cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Adaptive Digital Twin for UAV-Assisted Integrated Sensing, Communication, and Computation Networks
Creators: name: Li, Bin
name: Liu, Wenshuai
name: Xie, Wancheng
name: Zhang, Ning
name: Zhang, Yan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Signal Processing (eess.SP)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In this paper, we study a digital twin (DT)-empowered integrated sensing, communication, and computation network. Specifically, the users perform radar sensing and computation offloading on the same spectrum, while unmanned aerial vehicles (UAVs) are deployed to provide edge computing service. We first formulate a multi-objective optimization problem to minimize the beampattern performance of multi-input multi-output (MIMO) radars and the computation offloading energy consumption simultaneously. Then, we explore the prediction capability of DT to provide intelligent offloading decision, where the DT estimation deviation is considered. To track this challenge, we reformulate the original problem as a multi-agent Markov decision process and design a multi-agent proximal policy optimization (MAPPO) framework to achieve a flexible learning policy. Furthermore, the Beta-policy and attention mechanism are used to improve the training performance. Numerical results show that the proposed method is able to balance the performance tradeoff between sensing and computation functions, while reducing the energy consumption compared with the existing studies.
description: 14 pages, 11 figures,
School-based interventions for increasing autistic pupils’ access to social participation: A systematic review
Creators: name: Louloumari, Angeliki
name: Yung-Ting Tsou
name: Kovács, Lilla Veronika
name: Rieffe, Carolien
Publisher: name: Open Science Framework
Year: 2021
Subjects: subject: Social and Behavioral Sciences
subject: Developmental Psychology
subject: Psychology
subject: FOS: Psychology
subject: Education
subject: Secondary Education
subject: Elementary Education
subject: school-based intervention
subject: social participation
subject: autism
subject: systematic review

description: A review protocol for a systematic review on interventions in primary and secondary mainstream school settings for increasing autistic pupils’ access to social participation.
Additional file 1 of Practice of oxygen use in anesthesiology – a survey of the European Society of Anaesthesiology and Intensive Care
Creators: name: Scharffenberg, Martin
name: Weiss, Thomas
name: Wittenstein, Jakob
name: Krenn, Katharina
name: Fleming, Magdalena
name: Biro, Peter
name: De Hert, Stefan
name: Hendrickx, Jan F. A.
name: Ionescu, Daniela
name: de Abreu, Marcelo Gama
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Supplementary Material 1. Complete set of Questions – Oxygen survey.
Non-dental health professionals and delivery of oral health interventions in early childhood: a scoping review protocol
Creators: name: Stormon, Nicole
name: Pukallus, Margaret
name: Dickinson, Alison
name: Lalloo, Ratilal
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences
subject: Pediatric Dentistry and Pedodontics
subject: Dentistry
subject: FOS: Clinical medicine
subject: Dental Public Health and Education
subject: Early childhood; prevention; dental decay; primary care; non-dental health professionals

description: Scoping Review Protocol
Secure short-term load forecasting for smart grids with transformer-based federated learning
Creators: name: Sievers, Jonas
name: Blank, Thomas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Electricity load forecasting is an essential task within smart grids to assist demand and supply balance. While advanced deep learning models require large amounts of high-resolution data for accurate short-term load predictions, fine-grained load profiles can expose users' electricity consumption behaviors, which raises privacy and security concerns. One solution to improve data privacy is federated learning, where models are trained locally on private data, and only the trained model parameters are merged and updated on a global server. Therefore, this paper presents a novel transformer-based deep learning approach with federated learning for short-term electricity load prediction. To evaluate our results, we benchmark our federated learning architecture against central and local learning and compare the performance of our model to long short-term memory models and convolutional neural networks. Our simulations are based on a dataset from a German university campus and show that transformer-based forecasting is a promising alternative to state-of-the-art models within federated learning.
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Creators: name: Auerbach, R. K.
name: Clawson, H.
name: Niu, W.
name: Van Nostrand, E. L.
name: Morris, M.
name: Brennan, J.
name: Lu, Z. J.
name: Gerstein, M. B.
name: Cheung, M.-S.
name: Alexander, R. P.
name: Arshinoff, B. I.
name: Cheng, C.
name: Barber, G.
name: Robilotto, R.
name: Perry, M.
name: Chateigner, A.
name: Dernburg, A. F.
name: Ikegami, K.
name: Brdlik, C. M.
name: Rechtsteiner, A.
name: Alves, P.
name: Brouillet, J. J.
name: Contrino, S.
name: Agarwal, A.
name: Vielle, A.
name: Carr, A.
name: Leng, J.
name: Dannenberg, L. O.
