cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
NLRX1 promotes immediate IRF1-directed antiviral responses by limiting dsRNA-activated translational inhibition mediated by PKR
Creators: name: Reid, Lola M.
name: Lemon, Stanley M.
name: Moorman, Nathaniel J.
name: Lenarcic, Erik M.
name: McGivern, David R.
name: Mo, Jinyao
name: Ting, Jenny P-Y
name: Wauthier, Eliane
name: Duncan, Joseph A.
name: Yamane, Daisuke
name: Misumi, Ichiro
name: Feng, Hui
name: Whitmire, Jason K.
name: Guo, Haitao
name: Gonzalez-Lopez, Olga
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: NLRX1 is unique among the nucleotide-binding-domain and leucine-rich-repeat (NLR) proteins in its mitochondrial localization and ability to negatively regulate antiviral innate immunity dependent on the adaptors MAVS and STING. However, some studies have suggested a positive regulatory role for NLRX1 in inducing antiviral responses. We found that NLRX1 exerted opposing regulatory effects on viral activation of the transcription factors IRF1 and IRF3, which might potentially explain such contradictory results. Whereas NLRX1 suppressed MAVS-mediated activation of IRF3, it conversely facilitated virus-induced increases in IRF1 expression and thereby enhanced control of viral infection. NLRX1 had a minimal effect on the transcription of IRF1 mediated by the transcription factor NF-kB and regulated the abundance of IRF1 post-transcriptionally by preventing translational shutdown mediated by the double-stranded RNA (dsRNA)-activated kinase PKR and thereby allowed virus-induced increases in the abundance of IRF1 protein.
Rare Feature Selection in High Dimensions
Creators: name: Yan, Xiaohan
name: Bien, Jacob
Publisher: name: arXiv
Year: 2018
Subjects: subject: Methodology (stat.ME)
subject: Statistics Theory (math.ST)
subject: Computation (stat.CO)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: It is common in modern prediction problems for many predictor variables to be counts of rarely occurring events. This leads to design matrices in which many columns are highly sparse. The challenge posed by such "rare features" has received little attention despite its prevalence in diverse areas, ranging from natural language processing (e.g., rare words) to biology (e.g., rare species). We show, both theoretically and empirically, that not explicitly accounting for the rareness of features can greatly reduce the effectiveness of an analysis. We next propose a framework for aggregating rare features into denser features in a flexible manner that creates better predictors of the response. Our strategy leverages side information in the form of a tree that encodes feature similarity. We apply our method to data from TripAdvisor, in which we predict the numerical rating of a hotel based on the text of the associated review. Our method achieves high accuracy by making effective use of rare words; by contrast, the lasso is unable to identify highly predictive words if they are too rare. A companion R package, called rare, implements our new estimator, using the alternating direction method of multipliers.
description: 42 pages, 10 figures
Decision problems for Clark-congruential languages
Creators: name: Kanazawa, Makoto
name: Kappé, Tobias
Publisher: name: arXiv
Year: 2018
Subjects: subject: Computation and Language (cs.CL)
subject: Formal Languages and Automata Theory (cs.FL)
subject: FOS: Computer and information sciences

description: A common question when studying a class of context-free grammars is whether equivalence is decidable within this class. We answer this question positively for the class of Clark-congruential grammars, which are of interest to grammatical inference. We also consider the problem of checking whether a given CFG is Clark-congruential, and show that it is decidable given that the CFG is a DCFG.
description: Version 2 incorporates revisions prompted by the comments of anonymous referees at ICGI and LearnAut
Additional file 3 of How symptoms of prolonged grief disorder, posttraumatic stress disorder, and depression relate to each other for grieving ICU families during the first two years of bereavement
Creators: name: Wen, Fur-Hsing
name: Prigerson, Holly G.
name: Chou, Wen-Chi
name: Huang, Chung-Chi
name: Hu, Tsung-Hui
name: Chiang, Ming Chu
name: Chuang, Li-Pang
name: Tang, Siew Tzuh
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 3. Table S3. Comparisons of patient characteristics across participation status during bereavement follow-ups (N = 303).
Kleene Algebra with Observations
Creators: name: Kappé, Tobias
name: Brunet, Paul
name: Rot, Jurriaan
name: Silva, Alexandra
name: Wagemaker, Jana
name: Zanasi, Fabio
Publisher: name: arXiv
Year: 2018
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Formal Languages and Automata Theory (cs.FL)
subject: FOS: Computer and information sciences

description: Kleene algebra with tests (KAT) is an algebraic framework for reasoning about the control flow of sequential programs. Generalising KAT to reason about concurrent programs is not straightforward, because axioms native to KAT in conjunction with expected axioms for concurrency lead to an anomalous equation. In this paper, we propose Kleene algebra with observations (KAO), a variant of KAT, as an alternative foundation for extending KAT to a concurrent setting. We characterise the free model of KAO, and establish a decision procedure w.r.t. its equational theory.
On Series-Parallel Pomset Languages: Rationality, Context-Freeness and Automata
Creators: name: Kappé, Tobias
name: Brunet, Paul
name: Luttik, Bas
name: Silva, Alexandra
name: Zanasi, Fabio
Publisher: name: arXiv
Year: 2018
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: FOS: Computer and information sciences

