cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region
Creators: name: Mathur, Anuja
name: Marquitz, Aron R.
name: Edwards, Rachel Hood
name: Raab-Traub, Nancy
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT In Epstein-Barr virus-infected epithelial cancers, the alternatively spliced BamHI A rightward transcripts (BARTs) are the most abundant viral polyadenylated RNA. The BART introns form the template for the production of 44 microRNAs (miRNAs), and the spliced and polyadenylated exons form nuclear non-protein-coding RNAs. Analysis of host cell transcription by RNA-seq during latency in AGS cells identified a large number of reproducibly changed genes. Genes that were downregulated were enriched for BART miRNA targets. Bioinformatics analysis predicted activation of the myc pathway and downregulation of XBP1 as likely mediators of the host transcriptional changes. Effects on XBP1 activity were not detected in these cells; however, myc activation was confirmed through use of a myc-responsive luciferase reporter. To identify potential regulatory properties of the spliced, polyadenylated BART RNAs, a full-length cDNA clone of one of the BART isoforms was obtained and expressed in the Epstein-Barr virus (EBV)-negative AGS cells. The BART cDNA transcript remained primarily nuclear yet induced considerable and consistent changes in cellular transcription, as profiled by RNA-seq. These transcriptional changes significantly overlapped the transcriptional changes induced during latent EBV infection of these same cells, where the BARTs are exclusively nuclear and do not encode proteins. These data suggest that the nuclear BART RNAs are functional long noncoding RNAs (lncRNAs). The abundant expression of multiple forms of noncoding RNAs that contribute to growth regulation without expression of immunogenic proteins would be an important mechanism for viral oncogenesis in the presence of a functional immune system. IMPORTANCE Infection with Epstein-Barr virus (EBV) is nearly ubiquitous in the human population; however, it does contribute to the formation of multiple types of cancer. In immunocompromised patients, EBV causes multiple types of lymphomas by expressing viral oncogenes that promote growth and survival of infected B lymphocytes. EBV-positive gastric carcinoma does not require immune suppression, and the viral oncoproteins that are frequent targets for an immunological response are not expressed. This study demonstrates using transcriptional analysis that the expression of various classes of viral non-protein-coding RNAs likely contribute to the considerable changes in the host transcriptional profile in the AGS gastric cancer cell line. This is the first report to show that the highly expressed polyadenylated BamHI A rightward transcripts (BART) viral transcript in gastric carcinoma is in fact a functional viral long noncoding RNA. These studies provide new insight into how EBV can promote transformation in the absence of viral protein expression.
Additional file 1 of The ovipositor cue indole inhibits animal host attraction in Aedes aegypti (Diptera: Culicidae) mosquitoes
Creators: name: Dekel, Amir
name: Sar-Shalom, Evyatar
name: Vainer, Yuri
name: Yakir, Esther
name: Bohbot, Jonathan D.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 1: Figure S1. Diagrams of the odor delivery system. A The odor delivery system is composed of interlocking top and bottom rings attached to a removable chemical holder (overview, top, bottom and side views are provided). Dimensions are provided in millimeters. B The rings are locked in place across the glove of the person conducting the experiment. The glove within the inner area of the ring is removed, exposing the skin surface. A plastic net is intercalated between the rings and serves to physically protect the skin from mosquito bites.
Coexistence of 3d-ferromagnetism and superconductivity in [(Li(1-x)Fex)OH](Fe(1-y)Liy)Se
Creators: name: Pachmayr, Ursula
name: Nitsche, Fabian
name: Luetkens, Hubertus
name: Kamusella, Sirko
name: Brückner, Felix
name: Sarkar, Rajib
name: Klauss, Hans-Hennig
name: Johrendt, Dirk
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Superconducting [(Li(1-x)Fex)OH](Fe(1-y)Liy)Se (x ~ 0.2, y ~ 0.08) was synthesized by hydrothermal methods and structurally characterized by single crystal X-ray diffraction. The crystal structure contains anti-PbO type (Fe(1-y)Liy)Se layers separated by layers of (Li(1-x)Fex)OH. Electrical resistivity and magnetic susceptibility measurements reveal superconductivity at 43 K. An anomaly in the diamagnetic shielding indicates ferromagnetic ordering near 10 K while superconductivity is retained. The ferromagnetism emerges from the iron atoms in the (Li(1-x)Fex)OH layer. Isothermal magnetization measurements confirm the superposition of ferromagnetic with superconducting hysteresis. The internal ferromagnetic field is larger than the lower, but smaller than the upper critical field of the superconductor, which gives evidence for a spontaneous vortex phase where both orders coexist. 57Fe-Mössbauer spectra, 7Li-NMR spectra, and muSR experiments consistently support this rare situation, especially in a bulk material where magnetism emerges from a 3d-element.