name: Liu, T.
name: Rhrissorrakrai, K.
name: Yip, K. Y.
name: Feng, X.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
Woofer-tweeter deformable mirror control for closed-loop adaptive optics: theory and practice
Creators: name: Gavel, Donald
name: Norton, Andrew
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Deformable mirrors with very high order correction generally have smaller dynamic range of motion than what is required to correct seeing over large aperture telescopes. As a result, systems will need to have an architecture that employs two deformable mirrors in series, one for the low-order but large excursion parts of the wavefront and one for the finer and smaller excursion components. The closed-loop control challenge is to a) keep the overall system stable, b) avoid the two mirrors using control energy to cancel each other's correction, c) resolve actuator saturations stably, d) assure that on average the mirrors are each correcting their assigned region of spatial frequency space. We present the control architecture and techniques for assuring that it is linear and stable according to the above criteria. We derived the analytic forms for stability and performance and show results from simulations and on-sky testing using the new ShaneAO system on the Lick 3-meter telescope.
description: 11 pages, 4 figures, Presented SPIE Astronomical Telescopes and Instrumentation Conference, paper #9148-174
Kinetic Scaffolding Mediated by a Phospholipase C-  and Gq Signaling Complex
Creators: name: Kozasa, T.
name: Wang, X.
name: Cheever, M. L.
name: Waldo, G. L.
name: Kawano, T.
name: Tsuboi, K.
name: Harden, T. K.
name: Sondek, J.
name: Hicks, S. N.
name: Montell, C.
name: Ricks, T. K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Transmembrane signals initiated by a broad range of extracellular stimuli converge on nodes that regulate phospholipase C (PLC)–dependent inositol lipid hydrolysis for signal propagation. We describe how heterotrimeric guanine nucleotide–binding proteins (G proteins) activate PLC-βs and in turn are deactivated by these downstream effectors. The 2.7-angstrom structure of PLC-β3 bound to activated Gαq reveals a conserved module found within PLC-βs and other effectors optimized for rapid engagement of activated G proteins. The active site of PLC-β3 in the complex is occluded by an intramolecular plug that is likely removed upon G protein–dependent anchoring and orientation of the lipase at membrane surfaces. A second domain of PLC-β3 subsequently accelerates guanosine triphosphate hydrolysis by Gαq, causing the complex to dissociate and terminate signal propagation. Mutations within this domain dramatically delay signal termination in vitro and in vivo. Consequently, this work suggests a dynamic catch-and-release mechanism used to sharpen spatiotemporal signals mediated by diverse sensory inputs.
Supplementary materials from Mapping threatened Thai bovids provides opportunities for improved conservation outcomes in Asia
Creators: name: Horpiencharoen, Wantida
name: Muylaert, Renata L.
name: Marshall, Jonathan C
name: John, Reju Sam
name: Lynam, Antony
name: Riggio, Alex
name: Godfrey, Alexander
name: Ngoprasert, Dusit
name: Gale, George A.
name: Ash, Eric
name: Bisi, Francesco
name: Cremonesi, Giacomo
name: Clements, Gopalasamy Reuben
name: Yindee, Marnoch
name: Shwe, Nay Myo
name: Pin, Chanratana
name: Gray, T. N. E.
name: Aung, Saw Soe
name: Nakbun, Seree
name: Manka, Stephanie G.
name: Steinmetz, Robert
name: Phoonjampa, Rungnapa
name: Seuaturien, Naret
name: Phumanee, Worrapan
name: Hayman, David
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310399
subject: Ecology not elsewhere classified

description: Supplementary materials for the manuscript "Mapping threatened bovids provides opportunities for improved conservation outcomes in Asia", including Tables S1-S9 and Figures S1-S11.
Additional file 2 of Practice of oxygen use in anesthesiology – a survey of the European Society of Anaesthesiology and Intensive Care
Creators: name: Scharffenberg, Martin
name: Weiss, Thomas
name: Wittenstein, Jakob
name: Krenn, Katharina
name: Fleming, Magdalena
name: Biro, Peter
name: De Hert, Stefan
name: Hendrickx, Jan F. A.
name: Ionescu, Daniela
name: de Abreu, Marcelo Gama
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2: Supplementary Table 1. FiO2 during induction, maintenance, and emergence from anaesthesia by geographical regions.
