cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Beauty of Repetition in Machine Composition Scenarios
Creators: name: Hu, Zhejing
name: Ma, Xiao
name: Liu, Yan
name: Chen, Gong
name: Liu, Yongxu
Publisher: name: arXiv
Year: 2022
Subjects: subject: Multimedia (cs.MM)
subject: FOS: Computer and information sciences

description: Repetition, a basic form of artistic creation, appears in most musical works and delivers enthralling aesthetic experiences.
description: Published on ACM Multimedia 2022
The Rad6/18 Ubiquitin Complex Interacts with the Epstein-Barr Virus Deubiquitinating Enzyme, BPLF1, and Contributes to Virus Infectivity
Creators: name: Pagano, J. S.
name: Whitehurst, C. B.
name: Kumar, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Epstein-Barr virus (EBV) encodes BPLF1, a lytic cycle protein with deubiquitinating activity that is contained in its N-terminal domain and conserved across the Herpesviridae. EBV replication is associated with cellular DNA replication and repair factors, and initiation of EBV lytic replication induces a DNA damage response, which can be regulated at least in part by BPLF1. The cellular DNA repair pathway, translesion synthesis (TLS), is disrupted by BPLF1, which deubiquitinates the DNA processivity factor, PCNA, and inhibits the recruitment of the TLS polymerase, polymerase eta (Pol eta), after damage to DNA by UV irradiation. Here we showed that the E3 ubiquitin ligase, which activates TLS repair by monoubiquitination of PCNA, is also affected by BPLF1 deubiquitinating activity. First, BPLF1 interacts directly with Rad18, and overexpression of BPLF1 results in increased levels of the Rad18 protein, suggesting that it stabilizes Rad18. Next, expression of functionally active BPLF1 caused relocalization of Rad18 into nuclear foci, which is consistent with sites of cellular DNA replication that occur during S phase. Also, levels of Rad18 remain constant during lytic reactivation of wild-type virus, but reactivation of BPLF1 knockout virus resulted in decreased levels of Rad18. Finally, the contribution of Rad18 levels to infectious virus production was examined with small interfering RNA (siRNA) targeting Rad18. Results demonstrated that reducing levels of Rad18 decreased production of infectious virus, and infectious titers of BPLF1 knockout virus were partially restored by overexpression of Rad18. Thus, BPLF1 interacts with and maintains Rad18 at high levels during lytic replication, which assists in production of infectious virus.
Measuring pulse times of arrival from broadband pulsar observations
Creators: name: Liu, K.
name: Desvignes, G.
name: Cognard, I.
name: Stappers, B. W.
name: Verbiest, J. P. W.
name: Lee, K. J.
name: Champion, D. J.
name: Kramer, M.
name: Freire, P. C. C.
name: Karuppusamy, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: In recent years, instrumentation enabling pulsar observations with unprecedentedly high fractional bandwidth has been under development which can be used to substantially improve the precision of pulsar timing experiments. The traditional template-matching method used to calculate pulse times-of-arrival (ToAs), may not function effectively on these broadband data due to a variety of effects such as diffractive scintillation in the interstellar medium, profile variation as a function of frequency, dispersion measure (DM) evolution and so forth. In this paper, we describe the channelised Discrete Fourier Transform method that can greatly mitigate the influence of the aforementioned effects when measuring ToAs from broadband timing data. The method is tested on simulated data, and its potential in improving timing precision is shown. We further apply the method to PSR J1909$-$3744 data collected at the Nançay Radio Telescope with the Nançay Ultimate Pulsar Processing Instrument. We demonstrate a removal of systematics due to the scintillation effect as well as improvement on ToA measurement uncertainties. Our method also determines temporal variations in dispersion measure, which are consistent with multi-channel timing approaches used earlier.
description: 10 pages, 13 figures, accepted for publication in MNRAS
Within-Host Evolution Results in Antigenically Distinct GII.4 Noroviruses
Creators: name: Debbink, K.
name: Ferris, M. T.
name: Lanzavecchia, A.
name: Lindesmith, L. C.
name: Beltramello, M.
name: Baric, R. S.
name: Corti, D.
name: Swanstrom, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Genogroup II, genotype 4 (GII.4) noroviruses are known to rapidly evolve, with the emergence of a new primary strain every 2 to 4 years as herd immunity to the previously circulating strain is overcome. Because viral genetic diversity is higher in chronic than in acute infection, chronically infected immunocompromised people have been hypothesized to be a potential source for new epidemic GII.4 strains. However, while some capsid protein residues are under positive selection and undergo patterned changes in sequence variation over time, the relationships between genetic variation and antigenic variation remains unknown. Based on previously published GII.4 strains from a chronically infected individual, we synthetically reconstructed virus-like particles (VLPs) representing early and late isolates from a small-bowel transplant patient chronically infected with norovirus, as well as the parental GII.4-2006b strain. We demonstrate that intrahost GII.4 evolution results in the emergence of antigenically distinct strains over time, comparable to the variation noted between the chronologically predominant GII.4 strains GII.4-2006b and GII.4-2009. Our data suggest that in some individuals the evolution that occurs during a chronic norovirus infection overlaps with changing antigenic epitopes that are associated with successive outbreak strains and may select for isolates that are potentially able to escape herd immunity from earlier isolates.
