cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Protease Inhibitors Block Multiple Functions of the NS3/4A Protease-Helicase during the Hepatitis C Virus Life Cycle
Creators: name: Hamlett, Chris
name: McGivern, David R.
name: Masaki, Takahiro
name: Graham, Brent
name: Lovell, William
name: Saalau-Bethell, Susanne
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Hepatitis C virus (HCV) NS3 is a multifunctional protein composed of a protease domain and a helicase domain linked by a flexible linker. Protease activity is required to generate viral nonstructural (NS) proteins involved in RNA replication. Helicase activity is required for RNA replication, and genetic evidence implicates the helicase domain in virus assembly. Binding of protease inhibitors (PIs) to the protease active site blocks NS3-dependent polyprotein processing but might impact other steps of the virus life cycle. Kinetic analyses of antiviral suppression of cell culture-infectious genotype 1a strain H77S.3 were performed using assays that measure different readouts of the viral life cycle. In addition to the active-site PI telaprevir, we examined an allosteric protease-helicase inhibitor (APHI) that binds a site in the interdomain interface. By measuring nucleotide incorporation into HCV genomes, we found that telaprevir inhibits RNA synthesis as early as 12 h at high but clinically relevant concentrations. Immunoblot analyses showed that NS5B abundance was not reduced until after 12 h, suggesting that telaprevir exerts a direct effect on RNA synthesis. In contrast, the APHI could partially inhibit RNA synthesis, suggesting that the allosteric site is not always available during RNA synthesis. The APHI and active-site PI were both able to block virus assembly soon (<12 h) after drug treatment, suggesting that they rapidly engage with and block a pool of NS3 involved in assembly. In conclusion, PIs and APHIs can block NS3 functions in RNA synthesis and virus assembly, in addition to inhibiting polyprotein processing. IMPORTANCE The NS3/4A protease of hepatitis C virus (HCV) is an important antiviral target. Currently, three PIs have been approved for therapy of chronic hepatitis C, and several others are in development. NS3-dependent cleavage of the HCV polyprotein is required to generate the mature nonstructural proteins that form the viral replicase. Inhibition of protease activity can block RNA replication by preventing expression of mature replicase components. Like many viral proteins, NS3 is multifunctional, but how PIs affect stages of the HCV life cycle beyond polyprotein processing has not been well studied. Using cell-based assays, we show here that PIs can directly inhibit viral RNA synthesis and also block a late stage in virus assembly/maturation at clinically relevant concentrations.
Grouped Adaptive Loss Weighting for Person Search
Creators: name: Tian, Yanling
name: Chen, Di
name: Liu, Yunan
name: Zhang, Shanshan
name: Yang, Jian
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Person search is an integrated task of multiple sub-tasks such as foreground/background classification, bounding box regression and person re-identification. Therefore, person search is a typical multi-task learning problem, especially when solved in an end-to-end manner. Recently, some works enhance person search features by exploiting various auxiliary information, e.g. person joint keypoints, body part position, attributes, etc., which brings in more tasks and further complexifies a person search model. The inconsistent convergence rate of each task could potentially harm the model optimization. A straightforward solution is to manually assign different weights to different tasks, compensating for the diverse convergence rates. However, given the special case of person search, i.e. with a large number of tasks, it is impractical to weight the tasks manually. To this end, we propose a Grouped Adaptive Loss Weighting (GALW) method which adjusts the weight of each task automatically and dynamically. Specifically, we group tasks according to their convergence rates. Tasks within the same group share the same learnable weight, which is dynamically assigned by considering the loss uncertainty. Experimental results on two typical benchmarks, CUHK-SYSU and PRW, demonstrate the effectiveness of our method.
description: Accepted by ACM MM
Additional file 2 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 2.
From Starburst to Quiescence: Testing AGN feedback in Rapidly Quenching Post-Starburst Galaxies
Creators: name: Yesuf, Hassen M.
name: Faber, S. M.
name: Trump, Jonathan R.
name: Koo, David C.
name: Fang, Jerome J.
name: Liu, F. S.
name: Wild, Vivienne
name: Hayward, Christopher C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Post-starbursts are galaxies in transition from the blue cloud to the red sequence. Although they are rare today, integrated over time they may be an important pathway to the red sequence. This work uses SDSS, GALEX, and WISE observations to identify the evolutionary sequence from starbursts to fully quenched post-starbursts in the narrow mass range $\log M(M_\odot) = 10.3-10.7$, and identifies "transiting" post-starbursts which are intermediate between these two populations. In this mass range, $\sim 0.3\%$ of galaxies are starbursts, $\sim 0.1\%$ are quenched post-starbursts, and $\sim 0.5\%$ are the transiting types in between. The transiting post-starbursts have stellar properties that are predicted for fast-quenching starbursts and morphological characteristics that are already typical of early-type galaxies. The AGN fraction, as estimated from optical line ratios, of these post-starbursts is about 3 times higher ($\gtrsim 36 \pm 8 \%$) than that of normal star-forming galaxies of the same mass, but there is a significant delay between the starburst phase and the peak of nuclear optical AGN activity (median age difference of $\gtrsim 200 \pm 100$ Myr), in agreement with previous studies. The time delay is inferred by comparing the broad-band near NUV-to-optical photometry with stellar population synthesis models. We also find that starbursts and post-starbursts are significantly more dust-obscured than normal star-forming galaxies in the same mass range. About $20\%$ of the starbursts and $15\%$ of the transiting post-starbursts can be classified as the "Dust-Obscured Galaxies" (DOGs), while only $0.8\%$ of normal galaxies are DOGs.The time delay between the starburst phase and AGN activity suggests that AGN do not play a primary role in the original quenching of starbursts but may be responsible for quenching later low-level star formation during the post-starburst phase.
description: 30 pages, 18 figures,accepted to ApJ
Resilience Assessment of Hyperconnected Parcel Logistic Networks Under Worst-Case Disruptions
Creators: name: Kulkarni, Onkar
name: Dahan, Mathieu
name: Montreuil, Benoit
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Hyperconnected networks
Resilience
Worst-case disruptions
Stackelberg game
Physical internet