Understanding the fibroblast to myofibroblast activation process using dynamic hydrogels and machine learning
Creators: name: Hillsley, Alexander Veltman
name: 0000-0001-7920-2104
Publisher: name: The University of Texas at Austin
Year: 2022
Subjects: Biomaterials
Machine learning
Single-cell

description: Cardiac fibrosis is a pathological process characterized by excessive tissue deposition, matrix remodeling, and tissue stiffening. On a cellular level, fibrosis is associated with myofibroblast persistence. Myofibroblasts are a highly secretory and contractile phenotype that arise from resident cardiac fibroblasts, among other cell types, after an initiating injury. Of specific interest is the relationship between environmental stiffness and the myofibroblast activation process. Excess ECM produced by myofibroblasts significantly increases the stiffness of the surrounding tissue. Interestingly, increasing tissue stiffness is also a known stimulus of fibroblast activation, initiating a positive feedback loop ultimately resulting in fibrosis. To better understand this process, the work began with the development of a dynamic stiffening 2D hydrogel model, which was shown to mechanically control myofibroblast activation. A machine learning model was then trained to identify and segment activated myofibroblasts from a population of cultured cells. Next, in order to better understand the activation process, we focused on individual cells, rather than population averages. We then fully characterized cell size and shape and used the measured features to create a model to predict activation state with high accuracy. Further, we used these features and other deep learning techniques to create a continuous classification system that more accurately captures the natural progression. Next, to study the behavior of these cell types in a more natural system, we moved to 3D cell culture. Hydrogels were designed to isolate the effects of environmental stiffness and degradability, and their effects on cell ECM secretion and contractility were quantified. Lastly, we combined our 3D cell culture system with collagen to create an IPN to promote the vasculogenesis of iPSC-EPs where we once again saw that hydrogel stiffness and degradability had a significant effect of the viability and behavior of this cell type.
Regulation of Cellular Metabolism by Protein Lysine Acetylation
Creators: name: Xu, W.
name: Yang, P.
name: Hancock, S. M.
name: Zhou, L.
name: Zhao, S.
name: Yu, W.
name: He, F.
name: Zeng, Y.
name: An, W.
name: Guan, K.-L.
name: Zhang, T.
name: Xiong, Y.
name: Shi, J.
name: Li, Y.
name: Chin, J.
name: Yao, J.
name: Lei, Q.
name: Li, H.
name: Jiang, W.
name: Lin, Y.
name: Chen, X.
name: Qin, L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Protein lysine acetylation has emerged as a key posttranslational modification in cellular regulation, in particular through the modification of histones and nuclear transcription regulators. We show that lysine acetylation is a prevalent modification in enzymes that catalyze intermediate metabolism. Virtually every enzyme in glycolysis, gluconeogenesis, the tricarboxylic acid (TCA) cycle, the urea cycle, fatty acid metabolism, and glycogen metabolism was found to be acetylated in human liver tissue. The concentration of metabolic fuels, such as glucose, amino acids, and fatty acids, influenced the acetylation status of metabolic enzymes. Acetylation activated enoyl–coenzyme A hydratase/3-hydroxyacyl–coenzyme A dehydrogenase in fatty acid oxidation and malate dehydrogenase in the TCA cycle, inhibited argininosuccinate lyase in the urea cycle, and destabilized phosphoenolpyruvate carboxykinase in gluconeogenesis. Our study reveals that acetylation plays a major role in metabolic regulation.
Step-Growth Polymerization of Inorganic Nanoparticles
Creators: name: Nie, Z.
name: Zhao, N.
name: Li, W.
name: Kumacheva, E.
name: Rubinstein, M.
name: Liu, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Self-organization of nanoparticles is an efficient strategy for producing nanostructures with complex, hierarchical architectures. The past decade has witnessed great progress in nanoparticle self-assembly, yet the quantitative prediction of the architecture of nanoparticle ensembles and of the kinetics of their formation remains a challenge. We report on the marked similarity between the self-assembly of metal nanoparticles and reaction-controlled step-growth polymerization. The nanoparticles act as multifunctional monomer units, which form reversible, noncovalent bonds at specific bond angles and organize themselves into a colloidal polymer. We show that the kinetics and statistics of step-growth polymerization enable a quantitative prediction of the architecture of linear, branched, and cyclic self-assembled nanostructures; their aggregation numbers and size distribution; and the formation of structural isomers.