description: Concurrent Kleene Algebra (CKA) is a formalism to study concurrent programs. Like previous Kleene Algebra extensions, developing a correspondence between denotational and operational perspectives is important, for both foundations and applications. This paper takes an important step towards such a correspondence, by precisely relating bi-Kleene Algebra (BKA), a fragment of CKA, to a novel type of automata, pomset automata (PAs). We show that PAs can implement the BKA semantics of series-parallel rational expressions, and that a class of PAs can be translated back to these expressions. We also characterise the behavior of general PAs in terms of context-free pomset grammars; consequently, universality, equivalence and series-parallel rationality of general PAs are undecidable.
description: Accepted manuscript
Additional file 1 of Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort
Creators: name: Lengyel, Anna
name: Pinti, Éva
name: Pikó, Henriett
name: Kristóf, Árvai
name: Abonyi, Tünde
name: Némethi, Zaránd
name: Fekete, György
name: Haltrich, Irén
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1
Human cytomegalovirus regulation of eIF2α kinases
Creators: name: Moorman, Nathaniel J.
name: Vincent, Heather A
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Viral infection is an inherently stressful event. Virus replication taxes cellular biosynthetic machinery and produces
ligands that activate antiviral responses which impair normal cell function. These virus-induced stressors alter
cell function, in part by activating a family of four kinases that phosphorylate the translation initiation factor
eIF2α, leading to a dramatic reduction in protein synthesis. While eIF2α kinase activation typically inhibits virus
replication, human cytomegalovirus (HCMV) efficiently replicates in the presence of persistent cell stress. Here we
review the ways in which HCMV infection induces cellular stress responses and the mechanisms HCMV uses to
evade and manipulate these responses to its own ends.
Additional file 2 of Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort
Creators: name: Lengyel, Anna
name: Pinti, Éva
name: Pikó, Henriett
name: Kristóf, Árvai
name: Abonyi, Tünde
name: Némethi, Zaránd
name: Fekete, György
name: Haltrich, Irén
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 2
Mutations in the E2 glycoprotein and the 3' untranslated region enhance chikungunya virus virulence in mice
Creators: name: Hawman, David W.
name: Moorman, Nathaniel J.
name: Carpentier, Kathryn S.
name: May, Nicholas A.
name: Diamond, Michael S.
name: Montgomery, Stephanie A.
name: Morrison, Thomas E.
name: Fox, Julie M.
name: Sanders, Wes
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes debilitating musculoskeletal pain and inflammation and can persist for months to years after acute infection. Although studies of humans and experimentally infected animals suggest that CHIKV infection persists in musculoskeletal tissues, the mechanisms for this remain poorly understood. To evaluate this further, we isolated CHIKV from the serum of persistently infected Rag1 -/- mice at day 28. When inoculated into naive wild-type (WT) mice, this persistently circulating CHIKV strain displayed a capacity for earlier dissemination and greater pathogenicity than the parental virus. Sequence analysis revealed a nonsynonymous mutation in the E2 glycoprotein (E2 K200R) and a deletion within the 3' untranslated region (3'-UTR). The introduction of these changes into the parental virus conferred enhanced virulence in mice, although primary tropism for musculoskeletal tissues was maintained. The E2 K200R mutation was largely responsible for enhanced viral dissemination and pathogenicity, although these effects were augmented by the 3'- UTR deletion. Finally, studies with Irf3/Irf7 -/- and Ifnar1 -/- mice suggest that the E2 K200R mutation enhances viral dissemination from the site of inoculation independently of interferon regulatory factor 3 (IRF3)-, IRF7-, and IFNAR1-mediated responses. As our findings reveal viral determinants of CHIKV dissemination and pathogenicity, their further study should help to elucidate host-virus interactions that determine acute and chronic CHIKV infection.
Tree Automata as Algebras: Minimisation and Determinisation
Creators: name: van Heerdt, Gerco
name: Kappé, Tobias
name: Rot, Jurriaan
name: Sammartino, Matteo
name: Silva, Alexandra
Publisher: name: arXiv
Year: 2019
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: FOS: Computer and information sciences