description: 13 pages, 7 Figures
Spectral broadening and shaping of nanosecond pulses: towards shaping of single photons from quantum emitters
Creators: name: Agha, Imad
name: Ates, Serkan
name: Sapienza, Luca
name: Srinivasan, Kartik
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We experimentally demonstrate spectral broadening and shaping of exponentially-decaying nanosecond pulses via nonlinear mixing with a phase-modulated pump in a periodically-poled lithium niobate (PPLN) waveguide. A strong, 1550~nm pulse is imprinted with a temporal phase and used to upconvert a weak 980 nm pulse to 600 nm while simultaneously broadening the spectrum to that of a Lorentzian pulse up to 10 times shorter. While the current experimental demonstration is for spectral shaping, we also provide a numerical study showing the feasibility of subsequent spectral phase correction to achieve temporal compression and re-shaping of a 1~ns mono-exponentially decaying pulse to a 250 ps Lorentzian, which would constitute a complete spectro-temporal waveform shaping protocol. This method, which uses quantum frequency conversion in PPLN with >100:1 signal-to-noise ratio, is compatible with single photon states of light.
description: 4 pages, 4 figures
Dynamic resource deployment in hyperconnected parcel logistic hub networks
Creators: name: Xu, Yujia
name: Klibi, Walid
name: Montreuil, Benoit
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Physical Internet
Hyperconnected parcel logistic hubs
Dynamic resource deployment
Dynamic workforce scheduling

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: With the development of e-commerce, one of the major challenges for many parcel logistics companies has revealed to be designing reliable and flexible scheduling and deployment approaches and algorithms to meet uncertainties of parcel arrivals and resource availability in logistic hubs. In this Paper, we want to present models to spatiotemporally adjust the available resource, like workforce and robots, across hyperconnected logistic hub networks using a rolling horizon approach. In most traditional parcel logistic hubs, workers are hired to enable the sorting, consolidation, transshipment, and crossdocking of parcels, and most resource scheduling is periodic (e.g., daily) and limited to single facility, thus the number of required resources in each hub is constrained to meet the peak demand with high variance. We here propose dynamic resource scheduling and deployment mechanisms, that are fed with updated data with sensors and dynamically updated parcel arrival predictions at hubs.
Inclusion of Flagellin during Vaccination against Influenza Enhances Recall Responses in Nonhuman Primate Neonates
Creators: name: Holbrook, Beth C.
name: Hayward, Sarah L.
name: Jorgensen, Matthew J.
name: Blevins, Lance K.
name: D'Agostino, Ralph B.
name: Mizel, Steven B.
name: Kim, Jong R.
name: Alexander-Miller, Martha A.
name: Parks, Griffith D.
name: Aycock, S. Tyler
name: Kock, Nancy D.
name: De Paris, Kristina
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Influenza virus can cause life-threatening infections in neonates and young infants. Although vaccination is a major countermeasure against influenza, current vaccines are not approved for use in infants less than 6 months of age, in part due to the weak immune response following vaccination. Thus, there is a strong need to develop new vaccines with improved efficacy for this vulnerable population. To address this issue, we established a neonatal African green monkey (AGM) nonhuman primate model that could be used to identify effective influenza vaccine approaches for use in young infants. We assessed the ability of flagellin, a Toll-like receptor 5 (TLR5) agonist, to serve as an effective adjuvant in this at-risk population. Four- to 6-day-old AGMs were primed and boosted with inactivated PR8 influenza virus (IPR8) adjuvanted with either wild-type flagellin or inactive flagellin with a mutation at position 229 (m229), the latter of which is incapable of signaling through TLR5. Increased IgG responses were observed following a boost, as well as at early times after challenge, in infants vaccinated with flagellin-adjuvanted IPR8. Inclusion of flagellin during vaccination also resulted in a significantly increased number of influenza virus-specific T cells following challenge compared to the number in infants vaccinated with the m229 adjuvant. Finally, following challenge infants vaccinated with IPR8 plus flagellin exhibited a reduced pathology in the lungs compared to that in infants that received IPR8 plus m229. This study provides the first evidence of flagellin-mediated enhancement of vaccine responses in nonhuman primate neonates. IMPORTANCE Young infants are particularly susceptible to severe disease as a result of influenza virus infection. Compounding this is the lack of effective vaccines for use in this vulnerable population. Here we describe a vaccine approach that results in improved immune responses and protection in young infants. Incorporation of flagellin during vaccination resulted in increased antibody and T cell responses together with reduced disease following virus infection. These results suggest that flagellin may serve as an effective adjuvant for vaccines targeted to this vulnerable population.