Additional file 1 of Epidemiology and outcomes of culture-positive bloodstream pathogens prior to and during the SARS-CoV-2 pandemic: a multicenter evaluation
Creators: name: Bauer, Karri A.
name: Puzniak, Laura A.
name: Yu, Kalvin C.
name: Finelli, Lyn
name: Moise, Pamela
name: Ai, ChinEn
name: Watts, Janet A.
name: Gupta, Vikas
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Computational Biology

description: Additional file 1: Table S1. Distribution of study hospitals.
Additional file 1 of Safety and efficacy of early beta-blocker initiation in acute heart failure and cardiogenic shock: systematic review and meta-analysis
Creators: name: Sinardja, Cyndiana Widia Dewi
name: Jagannatha, Gusti Ngurah Prana
name: de Liyis, Bryan Gervais
name: Kosasih, Anastasya Maria
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Marine Biology

description: Additional file 1.
Multicasting in Cognitive Radio Networks: Algorithms, Techniques and Protocols
Creators: name: Qadir, Junaid
name: Baig, Adeel
name: Ali, Asad
name: Shafi, Quratulain
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Multicasting is a fundamental networking primitive utilized by numerous applications. This also holds true for cognitive radio networks (CRNs) which have been proposed as a solution to the problems that emanate from the static non-adaptive features of classical wireless networks. A prime application of CRNs is dynamic spectrum access (DSA), which improves the efficiency of spectrum allocation by allowing a secondary network, comprising of secondary users (SUs), to share spectrum licensed to a primary licensed networks comprising of primary users (PUs). Multicasting in CRNs is a challenging problem due to the dynamic nature of spectrum opportunities available to the SUs. Various approaches, including those based in optimization theory, network coding, algorithms, have been proposed for performing efficient multicast in CRNs. In this paper, we provide a self-contained tutorial on algorithms and techniques useful for solving the multicast problem, and then provide a comprehensive survey of protocols that have been proposed for multicasting in CRNs. We conclude this paper by identifying open research questions and future research directions.
Prerequisites for Data Sharing and Realizing Off-peak Deliveries
Creators: name: Hultåker, Annette
name: Blinge, Magnus
name: Jabarkhel, Ibrahim
name: Sandberg, Minna
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Off-peak deliveries
Urban freight
Freight efficiency
Night-time distribution
Unmanned delivery
Connected goods
Data sharing

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Off-Peak is an efficient way to transport goods to dense urban environments where congestion and lack of space have a major impact on the productivity of the delivery. Battery Electric Vehicles are quiet and have opened the possibilities for freight deliveries in cities at night. One challenge is that the deliveries must be possible to make without having staff at night to receive the delivery. In the HITS (Sustainable & Integrated Urban Transport System) project, we have accomplished a successful test and proven that unmanned off-peak deliveries can start to be implemented for many applications and can reduce delivery time by 30 percent. One-time encrypted digital smart lock solutions enable the right goods, from the right truck, at the right time, in the right location to get access to, e.g., restaurants after closing hours. In order for offpeak deliveries in a “Physical Internet”-setup to work, data needs to be shared between the actors. One part of the project has studied the prerequisites for data sharing to enable a trustful collaboration between different stakeholders in general. Important factors are the willingness to apply data-driven decision making and trust between the different actors within a supply chain.
Explicit tragoedia. The Undressing of the King’s Body Xerxes, Constantine XI Palaeologus, Richard II
Creators: name: Centanni, Monica
Publisher: name: La Rivista di Engramma
Year: 2023
Subjects: Ernst Kantorowicz
Aeschylus
Persians
Constantinople Fall
Skakespeare
King Richard II

description: Three pictures, three personae – Xerxes, Constantine XI Palaeologus, Richard the Second – staging three divestments of the royal body: three times, on the augmented stage of the tragic theatre in Athens in 472 BC; in London in 1599; and on 29 May, 1453, in Constantinople, in the last theatrical act of the last Byzantine emperor, in which the monarch strips himself naked and, deprived of his double, icastically shows the end of royalty. The monarchy thus ends three times. The battle of Salamis, in Aeschylus’ Persians, is presented (anti-historically, but that does not matter here) as the absolute end of the Persian monarchy. No matter how far-fetched and anti-historical the representation is, what Aeschylus presents on stage is the end of Persian monarchic power (“no one obeys the Sovereign any more [...] all Persia is buried”). The queen breaks her promise and does not appear onstage again to return her son-king the new robe: Xerxes is naked. The death of Constantine XI sanctions the end of the Second Rome and of the millennial Roman empire: Constantine Palaeologus understands the importance of the symbolic struggle and, on his last day in Constantinople, stages the figurative death of the monarch’s divine body. Richard II, with his divestment emphasised by perfect ceremonial gestures and formulas, stages the inverted ritual of kingship: “It is bankrupt of his majesty” (Richard II). For three times, Western theatre – both tragic and historical – blatantly stages the death of the king’s divine body and the end of kingship itself. Yet the ghosts of royalty can return to disturb the world, from past and future, from near and far. The death of the king’s divine body and the end of monarchy demand to be continually presented and performed, as the glow of kingship is resilient. Aeschylus, Shakespeare, and the scenario of the last day of Constantinople aptly present the allure and danger of royalty: the splendour of kingship becomes epiphany in the instant in which it implodes, in the last glow of its end.