description: We study a categorical generalisation of tree automata, as $Σ$-algebras for a fixed endofunctor $Σ$ endowed with initial and final states. Under mild assumptions about the base category, we present a general minimisation algorithm for these automata. We then build upon and extend an existing generalisation of the Nerode equivalence to a categorical setting and relate it to the existence of minimal automata. Finally, we show that generalised types of side-effects, such as non-determinism, can be captured by this categorical framework, leading to a general determinisation procedure.
Do Kernel and Neural Embeddings Help in Training and Generalization?
Creators: name: Rahbar, Arman
name: Jorge, Emilio
name: Dubhashi, Devdatt
name: Chehreghani, Morteza Haghir
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Recent results on optimization and generalization properties of neural networks showed that in a simple two-layer network, the alignment of the labels to the eigenvectors of the corresponding Gram matrix determines the convergence of the optimization during training. Such analyses also provide upper bounds on the generalization error. We experimentally investigate the implications of these results to deeper networks via embeddings. We regard the layers preceding the final hidden layer as producing different representations of the input data which are then fed to the two-layer model. We show that these representations improve both optimization and generalization. In particular, we investigate three kernel representations when fed to the final hidden layer: the Gaussian kernel and its approximation by random Fourier features, kernels designed to imitate representations produced by neural networks and finally an optimal kernel designed to align the data with target labels. The approximated representations induced by these kernels are fed to the neural network and the optimization and generalization properties of the final model are evaluated and compared.
description: This work is published by Neural Processing Letters
Whole Genome Sequencing and Haplotyping of Blastocyst Biopsies
Creators: name: BGI
Publisher: name: CNGB
Year: 2015
Subjects: Phenotype or Genotype
Multiisolate

description: Current methods available for pre-implantation genetic diagnosis (PGD) of in vitro fertilized (IVF) embryos do not detect de novo. Detection of these types of mutations requires whole genome sequencing (WGS). In this study advanced massively parallel WGS was performed on three 5-10 cell biopsies from two blastocyst-stage embryos. Overall, greater than 95% of each genome was called and experimentally derived haplotypes and barcoded read data were used to detect and phase up to 82% of de novo single base mutations with a false positive rate of ~1 error per Gb. These results suggest that phased WGS using barcoded DNA could be used in the future as part of the PGD process to maximize comprehensiveness in detecting disease causing mutations and reduce the incidence of genetic diseases.
Additional file 4 of Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort
Creators: name: Lengyel, Anna
name: Pinti, Éva
name: Pikó, Henriett
name: Kristóf, Árvai
name: Abonyi, Tünde
name: Némethi, Zaránd
name: Fekete, György
name: Haltrich, Irén
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 4
Completeness and Incompleteness of Synchronous Kleene Algebra
Creators: name: Wagemaker, Jana
name: Bonsangue, Marcello
name: Kappé, Tobias
name: Rot, Jurriaan
name: Silva, Alexandra
Publisher: name: arXiv
Year: 2019
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: Synchronous Kleene algebra (SKA), an extension of Kleene algebra (KA), was proposed by Prisacariu as a tool for reasoning about programs that may execute synchronously, i.e., in lock-step. We provide a countermodel witnessing that the axioms of SKA are incomplete w.r.t. its language semantics, by exploiting a lack of interaction between the synchronous product operator and the Kleene star. We then propose an alternative set of axioms for SKA, based on Salomaa's axiomatisation of regular languages, and show that these provide a sound and complete characterisation w.r.t. the original language semantics.
description: Accepted at MPC 2019
Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR
Creators: name: Phillips, Gabriela
name: Halvorsen, Matthew
name: Laederach, Alain
name: Solem, Amanda
name: Kutchko, Katrina M
name: Moorman, Nathaniel
name: Sanders, Wes
name: Weeks, Kevin M.
name: Ziehr, Ben
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Folding to a well-defined conformation is essential for the function of structured ribonucleic acids (RNAs) like the ribosome and tRNA. Structured elements in the untranslated regions (UTRs) of specific messenger RNAs (mRNAs) are known to control expression. The importance of unstructured regions adopting multiple conformations, however, is still poorly understood. High-resolution SHAPE-directed Boltzmann suboptimal sampling of the Homo sapiens Retinoblastoma 1 (RB1) 5' UTR yields three distinct conformations compatible with the experimental data. Private single nucleotide variants (SNVs) identified in two patients with retinoblastoma each collapse the structural ensemble to a single but distinct well-defined conformation. The RB1 5' UTRs from Bos taurus (cow) and Trichechus manatus latirostris (manatee) are divergent in sequence from H. sapiens (human) yet maintain structural compatibility with high-probability base pairs. SHAPE chemical probing of the cow and manatee RB1 5' UTRs reveals that they also adopt multiple conformations. Luciferase reporter assays reveal that 5' UTR mutations alter RB1 expression. In a traditional model of disease, causative SNVs disrupt a key structural element in the RNA. For the subset of patients with heritable retinoblastoma-associated SNVs in the RB1 5' UTR, the absence of multiple structures is likely causative of the cancer. Our data therefore suggest that selective pressure will favor multiple conformations in eukaryotic UTRs to regulate expression.
title: Petrarca e l'Umanesimo latino
Creators: name: Cascio, Giovanni
name: Capirossi, Arianna
name: Brovia, Romana
name: Marsico, Clementina
name: Refe, Laura
name: Tinelli, Elisa
name: Geri, Lorenzo
name: Bernardi, Veronica
name: Zimarino, Valentina
Publisher: name: Dipartimento di Filologia Classica e Italianistica - Università di Bologna
Year: 2023