PI Containers: Assessment of Functions and Development from an Engineering Design Related Perspective
Creators: name: Mahringer, Gerald
name: Landschützer, Christian
name: Cichocki, Max
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Containerization
Physical internet
Physical internet container
Transportation
Modularization

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: The idea of containerizing goods is a central component of the Physical Internet philosophy, as this containerization serves to abstract and standardize goods and shipments. This approach promises to simplify the handling of shipments on the one hand and deliver shipments more efficiently throughout the transport network. In the present work, scientific publications were evaluated according to the terms Physical Internet, PI Container and containerization. Out of almost 300 examined scientific publications, more than 25 could be identified that had a strong focus on the topics of PI Containers and containerization. These identified articles were methodically compared by categorizing them according to aspects highlighting the technical view on the current state of development of PI containers. Our research shows that over the past 12 years, just a few cases were documented where specific engineering design solutions of a PI container were presented and tested in real-life applications. Thus, we conclude that further research into the technical design of PI Containers is needed to identify use cases where the deployment of PI Containers has a significant positive impact, is accepted by users, and is accessible under economic, ecological, and technical aspects.
Alternate stabilization methods for CZTSSe photovoltaic devices by thermal treatment, dark electric bias and illumination
Creators: name: Ananda, W.
name: Rennhofer, M.
name: Mittal, A.
name: Zechner, N.
name: Lang, W.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Reliable measurement routines are crucial for power rating and yield prediction of photovoltaic emerging thinfilm technologies. Copper-Zinc-Tin-Sulfur-Selenium (CZTSSe) thin-film photovoltaic devices are an emerging technology made of abundant elements. Still, sufficient stabilization methods prior to electric power measurement are missing in the international standardization, while existing standards for other thin-film technologies do not work properly for CZTSSe. This study investigated methods for achieving power stabilization of the CZTSSe solar devices. Three complementary stabilization routines for the kesterite-based solar devices were investigated as an alternative to the existing international device testing standards: rapid annealing, dark electric biasing and different operating points under illumination. The typical number of stabilization cycles for power stabilization was between 3 and 6 cycles of rapid annealing, dark electric bias and illumination with a power loss of -19.5%, -11.4%, and -1.9%, for the respective methods. The dark electric bias method was found to provide the most reliable average result for power stabilization. All stabilization methods proved to have the potential to work sufficiently in stabilizing the CZTSSe devices for standardized power measurement.
Insight into the Mechanism of Inhibition of Adeno-Associated Virus by the Mre11/Rad50/Nbs1 Complex
Creators: name: Samulski, R. Jude
name: Lentz, Thomas B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Adeno-associated virus (AAV) is a dependent virus of the family Parvoviridae . The gene expression and replication of AAV and derived recombinant AAV (rAAV) vectors are severely limited (>10-fold) by the cellular DNA damage-sensing complex made up of Mre11, Rad50, and Nbs1 (MRN). The AAV genome does not encode the means to circumvent this block to productive infection but relies on coinfecting helper virus to do so. Using adenovirus helper proteins E1B55k and E4orf6, which enhance the transduction of AAV via degradation of MRN, we investigated the mechanism through which this DNA damage complex inhibits gene expression from rAAV. We tested the substrate specificity of inhibition and the contribution of different functions of the MRN complex. Our results demonstrate that both single- and double-stranded rAAV vectors are inhibited by MRN, which is in contrast to the predominant model that inhibition is the result of a block to second-strand synthesis. Exploring the contribution of known functions of MRN, we found that inhibition of rAAV does not require downstream DNA damage response factors, including signaling kinases ATM and ATR. The nuclease domain of Mre11 appears to play only a minor role in inhibition, while the DNA binding domain makes a greater contribution. Additionally, mutation of the inverted terminal repeat of the rAAV genome, which has been proposed to be the signal for interaction with MRN, is tolerated by the mechanism of inhibition. These results articulate a model of inhibition of gene expression in which physical interaction is more important than enzymatic activity and several key downstream damage repair factors are dispensable. IMPORTANCE Many viruses modulate the host DNA damage response (DDR) in order to create a cellular environment permissive for infection. The MRN complex is a primary sensor of damage in the cell but also responds to invading viral genomes, often posing a block to infection. AAV is greatly inhibited by MRN and dependent on coinfecting helper virus, such as adenovirus, to remove this factor. Currently, the mechanism through which MRN inhibits AAV and other viruses is poorly understood. Our results reform the predominant model that inhibition of rAAV by MRN is due to limiting second-strand DNA synthesis. Instead, a novel mechanism of inhibition of gene expression independent of a block in rAAV DNA synthesis or downstream damage factors is indicated. These findings have clear implications for understanding this restriction to transduction of AAV and rAAV vectors, which have high therapeutic relevance and likely translate to other viruses that must navigate the DDR.