Fair collaborative vehicle routing: A deep multi-agent reinforcement learning approach
Creators: name: Mak, Stephen
name: Xu, Liming
name: Pearce, Tim
name: Ostroumov, Michael
name: Brintrup, Alexandra
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Collaborative vehicle routing occurs when carriers collaborate through sharing their transportation requests and performing transportation requests on behalf of each other. This achieves economies of scale, thus reducing cost, greenhouse gas emissions and road congestion. But which carrier should partner with whom, and how much should each carrier be compensated? Traditional game theoretic solution concepts are expensive to calculate as the characteristic function scales exponentially with the number of agents. This would require solving the vehicle routing problem (NP-hard) an exponential number of times. We therefore propose to model this problem as a coalitional bargaining game solved using deep multi-agent reinforcement learning, where - crucially - agents are not given access to the characteristic function. Instead, we implicitly reason about the characteristic function; thus, when deployed in production, we only need to evaluate the expensive post-collaboration vehicle routing problem once. Our contribution is that we are the first to consider both the route allocation problem and gain sharing problem simultaneously - without access to the expensive characteristic function. Through decentralised machine learning, our agents bargain with each other and agree to outcomes that correlate well with the Shapley value - a fair profit allocation mechanism. Importantly, we are able to achieve a reduction in run-time of 88%.
description: Final, published version can be found here: https://www.sciencedirect.com/science/article/pii/S0968090X23003662
Pricey Therefore Good? Price Affects Expectations, But Not Quality Perceptions and Liking
Creators: name: Efendic, Emir
name: Kurz, Jacqueline
name: Goukens, Caroline
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: A mini meta-analysis will be carried out for the project titled Pricey Therefore Good? Price Affects Expectations, But Not Actual Liking And Perceived Product Quality. This project collected data from six studies investigating the effect of price attribute information on consumer product judgements. The judgments were liking and perceived quality.
Communion/Agency, Nursing, COVID
Creators: name: Amodio, David
name: Block, Katharina
name: Rösler, Inga K.
name: Berkebile, Michael
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology
subject: Arts and Humanities
subject: nursing
subject: agency
subject: gender
subject: covid
subject: communion

description: This is the pre-registration for this project. Hypotheses and analyses plans are attached as a document.
Additional file 3 of Practice of oxygen use in anesthesiology – a survey of the European Society of Anaesthesiology and Intensive Care
Creators: name: Scharffenberg, Martin
name: Weiss, Thomas
name: Wittenstein, Jakob
name: Krenn, Katharina
name: Fleming, Magdalena
name: Biro, Peter
name: De Hert, Stefan
name: Hendrickx, Jan F. A.
name: Ionescu, Daniela
name: de Abreu, Marcelo Gama
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3: Supplementary Table 2. Post-surgical oxygen management by geographical regions.
Gender, COVID, Comparative Careers
Creators: name: Berkebile, Michael
name: Block, Katharina
name: Rösler, Inga K.
name: Amodio, David
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Social Psychology
subject: Psychology
subject: FOS: Psychology
subject: covid
subject: gender
subject: nursing
subject: NLP

description: This is the pre-registration for this project. Hypotheses and analyses plans are attached as a document.
The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA–viral peptide interaction as the major factor modulating durable control of HIV infection.
Tuberculous Granuloma Induction via Interaction of a Bacterial Secreted Protein with Host Epithelium
Creators: name: Pozos, T. C.
name: Ramakrishnan, L.
name: Volkman, H. E.
name: Zheng, J.
name: Rawls, J. F.
name: Davis, J. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Granulomas, organized aggregates of immune cells, are a hallmark of tuberculosis, and have traditionally been thought to restrict mycobacterial growth. However, analysis of Mycobacterium marinum in zebrafish has shown that the early granuloma facilitates mycobacterial growth; uninfected macrophages are recruited to the granuloma where they are productively infected by M. marinum. Here, we identified the molecular mechanism by which mycobacteria induce granulomas: the bacterial secreted protein ESAT-6, which has long been implicated in virulence, induced matrix metalloproteinase-9 (MMP9) in epithelial cells neighboring infected macrophages. MMP9 enhanced recruitment of macrophages, which contributed to nascent granuloma maturation and bacterial growth. Disruption of MMP9 function attenuated granuloma formation and bacterial growth. Thus, interception of epithelial MMP9 production could hold promise as a host-targeting tuberculosis therapy.
The use of Inertial Measurement Units in traumatic spinal cord injuries. A scoping review protocol.
Creators: name: Shalchian-Tehran, Paiman
name: Mavrovounis, Georgios
name: Demetriades Andreas
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences

description: The aim of the present scoping review of the literature is to highlight the available evidence regarding the use of inertial measurement units (IMUs) in the post-injury period and rehabilitation process of patients with traumatic spinal cord injuries.