Extracting Hidden Hierarchies in 3D Distribution Networks
Creators: name: Modes, Carl D.
name: Magnasco, Marcelo O.
name: Katifori, Eleni
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences

description: Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function. Yet, the set of tools that can characterize such a weighted cycle-rich architecture in a physically relevant, mathematically compact way is sparse. In order to fill this void, we have developed a new algorithm that rests on an abstraction of the physical `tiling' in the case of a two dimensional network to an effective tiling of an abstract surface in space that the network may be thought to sit in. Generically these abstract surfaces are richer than the flat plane and as a result there are now two families of fundamental units that may aggregate upon cutting weakest links -- the plaquettes of the tiling and the longer `topological' cycles associated with the abstract surface itself. Upon sequential removal of the weakest links, as determined by the edge weight, neighboring plaquettes merge and a tree characterizing this merging process results. The properties of this characteristic tree can provide the physical and topological data required to describe the architecture of the network and to build physical models. The new algorithm can be used for automated phenotypic characterization of any weighted network whose structure is dominated by cycles, such as mammalian vasculature in the organs, the root networks of clonal colonies like quaking aspen, or the force networks in jammed granular matter.
Breast Milk of HIV-Positive Mothers Has Potent and Species-Specific In Vivo HIV-Inhibitory Activity
Creators: name: Kuhn, Louise
name: Garcia, J. Victor
name: Fouda, Genevieve G.
name: Baker, Caroline
name: Permar, Sallie R.
name: Stamper, Lisa W.
name: Hinde, Katie
name: Wahl, Angela
name: Spagnuolo, Rae Ann
name: Aldrovandi, Grace M.
name: Bode, Lars
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Despite the nutritional and health benefits of breast milk, breast milk can serve as a vector for mother-to-child HIV transmission. Most HIV-infected infants acquire HIV through breastfeeding. Paradoxically, most infants breastfed by HIV-positive women do not become infected. This is potentially attributed to anti-HIV factors in breast milk. Breast milk of HIV-negative women can inhibit HIV infection. However, the HIV-inhibitory activity of breast milk from HIV-positive mothers has not been evaluated. In addition, while significant differences in breast milk composition between transmitting and nontransmitting HIV-positive mothers have been correlated with transmission risk, the HIV-inhibitory activity of their breast milk has not been compared. This knowledge may significantly impact the design of prevention approaches in resource-limited settings that do not deny infants of HIV-positive women the health benefits of breast milk. Here, we utilized bone marrow/liver/thymus humanized mice to evaluate the in vivo HIV-inhibitory activity of breast milk obtained from HIV-positive transmitting and nontransmitting mothers. We also assessed the species specificity and biochemical characteristics of milk's in vivo HIV-inhibitory activity and its ability to inhibit other modes of HIV infection. Our results demonstrate that breast milk of HIV-positive mothers has potent HIV-inhibitory activity and indicate that breast milk can prevent multiple routes of infection. Most importantly, this activity is unique to human milk. Our results also suggest multiple factors in breast milk may contribute to its HIV-inhibitory activity. Collectively, our results support current recommendations that HIV-positive mothers in resource-limited settings exclusively breastfeed in combination with antiretroviral therapy. IMPORTANCE Approximately 240,000 children become infected with HIV annually, the majority via breastfeeding. Despite daily exposure to virus in breast milk, most infants breastfed by HIV-positive women do not acquire HIV. The low risk of breastfeeding-associated HIV transmission is likely due to antiviral factors in breast milk. It is well documented that breast milk of HIV-negative women can inhibit HIV infection. Here, we demonstrate, for the first time, that breast milk of HIV-positive mothers (nontransmitters and transmitters) inhibits HIV transmission. We also demonstrate that breast milk can prevent multiple routes of HIV acquisition and that this activity is unique to human milk. Collectively, our results support current guidelines which recommend that HIV-positive women in resource-limited settings exclusively breastfeed in combination with infant or maternal antiretroviral therapy.