R-matrices of three-state Hamiltonians solvable by Coordinate Bethe Ansatz
Creators: name: Fonseca, T.
name: Frappat, L.
name: Ragoucy, E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We review some of the strategies that can be implemented to infer an $R$-matrix from the knowledge of its Hamiltonian. We apply them to the classification achieved in arXiv:1306.6303, on three state $U(1)$-invariant Hamiltonians solvable by CBA, focusing on models for which the $S$-matrix is not trivial. For the 19-vertex solutions, we recover the $R$-matrices of the well-known Zamolodchikov--Fateev and Izergin--Korepin models. We point out that the generalized Bariev Hamiltonian is related to both main and special branches studied by Martins in arXiv:1303.4010, that we prove to generate the same Hamiltonian. The 19-vertex SpR model still resists to the analysis, although we are able to state some no-go theorems on its $R$-matrix. For 17-vertex Hamiltonians, we produce a new $R$-matrix.
description: 22 pages
Odium regni, fons olei e reges uncti da Augustus alla res publica christianorum. Spigolature tra il sacro e il profano (giuridico)
Creators: name: Licandro, Orazio
Publisher: name: La Rivista di Engramma
Year: 2023
Subjects: Roman Empire
Kingship
Holy oil
Investiture

description: Drawing on the research of Marc Bloch and Ernst H. Kantorowicz, the paper investigates the origins of anointing (holy oil) in the investiture of new kings in the post-Roman West, a rite that later penetrated the Eastern liturgy of imperial investiture.
Additional file 1 of A 2-year follow-up to a randomized controlled trial on resistance training in postmenopausal women: vasomotor symptoms, quality of life and cardiovascular risk markers
Creators: name: Nilsson, Sigrid
name: Henriksson, Moa
name: Hammar, Mats
name: Berin, Emilia
name: Lawesson, Sofia Sederholm
name: Ward, Liam J.
name: Li, Wei
name: Holm, Anna-Clara Spetz
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy
subject: Mental Health

description: Supplementary Material 1.
Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 1 Interacts with a Member of the Interferon-Stimulated Gene 15 Pathway
Creators: name: Jacobs, Sarah R.
name: Giffin, Louise
name: Damania, Blossom
name: Bennett, Christopher L.
name: West, John A.
name: Stopford, Charles M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) is a gammaherpesvirus known to establish lifelong latency in the human host. We and others have previously shown that three KSHV homologs of cellular interferon regulatory factors (IRFs), known as viral IRFs (vIRFs), participate in evasion of the host interferon (IFN) response. We report that vIRF1 interacts with the cellular interferon-stimulated gene 15 (ISG15) E3 ligase, HERC5, in the context of Toll-like receptor 3 (TLR3) activation and IFN induction. The ISG15 protein is covalently conjugated to target proteins upon activation of the interferon response. Interaction between vIRF1 and HERC5 was confirmed by immunoprecipitation, and the region between amino acids 224 and 349 of vIRF1 was required for interaction with HERC5. We further report that expression of vIRF1 in the context of TLR3 activation results in decreased ISG15 conjugation of proteins. Specifically, TLR3-induced ISG15 conjugation and protein levels of cellular IRF3, a known ISG15 target, were decreased in the presence of vIRF1 compared to the control. vIRF1 itself was also identified as a target of ISG15 conjugation. KSHV-infected cells exhibited increased ISG15 conjugation upon reactivation from latency in coordination with increased IFN. Furthermore, knockdown of ISG15 in latently infected cells resulted in a higher level of KSHV reactivation and an increase in infectious virus. These data suggest that the KSHV vIRF1 protein affects ISG15 conjugation and interferon responses and may contribute to effective KSHV replication. IMPORTANCE The KSHV vIRF1 protein can inhibit interferon activation in response to viral infection. We identified a cellular protein named HERC5, which is the major ligase for ISG15, as a vIRF1 binding partner. vIRF1 association with HERC5 altered ISG15 modification of cellular proteins, and knockdown of ISG15 augmented reactivation of KSHV from latency.
Combining Motion Matching and Orientation Prediction to Animate Avatars for Consumer-Grade VR Devices
Creators: name: Ponton, Jose Luis
name: Yun, Haoran
name: Andujar, Carlos
name: Pelechano, Nuria
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Graphics (cs.GR)
subject: FOS: Computer and information sciences

description: The animation of user avatars plays a crucial role in conveying their pose, gestures, and relative distances to virtual objects or other users. Self-avatar animation in immersive VR helps improve the user experience and provides a Sense of Embodiment. However, consumer-grade VR devices typically include at most three trackers, one at the Head Mounted Display (HMD), and two at the handheld VR controllers. Since the problem of reconstruction the user pose from such sparse data is ill-defined, especially for the lower body, the approach adopted by most VR games consists of assuming the body orientation matches that of the HMD, and applying animation blending and time-warping from a reduced set of animations. Unfortunately, this approach produces noticeable mismatches between user and avatar movements. In this work we present a new approach to animate user avatars that is suitable for current mainstream VR devices. First, we use a neural network to estimate the user's body orientation based on the tracking information from the HMD and the hand controllers. Then we use this orientation together with the velocity and rotation of the HMD to build a feature vector that feeds a Motion Matching algorithm. We built a MoCap database with animations of VR users wearing a HMD and used it to test our approach on both self-avatars and other users' avatars. Our results show that our system can provide a large variety of lower body animations while correctly matching the user orientation, which in turn allows us to represent not only forward movements but also stepping in any direction.