Chemoenzymatic Synthesis of Homogeneous Ultralow Molecular Weight Heparins
Creators: name: Liu, R.
name: Mousa, S. A.
name: Takieddin, M.
name: Liu, J.
name: Jing, J.
name: Masuko, S.
name: Linhardt, R. J.
name: Xu, Y.
name: Xu, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Ultralow molecular weight (ULMW) heparins are sulfated glycans that are clinically used to treat thrombotic disorders. ULMW heparins range from 1500 to 3000 daltons, corresponding from 5 to 10 saccharide units. The commercial drug Arixtra (fondaparinux sodium) is a structurally homogeneous ULMW heparin pentasaccharide that is synthesized through a lengthy chemical process. Here, we report 10- and 12-step chemoenzymatic syntheses of two structurally homogeneous ULMW heparins (MW = 1778.5 and 1816.5) in 45 and 37% overall yield, respectively, starting from a simple disaccharide. These ULMW heparins display excellent in vitro anticoagulant activity and comparable pharmacokinetic properties to Arixtra, as demonstrated in a rabbit model. The chemoenzymatic approach is scalable and shows promise for a more efficient route to synthesize this important class of medicinal agent.
Statistical immersions between statistical manifolds of constant curvature
Creators: name: Min, Chol Rim
name: Choe, Song Ok
name: An, Yun Ho
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53A15, 53C42, 53B05

description: The condition for the curvature of a statistical manifold to admit a kind of standard hypersurface is given. We study the statistical hypersurfces of some types of the statistical manifolds $(M, \nabla, g )$, which enable $(M, \nabla^{(α)}, g ), \forallα\in\mathbf{R}$ to admit the structure of a constant curvature.
description: 10 pages
Discovery of a Viral NLR Homolog that Inhibits the Inflammasome
Creators: name: Davis, B. K.
name: Matsuzawa, S.-i.
name: Damania, B.
name: Gregory, S. M.
name: West, J. A.
name: Ting, J. P. Y.
name: Taxman, D. J.
name: Reed, J. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The nucleotide-binding and oligomerization, leucine-rich repeat (NLR) family of proteins sense microbial infections and activate the inflammasome, a multi-protein complex that promotes microbial clearance. Kaposi's sarcoma-associated herpesvirus (KSHV) is linked to several human malignancies. We report that KSHV Orf63 is a viral homolog of human NLRP1. Orf63 blocked NLRP1-dependent innate immune responses, including caspase-1 activation and processing of interleukin (IL)-1β and IL-18. KSHV Orf63 interacted with NLRP1, NLRP3, and NOD2. Inhibition of Orf63 expression resulted in increased expression of IL-1β during the KSHV lifecycle. Furthermore, inhibition of NLRP1 was necessary for efficient reactivation and generation of progeny virus. The viral homolog subverts the function of cellular NLRs, which suggests that modulation of NLR-mediated innate immunity is important for the life-long persistence of herpesviruses.
DNA Synthesis Generates Terminal Duplications That Seal End-to-End Chromosome Fusions
Creators: name: Flibotte, S.
name: Ahmed, S.
name: Lowden, M. R.
name: Moerman, D. G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: End-to-end chromosome fusions that occur in the context of telomerase deficiency can trigger genomic duplications. For over 70 years these duplications have been attributed solely to Breakage-Fusion-Bridge cycles. To test this hypothesis, we examined end-to-end fusions isolated from C. elegans telomere replication mutants. Genome level rearrangements revealed fused chromosome ends possessing interrupted terminal duplications accompanied by template switching events. These features are very similar to disease-associated duplications of interstitial segments of the human genome. A model termed Fork Stalling and Template Switching has been proposed previously to explain such duplications, where promiscuous replication of large, non-contiguous segments of the genome occurs. Thus, a DNA synthesis-based process may create duplications that seal end-to-end fusions, in the absence of Breakage-Fusion-Bridge cycles.
Controllable Generation of Artificial Speaker Embeddings through Discovery of Principal Directions
Creators: name: Lux, Florian
name: Tilli, Pascal
name: Meyer, Sarina
name: Vu, Ngoc Thang
Publisher: name: arXiv
Year: 2023
Subjects: subject: Sound (cs.SD)
subject: Machine Learning (cs.LG)
subject: Audio and Speech Processing (eess.AS)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Customizing voice and speaking style in a speech synthesis system with intuitive and fine-grained controls is challenging, given that little data with appropriate labels is available. Furthermore, editing an existing human's voice also comes with ethical concerns. In this paper, we propose a method to generate artificial speaker embeddings that cannot be linked to a real human while offering intuitive and fine-grained control over the voice and speaking style of the embeddings, without requiring any labels for speaker or style. The artificial and controllable embeddings can be fed to a speech synthesis system, conditioned on embeddings of real humans during training, without sacrificing privacy during inference.
description: Published at ISCA Interspeech 2023 https://www.isca-speech.org/archive/interspeech_2023/lux23_interspeech.html
Additional file 1 of Neuroinflammation regulates the balance between hippocampal neuron death and neurogenesis in an ex vivo model of thiamine deficiency
Creators: name: Cassiano, Larissa M. G.