Motion Guided Deep Dynamic 3D Garments
Creators: name: Zhang, Meng
name: Ceylan, Duygu
name: Mitra, Niloy J.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Graphics (cs.GR)
subject: FOS: Computer and information sciences

description: Realistic dynamic garments on animated characters have many AR/VR applications. While authoring such dynamic garment geometry is still a challenging task, data-driven simulation provides an attractive alternative, especially if it can be controlled simply using the motion of the underlying character. In this work, we focus on motion guided dynamic 3D garments, especially for loose garments. In a data-driven setup, we first learn a generative space of plausible garment geometries. Then, we learn a mapping to this space to capture the motion dependent dynamic deformations, conditioned on the previous state of the garment as well as its relative position with respect to the underlying body. Technically, we model garment dynamics, driven using the input character motion, by predicting per-frame local displacements in a canonical state of the garment that is enriched with frame-dependent skinning weights to bring the garment to the global space. We resolve any remaining per-frame collisions by predicting residual local displacements. The resultant garment geometry is used as history to enable iterative rollout prediction. We demonstrate plausible generalization to unseen body shapes and motion inputs, and show improvements over multiple state-of-the-art alternatives.
description: 11 pages
Modeling and optimization of the omnichannel retailing problem
Creators: name: Kolyaei, Maryam
name: Zhang, Lele
name: Anjomshoa, Hamideh
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Omnichannel retailer
Optimization
Inventory management
Replenishment
Fulfillment

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: In this Paper, we focus on a problem faced by an omnichannel retailer that operates multiple stores and a fulfillment center. The retailer sells products to customers over a selling horizon of the period through online and physical channels. This study aims to determine the joint tactical and operational decisions on fulfillment optimization and inventory management services in an integrated model. The multi-period horizon in our model allows more realistic planning, where various decisions can be taken at different periods. Besides, our model considers the lost-demand sale to reflect the actual sale. The proposed model helps omnichannel retailers to have an integrated tool for inventory management and fulfillment service with real-time monitoring the inventory levels across locations.
Additional file 2 of Epidemiology and outcomes of culture-positive bloodstream pathogens prior to and during the SARS-CoV-2 pandemic: a multicenter evaluation
Creators: name: Bauer, Karri A.
name: Puzniak, Laura A.
name: Yu, Kalvin C.
name: Finelli, Lyn
name: Moise, Pamela
name: Ai, ChinEn
name: Watts, Janet A.
name: Gupta, Vikas
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Computational Biology

description: Additional file 2: Table S2. Laboratory criteria used as surrogates for admission-period clinical conditions.
Additional file 1 of Evaluating the implementation of the Pediatric Acute Care Education (PACE) program in northwestern Tanzania: a mixed-methods study guided by normalization process theory
Creators: name: Mwanga, Joseph R.
name: Hokororo, Adolfine
name: Ndosi, Hanston
name: Masenge, Theopista
name: Kalabamu, Florence S.
name: Tawfik, Daniel
name: Mediratta, Rishi P.
name: Rozenfeld, Boris
name: Berg, Marc
name: Smith, Zachary H.
name: Chami, Neema
name: Mkopi, Namala P.
name: Mwanga, Castory
name: Diocles, Enock
name: Agweyu, Ambrose
name: Meaney, Peter A.
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Material 1.
A Preliminary Investigation of MLOps Practices in GitHub
Creators: name: Calefato, Fabio
name: Lanubile, Filippo
name: Quaranta, Luigi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Software Engineering (cs.SE)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Background. The rapid and growing popularity of machine learning (ML) applications has led to an increasing interest in MLOps, that is, the practice of continuous integration and deployment (CI/CD) of ML-enabled systems. Aims. Since changes may affect not only the code but also the ML model parameters and the data themselves, the automation of traditional CI/CD needs to be extended to manage model retraining in production. Method. In this paper, we present an initial investigation of the MLOps practices implemented in a set of ML-enabled systems retrieved from GitHub, focusing on GitHub Actions and CML, two solutions to automate the development workflow. Results. Our preliminary results suggest that the adoption of MLOps workflows in open-source GitHub projects is currently rather limited. Conclusions. Issues are also identified, which can guide future research work.