description: I saggi qui raccolti mettono in dialogo opere e fonti petrarchesche con testi e autori successivi, si interrogano ancora una volta sul metodo di lavoro petrarchesco e tentano di esplorare l’incessante colloquio fra Petrarca e gli umanisti. La scelta di concentrare l’indagine sull’Umanesimo latino muove dalla necessità di stimolare una nuova lettura di alcune opere tutt’altro che secondarie nella produzione del poeta aretino: in alcuni contributi, infatti, si mettono in luce le riflessioni del Petrarca autoesegeta, mentre in altri vengono approfonditi i tempi, i luoghi e le forme della ricezione dei modelli petrarcheschi. Il risultato è un volume miscellaneo che da un lato arricchisce la non esigua bibliografia degli studi e dall’altro apre il campo a nuove indagini e nuovi spunti per il futuro della ricerca futura.
1964-Aghajanian-Bing-Persistence Of LSD In Plasma In Human Subjects
Creators: name: Aghajanian, G
Publisher: name: QUBES Educational Resources
Year: 2023

description: Two micrograms per kilogram of LSD-25 was administered intravenously to five normal human subjects. The concentration of[ drug in plasma was determined serially over the subsequent 8 hours. We model this.
Additional file 5 of Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort
Creators: name: Lengyel, Anna
name: Pinti, Éva
name: Pikó, Henriett
name: Kristóf, Árvai
name: Abonyi, Tünde
name: Némethi, Zaránd
name: Fekete, György
name: Haltrich, Irén
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 5
A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation
Creators: name: Shenk, Thomas
name: Moorman, Nathaniel J.
name: Cristea, Ileana M.
name: Sharon-Friling, Ronit
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The assembly of infectious virus particles is a complex event. For human cytomegalovirus (HCMV) this process requires the coordinated expression and localization of at least 60 viral proteins that comprise the infectious virion. To gain insight into the mechanisms controlling this process, we identified protein binding partners for two viral proteins, pUL99 (also termed pp28) and pUL32 (pp150), which are essential for HCMV virion assembly. We utilized HCMV strains expressing pUL99 or pUL32 carboxyl-terminal green fluorescent protein fusion proteins from their native location in the HCMV genome. Based on the presence of ubiquitin in the pUL99 immunoisolation, we discovered that this viral protein colocalizes with components of the cellular endosomal sorting complex required for transport (ESCRT) pathway during the initial stages of virion assembly. We identified the nucleocapsid and a large number of tegument proteins as pUL32 binding partners, suggesting that events controlling trafficking of this viral protein in the cytoplasm regulate nucleocapsid/ tegument maturation. The finding that pUL32, but not pUL99, associates with clathrin led to the discovery that the two viral proteins traffic via distinct pathways during the early stages of virion assembly. Additional investigation revealed that the majority of the major viral glycoprotein gB initially resides in a third compartment. Analysis of the trafficking of these three viral proteins throughout a time course of virion assembly allowed us to visualize their merger into a single large cytoplasmic structure during the late stages of viral assembly. We propose a model of HCMV virion maturation in which multiple components of the virion traffic independently of one another before merging.
D4.1 Analytical framework detailed and specified for application within BioValue
Creators: name: Locher-Krause, Karla E
name: Zhu, Yuanzao
name: Wittmer, Heidi
Publisher: name: Zenodo
Year: 2023

description: This report documents the adaptation of the analytical framework developed by UFZ (Wittmer et al., 2021) to the project context. Section 4 seeks to set up the base and provide the theoretical background of the concepts of transformative change, transformative change for biodiversity and transformative change in the context of spatial planning used in BioValue. Section 5 provides a detailed description of the Wittmer et al. 2021 framework, together with the adapted version for the projects developed based on a series of discussions among the BioValue consortium. The last sections provide conclusions and the next steps that will be followed to continuously revisit and reflect upon this adapted framework to truly identify and provide recommendations seeking to leverage the transformative potential of spatial planning practices and instruments to enhance biodiversity.
Transcriptomic change in response to high ambient temperature in two Arabidopsis thaliana ecotypes
Creators: name: BGI
Publisher: name: CNGB
Year: 2015
Subjects: transcriptome
Monoisolate

