no effect on ethanol consumption was seen after DREADD manipulation in the BLA. Moreover, CeA CRF-neuronal inhibition had no effect on sucrose consumption. The effects of silencing CRF neurons in the CeA on ethanol consumption are not secondary to changes in motor function or anxiety-like behaviors as assessed in the open-field test (OFT). Finally, the DREADD construct's functional ability to inhibit CRF-neuronal activity was demonstrated by reduced ethanol-induced c-Fos following DREADD activation. Together, these data suggest that the CRF neurons in the CeA play an important role in binge ethanol consumption and that inhibition of the CRF-signaling pathway remains a viable target for manipulating binge-like ethanol consumption.
A generic neural network model to estimate populational neural activity for robust neural decoding
Creators: name: Xu, Feng
name: Kamper, Derek G
name: Hu, Xiaogang
name: Roy, Rinku
Publisher: name: Elsevier
Year: 2022

description: BACKGROUND: Robust and continuous neural decoding is crucial for reliable and intuitive neural-machine interactions. This study developed a novel generic neural network model that can continuously predict finger forces based on decoded populational motoneuron firing activities. METHOD: We implemented convolutional neural networks (CNNs) to learn the mapping from high-density electromyogram (HD-EMG) signals of forearm muscles to populational motoneuron firing frequency. We first extracted the spatiotemporal features of EMG energy and frequency maps to improve learning efficiency, given that EMG signals are intrinsically stochastic. We then established a generic neural network model by training on the populational neuron firing activities of multiple participants. Using a regression model, we continuously predicted individual finger forces in real-time. We compared the force prediction performance with two state-of-the-art approaches: a neuron-decomposition method and a classic EMG-amplitude method. RESULTS: Our results showed that the generic CNN model outperformed the subject-specific neuron-decomposition method and the EMG-amplitude method, as demonstrated by a higher correlation coefficient between the measured and predicted forces, and a lower force prediction error. In addition, the CNN model revealed more stable force prediction performance over time. CONCLUSIONS: Overall, our approach provides a generic and efficient continuous neural decoding approach for real-time and robust human-robot interactions.
Microphotus angustus LeConte 1874
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Microphotus
Microphotus angustus

description: Microphotus angustus LeConte, 1874
USA; MEXICO: BC
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 3: Table S2. of Identification of genomic variants putatively targeted by selection during dog domestication
Creators: name: Cagan, Alex
name: Blass, Torsten
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Results of Tukey’s range test for ANOVA of Mean Fst in 50kb windows around functional categories of sites with Fst > = 0.75. (DOCX 99 kb)
A minimal physiologically based pharmacokinetic model that predicts anti-PEG IgG-mediated clearance of PEGylated drugs in human and mouse
Creators: name: Ciociola, E.C.
name: Lai, S.K.
name: Zamboni, W.C.
name: Herity, L.B.
name: Forest, M.G.
name: Piscitelli, J.A.
name: Cao, Y.
name: McSweeney, M.D.
name: Price, L.S.L.
name: Wessler, T.
Publisher: name: Elsevier
Year: 2018