description: Project Website: https://github.com/UPC-ViRVIG/MMVR
LMP1 Promotes Expression of Insulin-Like Growth Factor 1 (IGF1) To Selectively Activate IGF1 Receptor and Drive Cell Proliferation
Creators: name: Raab-Traub, Nancy
name: Tworkoski, Kathryn
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Epstein-Barr Virus (EBV) is a gammaherpesvirus that infects the majority of the human population and is linked to the development of multiple cancers, including nasopharyngeal carcinoma. Latent membrane protein 1 (LMP1) is considered the primary oncoprotein of EBV, and in epithelial cells it induces the expression and activation, or phosphorylation, of the epidermal growth factor receptor kinase. To identify effects on additional kinases, an unbiased screen of receptor tyrosine kinases potentially activated by LMP1 was performed. Using a protein array, it was determined that LMP1 selectively activates insulin-like growth factor 1 receptor (IGF1R). This activation takes place in fibroblast, epithelial, and nasopharyngeal cell lines that express LMP1 stably and transiently. Of note, LMP1 altered the phosphorylation, but not the expression, of IGF1R. The use of LMP1 mutants with defective signaling domains revealed that the C-terminal activating region 2 domain of LMP1 increased the mRNA expression and the secretion of the ligand IGF1, which promoted phosphorylation of IGF1R. IGF1R phosphorylation was dependent upon activation of canonical NF-κB signaling and was suppressed by IκBα and a dominant negative form of TRAF6. Inhibition of IGF1R activation with two small-molecule inhibitors, AG1024 and picropodophyllin (PPP), or with short hairpin RNA (shRNA) directed against IGF1R selectively reduced proliferation, focus formation, and Akt activation in LMP1-positive cells but did not impair LMP1-induced cell migration. Expression of constitutively active Akt rescued cell proliferation in the presence of IGF1R inhibitors. These findings suggest that LMP1-mediated activation of IGF1R contributes to the ability of LMP1 to transform epithelial cells. IMPORTANCE EBV is linked to the development of multiple cancers in both lymphoid and epithelial cells, including nasopharyngeal carcinoma. Nasopharyngeal carcinoma is a major cancer that develops in specific populations, with nearly 80,000 new cases reported annually. LMP1 is consistently expressed in early lesions and continues to be detected within 50 to 80% of these cancers at later stages. It is therefore of paramount importance to understand the mechanisms through which LMP1 alters cell growth and contributes to tumorigenesis. This study is the first to determine that LMP1 activates the IGF1R tyrosine kinase by regulating expression of the ligand IGF1. Additionally, the data in this paper reveal that specific targeting of IGF1R selectively impacts LMP1-positive cells. These findings suggest that therapies directed against IGF1R may specifically impair the growth of EBV-infected cells.
Additional file 1 of scBubbletree: computational approach for visualization of single cell RNA-seq data
Creators: name: Kitanovski, Simo
name: Cao, Yingying
name: Ttoouli, Dimitris
name: Farahpour, Farnoush
name: Wang, Jun
name: Hoffmann, Daniel
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Space Science
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Plant Biology

description: Additional file 1:
A theoretical calculation of microlensing signatures caused by free-floating planets towards the Galactic bulge
Creators: name: Hamolli, L.
name: Hafizi, M.
name: Nucita, A. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Free-floating planets are recently drawing a special interest of the scientific community. Gravitational microlensing is up to now the exclusive method for the investigation of free-floating planets, including their spatial distribution function and mass function. In this work, we examine the possibility that the future Euclid space-based observatory may allow to discover a substantial number of microlensing events caused by free-floating planets. Based on latest results about the free-floating planet mass function in the mass range $[10^{-5}, 10^{-2}]M_{\odot}$, we calculate the optical depth towards the Galactic bulge as well as the expected microlensing rate and find that Euclid may be able to detect hundreds to thousands of these events per month. Making use of a synthetic population, we also investigate the possibility of detecting parallax effect in simulated microlensing events due to free-floating planets and find a significant efficiency for the parallax detection that turns out to be around 30%.
description: Paper published in IJMPD 22, 1350072, 2013; 14 pages, 3 tables, 3 figures
Additional file 4 of The ovipositor cue indole inhibits animal host attraction in Aedes aegypti (Diptera: Culicidae) mosquitoes
Creators: name: Dekel, Amir
name: Sar-Shalom, Evyatar
name: Vainer, Yuri
name: Yakir, Esther
name: Bohbot, Jonathan D.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 4: Table S1. Scripts and functions used to calculate flight parameters.