description: To observe the transcriptomic change in response to ambient high temeprature in two different Arabidopsis thaliana accessions: Col-0 and Sij-4.
Additional file 1 of False discovery rate estimation using candidate peptides for each spectrum
Creators: name: Lee, Sangjeong
name: Park, Heejin
name: Kim, Hyunwoo
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Additional file 1: Supplementary tables and figures.
IEEE 802.15.7-Compliant Ultra-low Latency Relaying VLC System for Safety-Critical ITS
Creators: name: Nawaz, Tassadaq
name: Seminara, Marco
name: Caputo, Stefano
name: Mucchi, Lorenzo
name: Cataliotti, Francesco
name: Catani, Jacopo
Publisher: name: arXiv
Year: 2019
Subjects: subject: Signal Processing (eess.SP)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The integration of Visible-Light Communications technology (VLC) in Intelligent Transportation Systems (ITS) is a very promising platform for a cost-effective implementation of revolutionary ITS and cooperative ITS protocols. In this paper, we propose an infrastructure-to-vehicle-to-vehicle (I2V2V) VLC system for ITS, implementing it through a regular LED traffic light serving as a transmitter and a digital Active Decode-and-Relay (ADR) stage for decoding and relaying the received information towards further incoming units. The proposed VLC system targets the challenging and important case of ultra-low latency ADR transmission of short packets, as this is needed for emerging applications of automatic braking, car platooning and other critical automatic and/or assisted driving applications. The experimental validation of the ADR VLC chain, as well as a thorough statistical analysis of errors distribution in the transmission, has been performed for short to medium distances, up to 50 meters. The performances of the designed system are evaluated by measuring the packet error rate (PER) and latency in the whole ADR transmission chain. Our analysis shows that our system attains ultra-low, sub-ms latencies at 99.9\% confidence level for PER as high as $5\times10^{-3}$, yet granting a latency below 10 ms even for distances of 50 m. The demonstrated system prototype is compatible with IEEE 802.15.7 standard.
description: 11 pages, 13 figures, published in journal
Guarded Kleene Algebra with Tests: Verification of Uninterpreted Programs in Nearly Linear Time
Creators: name: Smolka, Steffen
name: Foster, Nate
name: Hsu, Justin
name: Kappé, Tobias
name: Kozen, Dexter
name: Silva, Alexandra
Publisher: name: arXiv
Year: 2019
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Guarded Kleene Algebra with Tests (GKAT) is a variation on Kleene Algebra with Tests (KAT) that arises by restricting the union ($+$) and iteration ($*$) operations from KAT to predicate-guarded versions. We develop the (co)algebraic theory of GKAT and show how it can be efficiently used to reason about imperative programs. In contrast to KAT, whose equational theory is PSPACE-complete, we show that the equational theory of GKAT is (almost) linear time. We also provide a full Kleene theorem and prove completeness for an analogue of Salomaa's axiomatization of Kleene Algebra.
description: Extended version with appendix
Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA
Creators: name: Rout, Michael P.
name: Shenk, Thomas
name: Moorman, Nathaniel J.
name: Chait, Brian T.
name: Cuevas-Bennett, Christian
name: Terhune, Scott S.
name: Savaryn, John Paul
name: Cristea, Ileana M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Histone deacetylation plays a pivotal role in regulating human cytomegalovirus gene expression. In this report, we have identified candidate HDAC1-interacting proteins in the context of infection by using a method for rapid immunoisolation of an epitope-tagged protein coupled with mass spectrometry. Putative interactors included multiple human cytomegalo- virus-coded proteins. In particular, the interaction of pUL38 and pUL29/28 with HDAC1 was confirmed by reciprocal immunoprecipitations. HDAC1 is present in numerous protein complexes, including the HDAC1-containing nucleosome remodeling and deacetylase protein complex, NuRD. pUL38 and pUL29/28 associated with the MTA2 component of NuRD, and shRNA-mediated knockdown of the RBBP4 and CHD4 constituents of NuRD inhibited HCMV immediate-early RNA and viral DNA accumulation; together this argues that multiple components of the NuRD complex are needed for efficient HCMV replication. Consistent with a positive acting role for the NuRD elements during viral replication, the growth of pUL29/28- or pUL38-deficient viruses could not be rescued by treating infected cells with the deacetylase inhibitor, trichostatin A. Transient expression of pUL29/28 enhanced activity of the HCMV major immediate-early promoter in a reporter assay, regardless of pUL38 expression. Importantly, induction of the major immediate-early reporter activity by pUL29/28 required functional NuRD components, consistent with the inhibition of immediate-early RNA accumulation within infected cells after knockdown of RBBP4 and CHD4. We propose that pUL29/28 modifies the NuRD complex to stimulate the accumulation of immediate-early RNAs.
A Compact theorem on the compactness of ultra-compact objects with monotonically decreasing matter fields
Creators: name: Hod, Shahar
Publisher: name: arXiv
Year: 2025
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Self-gravitating horizonless ultra-compact objects that possess light rings have attracted the attention of physicists and mathematicians in recent years. In the present compact paper we raise the following physically interesting question: Is there a lower bound on the global compactness parameters ${\cal C}\equiv\text{max}_r\{2m(r)/r\}$ of spherically symmetric ultra-compact objects? Using the non-linearly coupled Einstein-matter field equations we explicitly prove that spatially regular ultra-compact objects with monotonically decreasing density functions (or monotonically decreasing radial pressure functions) are characterized by the lower bound ${\cal C}\geq1/3$ on their dimensionless compactness parameters.
description: 5 pages
Mehr Grundlagendaten für eine nachhaltige Wasserkraft
Creators: name: Schaefli, Bettina
name: Wechsler, Tobias
name: Seibert, Jan
Publisher: name: Zenodo
Year: 2022
Subjects: Wasserkraft
Schweiz
Hydrologie
Restwasser
Grundwasser