description: Presented at ESEM '22, the 16th ACM / IEEE International Symposium on Empirical Software Engineering and Measurement
Dissecting the Roles of the 5′ Exoribonucleases Xrn1 and Xrn2 in Restricting Hepatitis C Virus Replication
Creators: name: Li, You
name: Yamane, Daisuke
name: Lemon, Stanley M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT The replication of hepatitis C virus (HCV) is uniquely dependent on a host microRNA, miR-122. Previous studies using genotype 1a H77S.3 virus demonstrated that miR-122 acts in part by protecting the RNA genome from 5′ decay mediated by the cytoplasmic 5′ exoribonuclease, Xrn1. However, this finding has been challenged by a recent report suggesting that a predominantly nuclear exoribonuclease, Xrn2, mediates the degradation of genotype 2a JFH1 RNA. Here, we dissect the roles of these two 5′ exoribonucleases in restricting the replication of different HCV strains and mediating the decay of HCV RNA. Small interfering RNA (siRNA) depletion experiments indicated that Xrn1 restricts replication of all HCV strains tested: JFH1, H77S.3, H77D (a robustly replicating genotype 1a variant), and HJ3-5 (a genotype 1a/2a chimeric virus). In contrast, the antiviral effects of Xrn2 were limited to JFH1 and H77D viruses. Moreover, such effects were not apparent in cells infected with a JFH1 luciferase reporter virus. Whereas Xrn1 depletion significantly slowed decay of JFH1 and HJ3-5 RNAs, Xrn2 depletion marginally enhanced the JFH1 RNA half-life and had no effect on HJ3-5 RNA decay. The positive effects of Xrn1 depletion on JFH1 replication were largely redundant and nonadditive with those of exogenous miR-122 supplementation, whereas Xrn2 depletion acted additively and thus independently of miR-122. We conclude that Xrn1 is the dominant 5′ exoribonuclease mediating decay of HCV RNA and that miR-122 provides protection against it. The restriction of JFH1 and H77D replication by Xrn2 is likely indirect in nature and possibly linked to cytopathic effects of these robustly replicating viruses. IMPORTANCE HCV is a common cause of liver disease both within and outside the United States. Its replication is dependent upon a small, liver-specific noncoding RNA, miR-122. Although this requirement has been exploited for the development of an anti-miR-122 antagomir as a host-targeting antiviral, the molecular mechanisms underpinning the host factor activity of miR-122 remain incompletely defined. Conflicting reports suggest miR-122 protects the viral RNA against decay mediated by distinct cellular 5′ exoribonucleases, Xrn1 and Xrn2. Here, we compare the roles of these two exoribonucleases in HCV-infected cells and confirm that Xrn1, not Xrn2, is primarily responsible for decay of RNA in cells infected with multiple virus strains. Our results clarify previously published research and add to the current understanding of the host factor requirement for miR-122.
MAKTABGACHA TAʻLIM SOHASI UCHUN PEDAGOG KADRLARNI YANGI YONDASHUVLAR ASOSIDA TAYYORLASH
Creators: name: Valiyeva, Feruza
Publisher: name: Zenodo
Year: 2023

description: Bugungi kunda maktabgacha taʼlim yangi taʼlim paradigmasiga mos kelish uchun, taʼlim oluvchilarni maqsadli ravishda ijodiy shaxs sifatida shakllantirishni oʻrganish juda muhim hisoblanadi. Taʼlim-tarbiya jarayonida taʼlim oluvchini nafaqat ijtimoiy-kasbiy bilimlar bilan taʼminlash, balki unda tanlagan kasbiga xos sifatlar shakllanishiga ham yordam berish lozim. Ushbu maqolada maktabgacha taʼlim sohasi uchun pedagog kadrlarni tayyorlash tamoyillari, muammolari, jahon miqyosidagi xorijiy tajribalar keltirilgan.
Data Sharing in the Physical Internet: A Capability-Based Approach for Trustless Logistic Networks
Creators: name: Cassan, Catherine
name: Michiels, Philippe
name: Sun, Shiqi
name: Lemos, Vitor
name: Van Bever, Dries
name: Cant, An
name: Fink, Joris
name: Macharis, Cathy
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Physical internet
Trust
Collaboration
Decentralized data sharing
Sustainable logistics
Capacity
Capability

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Physical Internet promises a more sustainable logistics network through hyperconnectivity between companies and high automatization. However, many logistic companies are reluctant to enter such a network, as they fear sharing sensitive commercial data with competitors and/or a central orchestrator. Therefore, we introduce a fixed set of ‘capabilities’ (services a specific company offers) which allow for the flexibility and exactness to define logistic companies. Based on these capabilities, we propose a decentralized scheme wherein 1) logistic companies only need to share these ‘capabilities’ openly with the network and 2) the logistic network is modelled based on these capabilities and routing algorithms can be applied. We tested this concept both by applying it in an ABM model based on real data and by in-depth interviews with potential participants for a real-life test. The approach shows promising preliminary results on both tests, although more research is needed to confirm these findings.