LMP1-Induced Sumoylation Influences the Maintenance of Epstein-Barr Virus Latency through KAP1
Creators: name: Moody, Cary A.
name: Pagano, Joseph S.
name: Whitehurst, Christopher B.
name: Moss, Charles Randall
name: Bentz, Gretchen L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT As a herpesvirus, Epstein-Barr virus (EBV) establishes a latent infection that can periodically undergo reactivation, resulting in lytic replication and the production of new infectious virus. Latent membrane protein-1 (LMP1), the principal viral oncoprotein, is a latency-associated protein implicated in regulating viral reactivation and the maintenance of latency. We recently found that LMP1 hijacks the SUMO-conjugating enzyme Ubc9 via its C-terminal activating region-3 (CTAR3) and induces the sumoylation of cellular proteins. Because protein sumoylation can promote transcriptional repression, we hypothesized that LMP1-induced protein sumoylation induces the repression of EBV lytic promoters and helps maintain the viral genome in its latent state. We now show that with inhibition of LMP1-induced protein sumoylation, the latent state becomes less stable or leakier in EBV-transformed lymphoblastoid cell lines. The cells are also more sensitive to viral reactivation induced by irradiation, which results in the increased production and release of infectious virus, as well as increased susceptibility to ganciclovir treatment. We have identified a target of LMP1-mediated sumoylation that contributes to the maintenance of latency in this context: KRAB-associated protein-1 (KAP1). LMP1 CTAR3-mediated sumoylation regulates the function of KAP1. KAP1 also binds to EBV OriLyt and immediate early promoters in a CTAR3-dependent manner, and inhibition of sumoylation processes abrogates the binding of KAP1 to these promoters. These data provide an additional line of evidence that supports our findings that CTAR3 is a distinct functioning regulatory region of LMP1 and confirm that LMP1-induced sumoylation may help stabilize the maintenance of EBV latency. IMPORTANCE Epstein-Barr virus (EBV) latent membrane protein-1 (LMP1) plays an important role in the maintenance of viral latency. Previously, we documented that LMP1 targets cellular proteins to be modified by a ubiquitin-like protein (SUMO). We have now identified a function for this LMP1-induced modification of cellular proteins in the maintenance of EBV latency. Because latently infected cells have to undergo viral reactivation in order to be vulnerable to antiviral drugs, these findings identify a new way to increase the rate of EBV reactivation, which increases cell susceptibility to antiviral therapies.
AvatarGo: Plug and Play self-avatars for VR
Creators: name: Ponton, Jose Luis
name: Monclus, Eva
name: Pelechano, Nuria
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Graphics (cs.GR)
subject: FOS: Computer and information sciences

description: The use of self-avatars in a VR application can enhance presence and embodiment which leads to a better user experience. In collaborative VR it also facilitates non-verbal communication. Currently it is possible to track a few body parts with cheap trackers and then apply IK methods to animate a character. However, the correspondence between trackers and avatar joints is typically fixed ad-hoc, which is enough to animate the avatar, but causes noticeable mismatches between the user's body pose and the avatar. In this paper we present a fast and easy to set up system to compute exact offset values, unique for each user, which leads to improvements in avatar movement. Our user study shows that the Sense of Embodiment increased significantly when using exact offsets as opposed to fixed ones. We also allowed the users to see a semitransparent avatar overlaid with their real body to objectively evaluate the quality of the avatar movement with our technique.
description: GitHub: https://github.com/UPC-ViRVIG/AvatarGo
Physical Internet based Hyperconnected Logistics Platform Enabling Heavy-Duty Machinery Sharing in the Composting Industry: A Simulation-Based Scenario Investigation
Creators: name: Cichocki, Max
name: Montreuil, Benoit
name: Barenji, Ali
name: Landschützer, Christian
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Physical internet
Hyperconnected logistic
Heavy-duty machinery
Simulation
Composting

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Composting plants face significant challenges in meeting increasing quality standards and production rates due to the high costs of essential composting machinery. To address these issues, a Physical Internet based Hyperconnected Logistic Platform for Heavy-Duty Machinery (HLHD) has been proposed. The HLHD system enables composting plant operators to share expensive machinery between plants, allowing for improved efficiency, cost-effectiveness, and enhanced compost production quality The HLHD operates by transporting composting machinery between designated hubs and participating composting plants, where they perform their specific tasks during the composting process. To evaluate the efficacy of the proposed HLHD system, a simulation-based study of three distinct scenarios has been conducted. The first scenario focused on small and medium-sized composting facilities, providing an accessible and cost-effective solution for smaller facilities. In the second scenario, all composting facilities participate in the HLHD to an equal extent, while the third scenario assumed that big composting plants already own the necessary equipment. However, since the utilization of machinery at these large farms is generally low, they participate in the HLHD by serving as hubs once their machinery is idle. Overall, the HLHD system shows great potential in addressing the challenges faced by composting plants. The proposed system can lead to improved resource utilization, enhanced efficiency, and reduced costs, ultimately leading to better quality compost production.