name: Oliveira, Marina S.
name: Pioline, Jeanne
name: Salim, Anna C. M.
name: Coimbra, Roney S.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 1. Central energy metabolism. ATP: adenosine triphosphate; NAD+: nicotinamide adenine dinucleotide (oxidized); NADH: nicotinamide adenine dinucleotide (reduced); NADPH: nicotinamide adenine dinucleotide phosphate; H+: hydrogen (proton); CoA: coenzyme A; TPP: thiamine pyrophosphate; Pi: inorganic phosphate group; CO2: carbon dioxide, H2O: water, FAD: flavin-adenine dinucleotide; FADH2: flavin-adenine dinucleotide (hydroquinone form). Created with BioRender.com.
Evidence for Network Evolution in an Arabidopsis Interactome Map
Creators: name: Ahn, Y.-Y.
name: Barabasi, A.-L.
name: Balumuri, P.
name: Gilles, P.
name: Gutierrez, B. J.
name: Galli, M.
name: Dricot, A.
name: MacWilliams, A.
name: Cusick, M. E.
name: Kim, R. C.
name: Gebreab, F.
name: Kim, C. J.
name: Byrdsong, D.
name: Gai, L.
name: Chen, H.
name: Dangl, J. L.
name: Carvunis, A.-R.
name: Dreze, M.
name: Hill, D. E.
name: Pevzner, S. J.
name: Chesnut, J. D.
name: Ecker, J. R.
name: Ghoshal, G.
name: Tasan, M.
name: Braun, P.
name: Bautista, V.
name: Lurin, C.
name: Duarte, M.
name: Fan, C.
name: Charloteaux, B.
name: Hao, T.
name: de los Reyes, C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.
Additional file 1 of Students’ learning experiences of three-dimensional printed models and plastinated specimens: a qualitative analysis
Creators: name: Radzi, Shairah
name: Chandrasekaran, Ramya
name: Peh, Zhen Kai
name: Rajalingam, Preman
name: Yeong, Wai Yee
name: Mogali, Sreenivasulu Reddy
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Focus group discussion guided questions (Moderator Version).
Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network
Creators: name: Roth, F. P.
name: Harbort, C. J.
name: Vidal, M.
name: Tasan, M.
name: Galli, M.
name: Nishimura, M. T.
name: Vandenhaute, J.
name: Epple, P.
name: Chen, H.
name: Moore, J.
name: Pevzner, S. J.
name: Hao, T.
name: Hill, D. E.
name: McDonald, N.
name: Gai, L.
name: Tam, S.
name: Gebreab, F.
name: Ecker, J. R.
name: Carvunis, A.-R.
name: He, Y.
name: Steinbrenner, J.
name: Santhanam, B.
name: Mukhtar, M. S.
name: Monachello, D.
name: Gutierrez, B. J.
name: Poulin, M. M.
name: Dreze, M.
name: Boxem, M.
name: Donovan, S. E.
name: Ghamsari, L.
name: Beynon, J.
name: Romero, V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. Pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. We generated a plant-pathogen immune system protein interaction network using effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins and ~8,000 other Arabidopsis proteins. We noted convergence of effectors onto highly interconnected host proteins, and indirect, rather than direct, connections between effectors and plant immune receptors. We demonstrated plant immune system functions for 15 of 17 tested host proteins that interact with effectors from both pathogens. Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life cycle strategies.
Additional file 1 of The hippocampal sparing subtype of Alzheimer’s disease assessed in neuropathology and in vivo tau positron emission tomography: a systematic review
Creators: name: Ferreira, Daniel
name: Mohanty, Rosaleena
name: Murray, Melissa E.
name: Nordberg, Agneta
name: Kantarci, Kejal
name: Westman, Eric
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Table S1. Search strategy. Table S2. Strategies followed to reduce the risk of bias. Table S3. List of fields covered for the collection of the data (data extraction template). Table S4. Reasons for excluding candidate records (inclusion stage in the study-selection flow). Table S5. Frequency of the hippocampal-sparing AD subtype – comparison of findings when using hippocampus versus entorhinal cortex for subtyping.