description: Dies ist ein Positionspapier. Ein Version dieses Textes ohne Referenzen ist in der Publikationsreihe «Carte Blanche - Forschende kommentieren» der Akademie der Naturwissenschaften Schweiz, SCNAT, publiziert worden, https://scnat.ch
title: Proteomics analysis of BT-474 and SKOV-3 cancer cell lines treated with purified compounds from bee pollen and cerumen
Creators: name: Ittiudomrak, Teeranai
Publisher: name: University of Liverpool Repository
Year: 2024

description: Breast and gynaecological cancers are the main causes of global cancer death in females. So far, several compounds have been identified from traditional medicine components and natural products that exhibited anticancer activity. Previously, α-mangostin (α-MG) and apigenin (APG) had been extracted and purified from cerumen of Tetragonula laeviceps and bee pollen of Apis mellifera respectively. Preliminary studies reported that these compounds express antiproliferative activity in several cancer cell lines. In this study, α-MG and APG were investigated for antiproliferation effect in breast cancer cell line BT-474 and ovarian adenocarcinoma cell line SKOV-3 using MTT assay, fluorescent staining coupled with flow cytometry analysis, caspase activity assay, and quantitative real-time PCR of interest genes. From BT-474 cell line results, both compounds caused necrotic death by induction of inflammation, as observation of COX2 gene upregulation. In SKOV-3 cell line, APG induced apoptosis via an intrinsic pathway while α-MG led to necrosis that was associated with upregulation of COX2 gene expression. Both compounds arrested the cell progression at G2/M phase. In addition, the half proximal inhibition concentration (IC50) of both compounds in normal cell lines was higher than cancer cell lines representing less cytotoxicity on normal cells. Regarding the antiproliferation effect of APG in SKOV-3, it is interesting how APG regulated cellular mechanisms to suppress cell proliferation. To clarify this question, 11-plex TMT labelling phosphoproteomics was performed at an early response time to observe the global changes of phosphoproteins after APG exposure. Gene set enrichment analysis appeared that APG treatment altered regulation of transcription via epigenetics, histone modification, and organisation associated with demethylation, and activated various signalling pathways especially signalling through mitogen-activated protein kinase (MAPK). APG inhibited cyclin-dependent kinase 1, 2, and 4 (CDK1, CDK2, and CDK4) activities, and activated stress response and cell survival signalling from NetworKIN and Kinase set enrichment analysis (KSEA). Notably, inhibition of pyruvate dehydrogenase complex activity by enhancing activities of pyruvate dehydrogenase kinase (PDK1 and PDK2) presumed that conversion of energy metabolism and aerobic glycolysis occurred in SKOV-3 cells after exposure with APG. Taken together, α-MG and APG exhibit antiproliferative activity on a different mechanism and knowledge from this study provide a better understanding of cellular response to the compounds that could become useful as a therapeutic or co-treatment agent for cancer medication.
Raw Data for the article "Chiral Trifluoromethylated Enamides: Synthesis and Applications"
Creators: name: Postole, Alexandru
name: Martínez-Pardo, Pablo
name: García-Vázquez, Víctor
name: Martín-Matute, Belén
Publisher: name: Zenodo
Year: 2023
Subjects: Catalysis
enamide
Raw data
ion pair

description: The raw data for our work on "Chiral Trifluoromethylated Enamides: Synthesis and Applications" is herein included. FIDs for 1H, 13C NMR. HRMS and HPLC raw data is also included.
Additional file 2 of A correlation map of genome-wide DNA methylation patterns between paired human brain and buccal samples
Creators: name: Sommerer, Yasmine
name: Ohlei, Olena
name: Dobricic, Valerija
name: Oakley, Derek H.
name: Wesse, Tanja
name: Sedghpour Sabet, Sanaz
name: Demuth, Ilja
name: Franke, Andre
name: Hyman, Bradley T.
name: Lill, Christina M.
name: Bertram, Lars
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 2. Supplementary Figures.
Quantum tunneling from rotating black holes with scalar hair in three dimensions
Creators: name: Sakalli, I.
name: Gursel, H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the Hawking radiation (HR) of scalar and Dirac particles (fermions) emitted from a rotating scalar hair black hole (RSHBH) within the context of three dimensional ($3D$) Einstein gravity using non-minimally coupled scalar field theory. Amalgamating the quantum tunneling approach with the Wentzel--Kramers--Brillouin (WKB) approximation, we obtain the tunneling rates of the outgoing particles across the event horizon. Inserting the resultant tunneling rates into the Boltzmann formula, we then obtain the Hawking temperature ($T_{H}$) of the $3D$ RSHBH.
Tensor Factorization with Label Information for Fake News Detection
Creators: name: Papanastasiou, Frosso
name: Katsimpras, Georgios
name: Paliouras, Georgios
Publisher: name: arXiv
Year: 2019
Subjects: subject: Social and Information Networks (cs.SI)
subject: Information Retrieval (cs.IR)
subject: FOS: Computer and information sciences