Non-Monotonic Reasoning and Story Comprehension
Creators: name: Diakidoy, Irene-Anna
name: Kakas, Antonis
name: Michael, Loizos
name: Miller, Rob
Publisher: name: arXiv
Year: 2014
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences
subject: I.2.3; I.2.4

description: This paper develops a Reasoning about Actions and Change framework integrated with Default Reasoning, suitable as a Knowledge Representation and Reasoning framework for Story Comprehension. The proposed framework, which is guided strongly by existing knowhow from the Psychology of Reading and Comprehension, is based on the theory of argumentation from AI. It uses argumentation to capture appropriate solutions to the frame, ramification and qualification problems and generalizations of these problems required for text comprehension. In this first part of the study the work concentrates on the central problem of integration (or elaboration) of the explicit information from the narrative in the text with the implicit (in the readers mind) common sense world knowledge pertaining to the topic(s) of the story given in the text. We also report on our empirical efforts to gather background common sense world knowledge used by humans when reading a story and to evaluate, through a prototype system, the ability of our approach to capture both the majority and the variability of understanding of a story by the human readers in the experiments.
Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations
Creators: name: Zhou, Shuntai
name: Swanstrom, Ronald
name: Jones, Corbin
name: Mieczkowski, Piotr
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Validating the sampling depth and reducing sequencing errors are critical for studies of viral populations using next-generation sequencing (NGS). We previously described the use of Primer ID to tag each viral RNA template with a block of degenerate nucleotides in the cDNA primer. We now show that low-abundance Primer IDs (offspring Primer IDs) are generated due to PCR/sequencing errors. These artifactual Primer IDs can be removed using a cutoff model for the number of reads required to make a template consensus sequence. We have modeled the fraction of sequences lost due to Primer ID resampling. For a typical sequencing run, less than 10% of the raw reads are lost to offspring Primer ID filtering and resampling. The remaining raw reads are used to correct for PCR resampling and sequencing errors. We also demonstrate that Primer ID reveals bias intrinsic to PCR, especially at low template input or utilization. cDNA synthesis and PCR convert ca. 20% of RNA templates into recoverable sequences, and 30-fold sequence coverage recovers most of these template sequences. We have directly measured the residual error rate to be around 1 in 10,000 nucleotides. We use this error rate and the Poisson distribution to define the cutoff to identify preexisting drug resistance mutations at low abundance in an HIV-infected subject. Collectively, these studies show that >90% of the raw sequence reads can be used to validate template sampling depth and to dramatically reduce the error rate in assessing a genetically diverse viral population using NGS. IMPORTANCE Although next-generation sequencing (NGS) has revolutionized sequencing strategies, it suffers from serious limitations in defining sequence heterogeneity in a genetically diverse population, such as HIV-1 due to PCR resampling and PCR/sequencing errors. The Primer ID approach reveals the true sampling depth and greatly reduces errors. Knowing the sampling depth allows the construction of a model of how to maximize the recovery of sequences from input templates and to reduce resampling of the Primer ID so that appropriate multiplexing can be included in the experimental design. With the defined sampling depth and measured error rate, we are able to assign cutoffs for the accurate detection of minority variants in viral populations. This approach allows the power of NGS to be realized without having to guess about sampling depth or to ignore the problem of PCR resampling, while also being able to correct most of the errors in the data set.
Additional file 7 of The ovipositor cue indole inhibits animal host attraction in Aedes aegypti (Diptera: Culicidae) mosquitoes
Creators: name: Dekel, Amir
name: Sar-Shalom, Evyatar
name: Vainer, Yuri
name: Yakir, Esther
name: Bohbot, Jonathan D.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 7: Figure S2. High indole concentrations exhibit significant repellency over time. Cumulative number of mosquito landings per elapsed minute (see Fig. 4b). Points represented are mean ± SEM (n = 3). Statistical significance was determined using a non-parametric test followed by a Dunn’s multiple comparisons test (P values shown on the histograms).