Enhanced Transgene Expression from Recombinant Single-Stranded D-Sequence-Substituted Adeno-Associated Virus Vectors in Human Cell Lines In Vitro and in Murine Hepatocytes In Vivo
Creators: name: Ling, Chen
name: Lentz, Thomas
name: Ma, Wenqin
name: Xiao, Xiao
name: Wang, Yuan
name: Aslanidi, George V.
name: Srivastava, Arun
name: Lu, Yuan
name: Samulski, R. Jude
name: Li, Baozheng
name: Ling, Changquan
name: Muzyczka, Nicholas
name: Wang, Lina
name: Jayandharan, Giridhara R.
name: Cheng, Binbin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT We have previously reported that the removal of a 20-nucleotide sequence, termed the D sequence, from both ends of the inverted terminal repeats (ITRs) in the adeno-associated virus serotype 2 (AAV2) genome significantly impairs rescue, replication, and encapsidation of the viral genomes (X. S. Wang, S. Ponnazhagan, and A. Srivastava, J Mol Biol 250:573–580, 1995; X. S. Wang, S. Ponnazhagan, and A. Srivastava, J Virol 70:1668–1677, 1996). Here we describe that replacement of only one D sequence in either ITR restores each of these functions, but DNA strands of only single polarity are encapsidated in mature progeny virions. Since most commonly used recombinant AAV vectors contain a single-stranded DNA (ssDNA), which is transcriptionally inactive, efficient transgene expression from AAV vectors is dependent upon viral second-strand DNA synthesis. We have also identified a transcription suppressor sequence in one of the D sequences, which shares homology with the binding site for the cellular NF-κB-repressing factor (NRF). The removal of this D sequence from, and replacement with a sequence containing putative binding sites for transcription factors in, single-stranded AAV (ssAAV) vectors significantly augments transgene expression both in human cell lines in vitro and in murine hepatocytes in vivo . The development of these genome-modified ssAAV vectors has implications not only for the basic biology of AAV but also for the optimal use of these vectors in human gene therapy. IMPORTANCE The results of the studies described here not only have provided novel insights into some of the critical steps in the life cycle of a human virus, the adeno-associated virus (AAV), that causes no known disease but have also led to the development of novel recombinant AAV vectors which are more efficient in allowing increased levels of gene expression. Thus, these studies have significant implications for the potential use of these novel AAV vectors in human gene therapy.
Continuum modeling of mechanically-induced creep in dense granular materials
Creators: name: Henann, David
name: Kamrin, Ken
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Recently, a new nonlocal granular rheology was successfully used to predict steady granular flows, including grain-size-dependent shear features, in a wide variety of flow configurations, including all variations of the split-bottom cell. A related problem in granular flow is that of mechanically-induced creep, in which shear deformation in one region of a granular medium fluidizes its entirety, including regions far from the sheared zone, effectively erasing the yield condition everywhere. This enables creep deformation when a force is applied in the nominally quiescent region through an intruder such as a cylindrical or spherical probe. We show that the nonlocal fluidity model is capable of capturing this phenomenology. Specifically, we explore creep of a circular intruder in a two-dimensional annular Couette cell and show that the model captures all salient features observed in experiments, including both the rate-independent nature of creep for sufficiently slow driving rates and the faster-than-linear increase in the creep speed with the force applied to the intruder.
Accreting neutron stars from the nuclear energy-density functional theory. II. Equation of state and global properties
Creators: name: Fantina, A. F.
name: Zdunik, J. L.
name: Chamel, N.
name: Pearson, J. M.
name: Suleiman, L.
name: Goriely, S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The accretion of matter onto the surface of a neutron star in a low-mass X-ray binary triggers X-ray bursts, whose ashes are buried and further processed thus altering the composition and the properties of the stellar crust. In this second paper of a series, the impact of accretion on the equation of state and on the global properties of neutron stars is studied in the framework of the nuclear energy-density functional theory. Considering ashes made of $^{56}$Fe, we calculated the equations of state using the same Brussels-Montreal nuclear energy-density functionals BSk19, BSk20, and BSk21, as those already employed for determining the crustal heating in our previous study for the same ashes. All regions of accreting neutron stars were treated in a unified and thermodynamically consistent way. With these equations of state, we determined the mass, radius, moment of inertia, and tidal deformability of accreted neutron stars and compared with catalyzed neutron stars for which unified equations of state based on the same functionals are available. The equation of state of accreted neutron stars is found to be significantly stiffer than that of catalyzed matter, with an adiabatic index $Γ\approx 4/3$ throughout the crust. For this reason, accreting neutron stars have larger radii. However, their crustal moment of inertia and their tidal deformability are hardly changed provided density discontinuities at the interface between adjacent crustal layers are properly taken into account. The enhancement of the stiffness of the equation of state of accreting neutron stars is mainly a consequence of nuclear shell effects, thus confirming the importance of a quantum treatment as stressed in our first study. With our previous calculations of crustal heating using the same functionals, we have thus obtained consistent microscopic inputs for simulations of accreting neutron stars.
description: 10 pages, 7 figures. The tables of the equations of state are available at the CDS
Assessing the Performance of Urban Freight Networks
Creators: name: Thompson, Russell G.