description: The buzz over the so-called "fake news" has created concerns about a degenerated media environment and led to the need for technological solutions. As the detection of fake news is increasingly considered a technological problem, it has attracted considerable research. Most of these studies primarily focus on utilizing information extracted from textual news content. In contrast, we focus on detecting fake news solely based on structural information of social networks. We suggest that the underlying network connections of users that share fake news are discriminative enough to support the detection of fake news. Thereupon, we model each post as a network of friendship interactions and represent a collection of posts as a multidimensional tensor. Taking into account the available labeled data, we propose a tensor factorization method which associates the class labels of data samples with their latent representations. Specifically, we combine a classification error term with the standard factorization in a unified optimization process. Results on real-world datasets demonstrate that our proposed method is competitive against state-of-the-art methods by implementing an arguably simpler approach.
description: Presented at the Workshop on Reducing Online Misinformation Exposure ROME 2019
Interferons regulate the phenotype of wild-type and mutant herpes simplex viruses in vivo
Creators: name: Laslo, Kathleen M.
name: Leib, David A.
name: Moorman, Nathaniel J.
name: Virgin, Herbert W.
name: Machalek, Michael A.
name: Harrison, Travis E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: Mechanisms responsible for neuroattenuation of herpes simplex virus (HSV) have been defined previously by studies of mutant viruses in cultured cells. The hypothesis that null mutations in host genes can override the attenuated phenotype of null mutations in certain viral genes was tested. Mutants such as those in infected cell protein (ICP) 0, thymidine kinase, ribonucleotide reductase, virion host shutoff, and ICP34.5 are reduced in their capacity to replicate in nondividing cells in culture and in vivo. The replication of these viruses was examined in eyes and trigeminal ganglia for 1-7 d after corneal inoculation in mice with null mutations (-/-) in interferon receptors (IFNR) for type I IFNs (IFN-α/βR), type II IFN (IFN- γR), and both type I and type II IFNs (IFN-α/β/γR). Viral titers in eyes and ganglia of IFN-γR(-/-) mice were not significantly different from congenic controls. However, in IFN-α/βR(-/-) or IFN-α/β/γR(-/-) mice, growth of all mutants, including those with significantly impaired growth in cell culture, was enhanced by up to 1,000-fold in eyes and trigeminal ganglia. Blepharitis and clinical signs of infection were evident in IFN- α/βR(-/-) and IFN-α/β/γR(-/-) but not control mice for all viruses. Also, IFNs were shown to significantly reduce productive infection of, and spread from intact, but not scarified, corneas. Particularly striking was restoration of near-normal trigeminal ganglion replication and neurovirulence of an ICP34.5 mutant in IFN-α/βR(-/-) mice. These data show that IFNs play a major role in limiting mutant and wild-type HSV replication in the cornea and in the nervous system. In addition, the in vivo target of ICP34.5 may be host IFN responses. These experiments demonstrate an unsuspected role for host factors in defining the phenotypes of some HSV mutants in vivo. The phenotypes of mutant viruses therefore cannot be interpreted based solely upon studies in cell culture but must be considered carefully in the context of host factors that may define the in vivo phenotype.
Controlled Generation of Nonlinear Resonances through Sinusoidal Lattice Modes in Bose-Einstein Condensate
Creators: name: Das, Priyam
name: Panigrahi, Prasanta K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We study Bose-Einstein condensate in the combined presence of time modulated optical lattice and harmonic trap in the mean-field approach. Through the self-similar method, we show the existence of sinusoidal lattice modes in this inhomogeneous system, commensurate with the lattice potential. A significant advantage of this system is wide tunability of the parameters through chirp management. The combined effect of the interaction, harmonic trap and lattice potential leads to the generation of nonlinear resonances, exactly where the matter wave changes its direction. When the harmonic trap is switched off, the BEC undergoes a nonlinear compression for the static optical lattice potential. For better understanding of chirp management and the nature of the sinusoidal excitation, we investigate the energy spectrum of the condensate, which clearly reveals the generation of nonlinear resonances in the appropriate regime. We have also identified a classical dynamical phase transition occurring in the system, where loss of superfluidity takes the superfluid phase to an insulating state.
description: 13 pages, 4 figures. arXiv admin note: text overlap with arXiv:1008.1847
The Assessment of Marketing Mix in Prompting Customer Satisfaction (A case study on the National Alcohol and Liquors Factory)
Creators: name: Zelalem Anley
Publisher: name: Zenodo
Year: 2011

description: Today’s companies (special regard to the National Alcohol and Liquors Factory) are facing toughest competition than ever. Companies can win the competition by doing a better job in order to satisfy the customers’ needs and wants, and customer-centered companies are adopt at building customers not just building a product. The study focuses on the assessments of marketing mix elements in prompting customer satisfaction for the case of the producer of the aforementioned factory, the National Alcohol and Liquors Factory. The main objective of the study was that to find out whether customers are satisfied with regard to the four controllable variable marketing mix factors (product, price promotion and distribution). This study helps to fill the gap related to the factory products and its level of customer satisfaction with regard to the 4p’s utilized by the factory. Such study helps the factory to be aware of its customer’s satisfaction level that will move in parallel with the changing customers need and want.
title: A postcritical reading of agency in contemporary British Muslim women’s fiction
Creators: name: Alrashidy, Fahimah
Publisher: name: University of Reading
Year: 2025