Sturm Liouville Problem with Moving Discontinuity Points
Creators: name: Hira, Fatma
name: Altinisik, Nihat
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 34B09, 34L10, 34L24, 34B27

description: In this paper, we present a new discontinuous Sturm Liouville problem with symmetrically located discontinuities which are defined depending on a neighborhood of a midpoint of the interval. Also the problem contains an eigenparameter in one of the boundary conditions and has coupled transmission conditions at the discontinuity points. We investigate the properties of the eigenvalues, obtain asymptotic formulas for the eigenvalues and the corresponding eigenfunctions and construct Green's function of this problem.
description: 19 pages. arXiv admin note: text overlap with arXiv:1210.4350 by other authors
Additional file 8 of The ovipositor cue indole inhibits animal host attraction in Aedes aegypti (Diptera: Culicidae) mosquitoes
Creators: name: Dekel, Amir
name: Sar-Shalom, Evyatar
name: Vainer, Yuri
name: Yakir, Esther
name: Bohbot, Jonathan D.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 8: Figure S3. Representative single flight trajectories of female mosquitoes exposed to CO2, 1-octen-3-ol and indole, respectively. A Schematic of the flight tunnel and the overall region of interest (ROI) located between 500 and 1300 mm on the X-axis (shaded gray box). The three odor treatments are color-coded. B Example trajectories of mosquitoes exposed to CO2 or to a combination of CO2 + 1-octen-3-ol, or CO2 + 1-octen-3-ol + indole. These trajectories were recorded in the ROI within the flight tunnel and projected into each of the three 2-dimensional planes (from left to right, Y-X, Z-X, and Z-Y). Speed is color-coded according to the speed index. The last coordinate of the trajectory is shown in black and marked with an arrow. The dashed line indicates trajectory segments outside the ROI.
Energy Transfer in Stability-Optimized Perovskite Nanocrystals
Creators: name: Greiner, Michèle G.
name: Singldinger, Andreas
name: Henke, Nina A.
name: Lampe, Carola
name: Leo, Ulrich
name: Gramlich, Moritz
name: Urban, Alexander S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Outstanding optoelectronic properties and a facile synthesis render halide perovskite nanocrystals (NCs) a promising material for nanostructure-based devices. However, the commercialization is hindered mainly by the lack of NC stability under ambient conditions and inefficient charge carrier injection. Here, we investigate solutions to both problems, employing methylammonium lead bromide (MAPbBr_3) NCs encapsulated in diblock copolymer core-shell micelles of tunable size. We confirm that the shell does not prohibit energy transfer, as FRET efficiencies between these NCs and 2D CsPbBr_3 nanoplatelets (NPLs) reach 73.6%. This value strongly correlates to the micelle size, with thicker shells displaying significantly reduced FRET efficiencies. Those high efficiencies come with a price, as the thinnest shells protect the encapsulated NCs less from environmentally induced degradation. Finding the sweet spot between efficiency and protection could lead to the realization of tailored energy funnels with enhanced carrier densities for high-power perovskite NC-based optoelectronic applications.
Physical Internet Enabled Hyperconnected Circular Supply Chains
Creators: name: Wu, Ziqing
name: Oger, Raphaël
name: Lauras, Matthieu
name: Montreuil, Benoit
name: Faugère, Louis
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Circular supply chain management
Physical internet
Hyperconnected circular
Supply chain
Circular economy
Sustainability
Conceptual framework

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Physical Internet (PI) and Circular Supply Chains (CSC) are both promising supply chain paradigms aiming toward the significant improvement of sustainability. PI potentially provides a set of solutions for implementing CSC as both emphasize interconnectivity. This Paper presents the Hyperconnected Circular Supply Chain (HCSC) framework, which aims to combine the strengths of both CSC and PI to create a comprehensive set of guidelines for supply chain stakeholders. The proposed HCSC framework encompasses nine core characteristics, addressing aspects such as product design for circularity, on-demand materialization in PI open production fabs, local material and energy recovery, hyperconnected logistics systems for materials and products, sharing economy enablement with PI, circular functionalities exploitation for existing facilities, open and hyperconnected sustainability performance monitoring, and technological and business model innovation.
Additional file 1 of Comparative effectiveness and safety of eplerenone and spironolactone in patients with heart failure: a systematic review and meta-analysis
Creators: name: Elshahat, Ahmed
name: Mansour, Ahmed
name: Ellabban, Mohamed
name: Diaa, Ahmed
name: Hassan, Atef
name: Fawzy, Ahmed
name: Saad, Omar Abdulrahman
name: Abouelmagd, Moaz
name: Eid, Mahmoud
name: Elaraby, Ahmed
name: Elkasaby, Mohamed Hamouda
name: Abdelaziz, Ahmed
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Hematology

description: Supplementary Material 1.
A restriction on the Alexander polynomials of $L$-space knots
Creators: name: Krcatovich, David
Publisher: name: arXiv
Year: 2014
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57

description: Using an invariant defined by Rasmussen, we extend an argument given by Hedden and Watson which further restricts which Alexander polynomials can be realized by $L$-space knots.
description: 11 pages, 2 figures