Replication-Dependent Loss of 5-Hydroxymethylcytosine in Mouse Preimplantation Embryos
Creators: name: Inoue, A.
name: Zhang, Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Although global erasure of DNA methylation has been observed in zygotes and primordial germ cells, the responsible enzyme(s) have been elusive. The demonstration that members of the Tet (ten eleven translocation) family of proteins are capable of catalyzing conversion of 5-methylcytosine (5mC) of DNA to 5-hydroxymethylcytosine (5hmC) raises the possibility that Tet proteins may participate in this process. Indeed, recent studies have implicated the involvement of Tet3 in the conversion of 5mC to 5hmC in zygotes. This result, combined with the demonstration that Tet proteins can further oxidize 5hmC to 5-carboxylcytosine followed by excision by thymine-DNA glycosylase, raises the possibility that active demethylation may take place in a process that involves Tet3-mediated oxidation followed by base excision repair. We demonstrated by immunostaining of mitotic chromosome spreads of preimplantation embryos that the 5hmC associated with the paternal genome in zygotes is gradually lost during preimplantation development. Our study suggests that, although the conversion of 5mC to 5hmC in zygotes is an enzyme-catalyzed process, loss of 5hmC during preimplantation appears to be a DNA replication-dependent passive process.
Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine
Creators: name: Wu, S. C.
name: Zhang, Y.
name: Collins, L. B.
name: Dai, Q.
name: Shen, L.
name: He, C.
name: Swenberg, J. A.
name: Ito, S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet proteins. Here we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity-dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse ES cells and mouse organs. The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins. Thus, we identify two new cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation.
Widespread RNA and DNA Sequence Differences in the Human Transcriptome
Creators: name: Li, Y.
name: Li, M.
name: Cheung, V. G.
name: Toung, J. M.
name: Bruzel, A.
name: Wang, I. X.
name: Richards, A. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The transmission of information from DNA to RNA is a critical process. We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. All 12 possible categories of discordances were observed. These differences were nonrandom as many sites were found in multiple individuals and in different cell types, including primary skin cells and brain tissues. Using mass spectrometry, we detected peptides that are translated from the discordant RNA sequences and thus do not correspond exactly to the DNA sequences. These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation.
Efficient generation of highly crystalline carbon quantum dots via electrooxidation of ethanol for rapid photodegradation of organic dyes
Creators: name: Barrionuevo, Santiago D.
name: Fioravanti, Federico
name: Nuñez, Jorge M.
name: Llaver, Mauricio
name: Aguirre, Myriam H.
name: Bellino, Martin G.
name: Lacconib, Gabriela I.
name: Ibañez, Francisco J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Achieving versatile routes to generate crystalline carbon-based nanostructures has become a fervent pursuit in photocatalysis-related fields. We demonstrate that the direct electrooxidation of ethanol, performed on Ni foam, yields ultra-small and highly crystalline graphene-like structures named carbon quantum dots (CQDs). We perform simulations of various sp2 and sp3 domains in order to understand the optical properties of CQDs by accounting their contribution as absorbance/luminescent centers in the overall optical response. Experiments and simulations reveal that absorbance bands for as-synthesized CQDs are dominated by small sp2 domains comprised of r7 aromatic-rings. After 48 h synthesis, the dispersion transition from yellow to red, exhibiting new and red shifted absorbance bands. Furthermore, fluorescence emission is governed by medium-sized sp 2 domains (with aromatic ring counts r12) and oxygen-containing groups. These oxygen-rich groups within the CQDs, confirmed by FT-IR and XPS, are responsible for the fast photodegradation of organic dyes, with B90% of methylene blue (MB) being degraded within the first 5 min of light exposure. Our work provides crucial insights about the electrochemical synthesis and overall optical properties of carbon nanostructures, while being effective and reliable toward the degradation of contaminants in water.
A Periciliary Brush Promotes the Lung Health by Separating the Mucus Layer from Airway Epithelia
Creators: name: Boucher, R. C.
name: Button, B.
name: Sheehan, J. K.
name: Hill, D. B.
name: Cai, L.-H.
name: Kesimer, M.
name: Ehre, C.
name: Rubinstein, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Mucus clearance is the primary defense mechanism that protects airways from inhaled infectious and toxic agents. In the current Gel-on-Liquid mucus clearance model mucus gel is propelled on top of a “watery” periciliary layer surrounding the cilia. However, this model fails to explain the formation of distinct mucus layer in health or why mucus clearance fails in disease. We propose a Gel-on-Brush model in which the periciliary layer is occupied by membrane spanning mucins and mucopolysaccharides densely tethered to the airway surface. This brush prevents mucus penetration into the periciliary space and causes mucus to form a distinct layer. The relative osmotic moduli of the mucus and periciliary brush layers explain both the stability of mucus clearance in health and its failure in airway disease.