description: This thesis studies five novels written by British Muslim women writers. Four of these novels have at their centre female characters who identify themselves as Muslim immigrants: Brick Lane (2003) by Monica Ali, Minaret (2005) by Leila Aboulela, My Name is Salma (2007) by Fadia Faqir, and Home Fire (2017) by Kamila Shamsie. The fifth narrative is This Green and Pleasant Land (2019) by Ayisha Malik, which is not about a female protagonist per se, but in which women play vital roles, especially in relation to issues of identity and cultural representation. I observe a tendency in the current body of criticism to read these novels instrumentally – as realist documents, or as interventions in contemporary political debates, whether reinforcing or challenging existing images of Muslim women. I argue that this approach is well-intentioned but ultimately reductive, resulting in an effective ghettoizing of the texts and their authors. Inspired by the interpretive approach of post-critique, which is advanced by Rita Felski, and by her use of Actor-Network theory, developed by Bruno Latour, I aim first to provide readings of the current criticism around the novels, analysing them from a postcritical perspective. I understand these texts instead to carry artistic autonomy which transcends the dichotomy of being either politically and socially useful or damaging to real Muslim communities. While the agency of the novels and their writers has been generally understood in the context of the message they supposedly deliver to their readers about Muslim woman, I stress that there are nuances to such agency that are overlooked. Employing Latour’s concept of Actor Network Theory as proposed by Felski, I want to bring to the surface the multiple kinds of agencies these narratives exhibit, and to do so while resisting the temptation to judge those agencies in terms of their utility to Muslim communities.
An epitaxial graphene platform for zero-energy edge state nanoelectronics
Creators: name: Prudkovskiy, Vladimir S.
name: Hu, Yiran
name: Hu, Yue
name: Zhang, Kaimin
name: Ji, Peixuan
name: Nunn, Grant
name: Zhao, Jian
name: Shi, Chenqian
name: Tejeda, Antonio
name: Wander, David
name: De Cecco, Alessandro
name: Winkelmann, Clemens B.
name: Jiang, Yuxuan
name: Zhao, Tianhao
name: Wakabayashi, Katsunori
name: Jiang, Zhigang
name: Ma, Lei
name: Berger, Claire
name: de Heer, Walt A.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Graphene's original promise to succeed silicon faltered due to pervasive edge disorder in lithographically patterned deposited graphene and the lack of a new electronics paradigm. Here we demonstrate that the annealed edges in conventionally patterned graphene epitaxially grown on a silicon carbide substrate (epigraphene) are stabilized by the substrate and support a protected edge state. The edge state has a mean free path that is greater than 50 microns, 5000 times greater that the bulk states and involves a theoretically unexpected Majorana-like zero-energy non-degenerate quasiparticle that does not produce a Hall voltage. In seamless integrated structures, the edge state forms a zero-energy one-dimensional ballistic network with essentially dissipationless nodes at ribbon-ribbon junctions. Seamless device structures offer a variety of switching possibilities including quantum coherent devices at low temperatures. This makes epigraphene a technologically viable graphene nanoelectronics platform that has the potential to succeed silicon nanoelectronics.
description: File contains article and supplementary. Nature Communications (in print)
“Musicalization of the Culture”: Is Music  Becoming Louder, More Repetitive, Monotonous and Simpler?
Creators: name: Yang, Yukun
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2020

description: “Musicalization of the culture” is the social science concept proposed by American philosopher George Stainer. He depicted the glooming future of music—it would become omnipresent while having increasing volume, repetitiveness, and monotony, which are ascribed to the debase of literal aesthetics. Although research that relates to one or some of these predictions exists, neither of them encompass all these “musicalization” manifestations, nor do they study the trend of these predictions over time. Therefore, this preliminary research tries to validate whether music has gained acoustic loudness, and lyrical repetitiveness, monotony, and simplicity in a computational fashion. Conducting time-series analysis with trend detection, we confirmed the increasing trends of acoustic loudness and repetitiveness but not monotony and simplicity from 1970 to 2016 using the MetroLyrics dataset and Spotify API. To investigate the simultaneity of these trends, we further conducted synchrony analysis and found little evidence indicating they would influence each other in a lagged fashion. In light of the results, we briefly discussed our findings by relating to the music industry change in reality. Our research made the first attempt to answer this music sociological preposition. On top of this, we also proposed novel metrics to quantify repetitiveness using closed frequent sequential pattern mining, which could be illuminating for future research.
Additional file 1 of A sterile insect technique pilot trial on Captiva Island: defining mosquito population parameters for sterile male releases using mark–release–recapture
Creators: name: Carvalho, Danilo O.
name: Morreale, Rachel
name: Stenhouse, Steven
name: Hahn, Daniel A.
name: Gomez, Maylen
name: Lloyd, Aaron
name: Hoel, David
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Zoology

description: Additional file 1: Text S1. Statistical analysis and R code.