name: Galkin, Andrii
name: Zhang, Joyce
name: Hassall, Kim
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Network design
Collaborative freight networks
Network performance measures

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Due to increasing concerns regarding rising emissions, urban congestion and financial costs it is important to develop and identify appropriate performance measures that can be used to aid the design of improved urban distribution networks. The Physical Internet (PI) concept involves transforming independent logistics networks into open and shared networks for improving sustainability. This involves designing new networks that are based on utilising multiple transport modes and transfer points. There is a need to compare the performance of typical urban freight networks with collaborative networks that involve shared use of warehouses and freight vehicles. This Paper presents an assessment of several criteria that can be used to quantify the performance of freight and logistics networks in cities. Multi-criteria analysis is conducted for common urban goods networks including retail swaps and retail distribution. The analysis contained in this Paper can be used to assist network planners and designers to identify the most appropriate criteria to aid the design of future urban freight networks for achieving net zero emissions. Such measures can provide direction for fleet managers, urban freight planners as well as communities.
Epstein-Barr Virus Latent Membrane Protein 2 Induces Autophagy To Promote Abnormal Acinus Formation
Creators: name: Fotheringham, Julie A.
name: Raab-Traub, Nancy
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Epstein-Barr virus latent membrane protein 2A (LMP2A) induces many characteristics of carcinoma, including transformation, migration, invasion, and impaired differentiation. The MCF10A cell line differentiates to form hollow acini when grown in Matrigel, and expression of LMP2A inhibited differentiation and anoikis induced by loss of matrix attachment. LMP2A-infected cells formed large, lobular structures rather than hollow acini. Autophagy inhibitors impaired this abnormal growth and induced caspase 3 activation and acinus formation. LMP2A also increased autophagosome formation and expression of proteins in the autophagosome pathway. These findings suggest that LMP2A may inhibit anoikis and luminal clearance in acini through induction of autophagy.
Gamma-delta T cells play a protective role in chikungunya virus-induced disease.
Creators: name: Heise, Mark T.
name: Lim, Jean K.
name: Whitmore, Alan C.
name: McGee, Charles E.
name: Ferris, Martin T.
name: Long, Kristin M.
name: Thurlow, Lance R.
name: Montgomery, Stephanie A.
name: Rodriguez, Carlos A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Chikungunya virus (CHIKV) is an alphavirus responsible for causing epidemic outbreaks of polyarthralgia in humans. As CHIKV is initially introduced into the skin where γδ T cells are prevalent, we evaluated their response to CHIKV infection. CHIKV infection led to a significant increase in γδ T cells in the infected foot and draining lymph node associated with the production of pro-inflammatory cytokines and chemokines in C57BL/6J mice. γδ T cell-/- mice demonstrated exacerbated CHIKV disease characterized by less weight gain and greater foot swelling compared to wild-type mice as well as a transient increase in monocytes and altered cytokine/chemokine expression in the foot. Histologically, γδ T cell-/- mice had increased inflammation-mediated oxidative damage in the ipsilateral foot and ankle joint of versus wild-type mice which was independent of differences in CHIKV replication. These results suggest that γδ T cells play a protective role in limiting the CHIKV-induced inflammatory response and subsequent tissue and joint damage. Recent epidemics including the 2004-2007 outbreak and the spread of CHIKV to naïve populations in the Caribbean, Central and South America with resultant cases imported into the U.S highlighted the capacity of CHIKV to cause explosive epidemics where the virus can spread to millions of people and rapidly move into new areas. These studies identify γδ T cells as being important to both recruitment of key inflammatory cell populations and dampening the tissue injury due to oxidative stress. Given the importance of these cells in the early response to CHIKV, this information may inform the development of CHIKV vaccines and therapeutics.