description: Circulating antibodies that specifically bind polyethylene glycol (PEG), a polymer routinely used in protein and nanoparticle therapeutics, have been associated with reduced efficacy and increased adverse reactions to some PEGylated therapeutics. In addition to acute induction of anti-PEG antibodies (APA) by PEGylated drugs, typically low but detectable levels of APA are also found in up to 70% of the general population. Despite the broad implications of APA, the dynamics of APA-mediated clearance of PEGylated drugs, and why many patients continue to respond to PEGylated drugs despite the presence of pre-existing APA, remains not well understood. Here, we developed a minimal physiologically based pharmacokinetic (mPBPK) model that incorporates various properties of APA and PEGylated drugs. Our mPBPK model reproduced clinical PK data of APA-mediated accelerated blood clearance of pegloticase, as well as APA-dependent elimination of PEGyated liposomes in mice. Our model predicts that the prolonged circulation of PEGylated drugs will be compromised only at APA concentrations greater than ~500â€¯ng/mL, providing a quantitative explanation to why the effects of APA on PEGylated treatments appear to be limited in most patients. This mPBPK model is readily adaptable to other PEGylated drugs and particles to predict the precise levels of APA that could render them ineffective, providing a powerful tool to support the development and interpretation of preclinical and clinical studies of various PEGylated therapeutics.
MOESM1 of Inhaled nitric oxide as adjunctive therapy for severe malaria: a randomized controlled trial
Creators: name: Hawkes, Michael
name: Conroy, Andrea
name: Opoka, Robert
name: Hermann, Laura
name: Thorpe, Kevin
name: McDonald, Chloe
name: Kim, Hani
name: Higgins, Sarah
name: Namasopo, Sophie
name: Chandy John
name: Miller, Chris
name: W. Liles
name: Kain, Kevin
Publisher: name: Figshare
Year: 2015
Subjects: subject: Neuroscience
subject: Pharmacology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Sensitivity analyses and quality measures for clinical trial â  Inhaled nitric oxide as adjunctive therapy for severe malariaâ  . Description: Sensitivity analyses on the primary and secondary (mortality) endpoints are provided. Measures of the quality of blinding and quality of clinical care in the trial are described.
Interpretable boosted-decision-tree analysis for the Majorana Demonstrator
Creators: name: Efremenko, Yu.
name: Giovanetti, G. K.
name: Paudel, L. S.
name: Xu, W
name: Hoppe, E. W.
name: Haufe, C. R.
name: Meijer, S. J.
name: Arnquist, I. J.
name: Hervas Aguilar, D
name: Vasilyev, S.
name: Barton, C. J.
name: Gruszko, J.
name: Hostiuc, A.
name: Wiseman, C
name: Guiseppe, V. E.
name: Oli, T. K.
name: Radford, D. C.
name: Varner, R. L.
name: Chan, Y-D.
name: Green, M. P.
name: Clark, M. L.
name: Lannen V, T E
name: Yu, C-H
name: Martin, E. L.
name: Busch, M.
name: Lopez-Castano, J M
name: Rielage, K.
name: Elliott, S. R.
name: Detwiler, J. A.
name: Othman, G.
name: Schaper, D. C.
name: Kouzes, R. T.
name: Caldwell, T. S.
name: Reine, A. L.
name: Henning, R.
name: Kidd, M. F.
name: Wilkerson, J. F.
name: Guinn, I. S.
name: Cuesta, C.
name: Barabash, A. S.
name: Poon, A. W. P.
name: Buuck, M.
name: Martin, R. D.
name: Massarczyk, R.
name: Chu, P.-H.
name: Li, A.
name: Pettus, W.
name: Blalock, E.
name: Bos, B.
name: Avignone, F. T.
name: Ruof, N. W.
name: Kim, I.
name: Tedeschi, D.
name: Christofferson, C. D.
name: Bhimani, K. H.
Publisher: name: American Physical Society (APS)
Year: 2023

description: The Majorana Demonstrator is a leading experiment searching for neutrinoless double-beta decay with high purity germanium (HPGe) detectors. Machine learning provides a new way to maximize the amount of information provided by these detectors, but the data-driven nature makes it less interpretable compared to traditional analysis. An interpretability study reveals the machine's decision-making logic, allowing us to learn from the machine to feed back to the traditional analysis. In this work, we present the first machine learning analysis of the data from the Majorana Demonstrator; this is also the first interpretable machine learning analysis of any germanium detector experiment. Two gradient boosted decision tree models are trained to learn from the data, and a game-theory-based model interpretability study is conducted to understand the origin of the classification power. By learning from data, this analysis recognizes the correlations among reconstruction parameters to further enhance the background rejection performance. By learning from the machine, this analysis reveals the importance of new background categories to reciprocally benefit the standard Majorana analysis. This model is highly compatible with next-generation germanium detector experiments like LEGEND since it can be simultaneously trained on a large number of detectors.
Microphotus curvophallus Zaragoza-Caballero,Vega-Badillo&Cifuentes-Ruiz 2021
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Microphotus
Microphotus curvophallus

description: Microphotuscurvophallus Zaragoza-Caballero,Vega-Badillo&Cifuentes-Ruiz,2021
MEXICO:BSEndemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269