An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
Creators: name: Ehm, M. G.
name: Nelson, M. R.
name: Li, Y.
name: Bacanu, S.-A.
name: Li, J.
name: Woollard, P.
name: Zawistowski, M.
name: Kessner, D.
name: Novembre, J.
name: Wegmann, D.
name: Shen, J.
name: Li, L.
name: Liu, X.
name: Nangle, K.
name: Fraser, D.
name: Zollner, S.
name: Wang, J.
name: Aponte, J.
name: Hall, M. D.
name: Chissoe, S. L.
name: Abecasis, G.
name: Cardon, L. R.
name: Warren, L.
name: Verzilli, C.
name: Zhang, Y.
name: Zhang, H.
name: Mooser, V.
name: Topp, S.
name: Whittaker, J. C.
name: St. Jean, P.
name: Tang, Z.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (one every 17 bases) and geographically localized, such that even with large sample sizes, rare variant catalogs will be largely incomplete. We used the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and mutation rates for each gene. Overall we conclude that, due to rapid population growth and weak purifying selection, human populations harbor an abundance of rare variants, many of which are deleterious and have relevance to understanding disease risk.
Opto-Mechanical Design of ShaneAO: the Adaptive Optics System for the 3-meter Shane Telescope
Creators: name: Ratliff, Christopher
name: Cabak, Jerry
name: Gavel, Donald
name: Kupke, Renate
name: Dillon, Daren
name: Gates, Elinor
name: Deich, William
name: Ward, Jim
name: Cowley, David
name: Pfister, Terry
name: Saylor, Mike
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: A Cassegrain mounted adaptive optics instrument presents unique challenges for opto-mechanical design. The flexure and temperature tolerances for stability are tighter than those of seeing limited instruments. This criteria requires particular attention to material properties and mounting techniques. This paper addresses the mechanical designs developed to meet the optical functional requirements. One of the key considerations was to have gravitational deformations, which vary with telescope orientation, stay within the optical error budget, or ensure that we can compensate with a steering mirror by maintaining predictable elastic behavior. Here we look at several cases where deformation is predicted with finite element analysis and Hertzian deformation analysis and also tested. Techniques used to address thermal deformation compensation without the use of low CTE materials will also be discussed.
description: 14 pages, 14 figures, 4 tables. Presented at SPIE Astronomical Telescopes + Instrumentation conference, paper 9148-119
Additional file 1 of Atheroprone fluid shear stress-regulated ALK1-Endoglin-SMAD signaling originates from early endosomes
Creators: name: Mendez, Paul-Lennard
name: Obendorf, Leon
name: Jatzlau, Jerome
name: Burdzinski, Wiktor
name: Reichenbach, Maria
name: Nageswaran, Vanasa
name: Haghikia, Arash
name: Stangl, Verena
name: Hiepen, Christian
name: Knaus, Petra
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Supplementary Figs. S1-S5. and primer sequences used in qPCR experiments. Figure S1. RNAseq analysis and HAoEC flow marker validation. Figure S2. Validation of used flow set up by comparison with existing data. Fig. S3. Human Serum experiment and additional flow regulated genes. Figure S4. Expression data of selected genes in Endoglin knock-down. Figure S5. Caveolin-1 positive early endosomes are signaling hotspots for FSS induced BMP signaling in HAoECs. Table S1. Primers used for quantitative PCR analysis.
Heat. A Distributed And Accelerated Tensor Framework For Data Analytics And Machine Learning
Creators: name: Comito, Claudia
name: Götz, Markus
name: Debus, Charlotte
name: Coquelin, Daniel
name: Tarnawa, Michael
name: Krajsek, Kai
name: Knechtges, Philipp
name: Siggel, Martin
name: Hagemeier, Björn
name: Basermann, Achim
name: Streit, Achim
Publisher: name: Zenodo
Year: 2021
Subjects: data-intensive science
GPU
methods and algorithms

description: Born out of a large-scale collaboration in applied sciences, Heat [1, 2] is an open-source Python library for high-performance data analytics, machine learning, and deep learning. It provides highly optimized algorithms and data structures for tensor computations using CPUs, GPUs and distributed cluster systems. Plus, with Heat, writing scalable scientific and data science applications is as straightforward as using NumPy.

 With as diverse a user base as, e.g., the Earth System Modeling, neuroscience, and aerospace research communities, Heat offers not only generalized solutions for data-intensive science, but also a platform for ever-expanding cross-discipline collaborations and knowledge transfer. We look forward to many interactions and possible collaborations at AI STAR.

 [1] Götz, M., Debus, C., Coquelin, et al.: "HeAT - a Distributed and GPU-accelerated Tensor Framework for Data Analytics". 2020 IEEE International Conference on Big Data (Big Data) (pp. 276-287)

 [2] https://github.com/helmholtz-analytics/heat