H3K27 Demethylation at the Proviral Promoter Sensitizes Latent HIV to the Effects of Vorinostat in Ex Vivo Cultures of Resting CD4 + T Cells
Creators: name: Margolis, David M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Histone methyltransferase inhibitors (HMTis) and histone deacetylase inhibitors (HDACis) are reported to synergistically induce the expression of latent human immunodeficiency virus type 1 (HIV-1), but studies have largely been performed with cell lines. As specific and potent HMTis directed at EZH1 (enhancer of zeste 2 Polycomb repressive complex 2 subunit 1)/EZH2 are now in human testing, we wished to rigorously test such an inhibitor in a primary resting T-cell model of HIV latency. We found that GSK343, a potent and selective EZH2/EZH1 inhibitor, reduced trimethylation of histone 3 at lysine 27 (H3K27) of the HIV provirus in resting cells. Remarkably, this epigenetic change was not associated with increased proviral expression in latently infected resting cells. However, following the reduction in H3K27 at the HIV long terminal repeat (LTR), subsequent exposure to the HDACi suberoylanilide hydroxamic acid or vorinostat (VOR) resulted in increases in HIV gag RNA and HIV p24 antigen production that were up to 2.5-fold greater than those induced by VOR alone. Therefore, in primary resting CD4 + T cells, true mechanistic synergy in the reversal of HIV latency may be achieved by the combination of HMTis and HDACis. Although other cellular effects of EZH2 inhibition may contribute to the sensitization of the HIV LTR to subsequent exposure to VOR, and to increase viral antigen production, this synergistic effect is directly associated with H3K27 demethylation at nucleosome 1 (Nuc-1). Based upon our findings, the combination of HMTis and HDACis should be considered for testing in animal models or clinical trials. IMPORTANCE Demethylation of H3K27 mediated by the histone methyltransferase inhibitor GSK343 in primary resting T cells is slow, occurring over 96 h, but by itself does not result in a significant upregulation of cell-associated HIV RNA expression or viral antigen production. However, following H3K27 demethylation, latent viral expression within infected primary resting CD4 + T cells is synergistically increased upon exposure to the histone deacetylase inhibitor vorinostat. Demethylation at H3K27 sensitizes the HIV promoter to the effects of an HDACi and provides a proof-of-concept for the testing of combination epigenetic approaches to disrupt latent HIV infection, a necessary step toward the eradication of HIV infection.
TeST: Test-time Self-Training under Distribution Shift
Creators: name: Sinha, Samarth
name: Gehler, Peter
name: Locatello, Francesco
name: Schiele, Bernt
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time Self-Training (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline test-time adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms, while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks: object detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new state-of-the art for test-time domain adaptation algorithms.
HIV-1 Env and Nef Cooperatively Contribute to Plasmacytoid Dendritic Cell Activation via CD4-Dependent Mechanisms
Creators: name: Sivaraman, Vijay
name: Su, Lishan
name: Zhang, Liguo
name: Reszka-Blanco, Natalia J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Plasmacytoid dendritic cells (pDCs) are the major source of type I IFN (IFN-I) in response to human immunodeficiency virus type 1 (HIV-1) infection. pDCs are rapidly activated during HIV-1 infection and are implicated in reducing the early viral load, as well as contributing to HIV-1-induced pathogenesis. However, most cell-free HIV-1 isolates are inefficient in activating human pDCs, and the mechanisms of HIV-1 recognition by pDCs and pDC activation are not clearly defined. In this study, we report that two genetically similar HIV-1 variants (R3A and R3B) isolated from a rapid progressor differentially activated pDCs to produce alpha interferon (IFN-α). The highly pathogenic R3A efficiently activated pDCs to induce robust IFN-α production, while the less pathogenic R3B did not. The viral determinant for efficient pDC activation was mapped to the V1V2 region of R3A Env, which also correlated with enhanced CD4 binding activity. Furthermore, we showed that the Nef protein was also required for the activation of pDCs by R3A. Analysis of a panel of R3A Nef functional mutants demonstrated that Nef domains involved in CD4 downregulation were necessary for R3A to activate pDCs. Our data indicate that R3A-induced pDC activation depends on (i) the high affinity of R3A Env for binding the CD4 receptor and (ii) Nef activity, which is involved in CD4 downregulation. Our findings provide new insights into the mechanism by which HIV-1 induces IFN-α in pDCs, which contributes to pathogenesis. IMPORTANCE Plasmacytoid dendritic cells (pDCs) are the major type I interferon (IFN-I)-producing cells, and IFN-I actually contributes to pathogenesis during chronic viral infections. How HIV-1 activates pDCs and the roles of pDCs/IFN-I in HIV-1 pathogenesis remain unclear. We report here that the highly pathogenic HIV R3A efficiently activated pDCs to induce IFN-α production, while most HIV-1 isolates are inefficient in activating pDCs. We have discovered that R3A-induced pDC activation depends on (i) the high affinity of R3A Env for binding the CD4 receptor and (ii) Nef activity, which is involved in CD4 downregulation. Our findings thus provide new insights into the mechanism by which HIV-1 induces IFN-α in pDCs and contributes to HIV-1 pathogenesis. These novel findings will be of great interest to those working on the roles of IFN and pDCs in HIV-1 pathogenesis in general and on the interaction of HIV-1 with pDCs in particular.
Transgender Inclusion and Feminism: Organizations and Innovation
Creators: name: Stepleton, Katherine S.
Publisher: name: Unknown
Year: 2006

description: As transgender issues become increasingly prominent, feminist organizations, many of which have restricted membership to women, are forced to consider how feminism is affected by changing gender identities. This article examines the how four feminist organizations in New York City considered the inclusion of transgender individuals. The groups examined here exhibited traits, such as decentralized, informal structures, that made them likely sites of social innovation. Additionally, by communicating with one another, the organizations influenced one another in discussions about transgender inclusion.