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Logistics networks that shape the Physical Internet’s logistics web are prone to potentially adversarial disruptions that impact their performance severely. In this article, we study a network interdiction problem on a multi-commodity flow network in which an adversary totally disrupts a set of network arcs with an intention to maximize the operational costs of delivering parcels. We formulate it as a two-stage mixed-integer linear program. To solve such complex large-scale program, we use linear programming duality and provide an algorithm based on the structure of the program that computes the set of network arcs that can be interdicted in order to reduce its size. Finally, we use the model and solution framework to evaluate the resilience capabilities of topology optimized hyperconnected networks and compare it with lean networks. We find that our developed solution methodology reduces the size of network interdiction program substantially and showcases superior computational performance against off-the-shelf optimization solvers. Furthermore, the resilience comparison between hyperconnected networks and lean networks depicts enhanced capabilities of the topology optimized hyperconnected networks to sustain worst-case disruptive events as opposed to that of lean logistics networks.
Additional file 1 of Cascade testing in mitochondrial diseases: a cross-sectional retrospective study
Creators: name: Haque, Sameen
name: Crawley, Karen
name: Schofield, Deborah
name: Shrestha, Rupendra
name: Sue, Carolyn M.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1
R5 Macrophage-Tropic HIV-1 in the Male Genital Tract
Creators: name: Eron, Joseph J.
name: Bednar, Maria M.
name: Dukhovlinova, Elena
name: Cohen, Myron S.
name: Zhou, Shuntai
name: Hoffman, Irving F.
name: Arrildt, Kathryn T.
name: Hauser, Blake M.
name: Swanstrom, Ronald
name: Ping, Li-Hua
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The entry tropism of HIV-1 Env proteins from virus isolated from the blood and genital tract of five men with compartmentalized lineages was determined. The Env proteins isolated from the genital tract of subject C018 were macrophage-tropic proteins, while the remaining cloned env genes encoded R5 T cell-tropic proteins. The detection of a macrophage-tropic lineage of HIV-1 within the male genital tract strongly suggests that evolution of macrophage-tropic viruses can occur in anatomically isolated sites outside the central nervous system.
Modular Containerization of Parcel Logistics Networks: Simulation-Based Impact Assessment
Creators: name: Shaikh, Sahrish Jaleel
name: Kim, Nayeon
name: Rababah, Mumen
name: Montreuil, Benoit
name: Smith, Jeffrey S.
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Hyperconnected logistics infrastructure
Containerization
Modularization
Mesh networks
Physical internet
Routing protocols
Network architecture
Multi-tier networks
Hyperconnected service network

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: The parcel industry has undergone significant changes in recent years, primarily driven by the surge of e-commerce and new technologies. The Physical Internet (PI) provides initiatives to optimize parcel flow and jointly address economic, operational, social, and environmental sustainability issues in the industry. Encapsulating parcels in modular PI containers is a promising method to enhance efficiency by consolidating parcel flows which can increase vehicle capacity utilization, leading to significant cost and transit time reductions. In this Paper, we investigate the potential benefits of containerization in the parcel industry using simulation-based scenario designs and assessments. The results are evaluated across several performance facets, such as transport efficiency, handling operations, induced costs, and greenhouse gas emissions. The simulation results focusing on the East Coast region of the USA demonstrated that containerization and tiered mesh networks lead to cost savings and efficient space utilization, with multiple container sizes and a mesh network approach being more effective. This approach also reduces driving time per leg, improving efficiency and driver well-being. In conclusion, the study offers conclusive remarks and suggests further research avenues in this domain.
Synchromodal transport re-planning using Agent-Based Modeling
Creators: name: Alaei, Shafagh
name: Durán-Micco, Javier
name: Macharis, Cathy
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Synchromodal transport
Agent-based modelling
Multimodal transport
Simulation

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Synchromodal Transport (ST) is an evolution of multimodal transport, where involves the flexible planning of transport processes and the ability to switch in real-time between modes of transport based on the the available resources, imposing complexity to the planning process. It offers integrated, optimal, and sustainable logistics solution.
title: Challenges to develop risk assessment schemes for Brazilian bees: multiple exposure routes
Creators: name: Nocelli, Roberta C. F.
name: De Oliveira Cham, Karina
name: Malaspina, Osmar
Publisher: name: Julius Kühn-Institut
Year: 2018

description: Julius-Kühn-Archiv, 462 (Hazards of pesticides to bees : 13th International Symposium of the ICP-PR Bee Protection Group ; 18. - 20. October 2017, València (Spain) - Proceedings -)
Additional file 1 of Changes in the intrinsic severity of severe acute respiratory syndrome coronavirus 2 according to the emerging variant: a nationwide study from February 2020 to June 2022, including comparison with vaccinated populations
Creators: name: Ryu, Boyeong
name: Shin, Eunjeong
name: Kim, Dong Hwi
name: Lee, HyunJu
name: Choi, So Young
name: Kim, Seong-Sun
name: Kim, Il-Hwan
name: Kim, Eun-Jin
name: Lee, Sangwon
name: Jeon, Jaehyun
name: Kwon, Donghyok
name: Cho, Sungil
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. The number of confirmed cases, including severe/critical cases and deaths.
Do bright SMGs do trace galaxy protoclusters?
Creators: name: Calvi, Rosa
name: Castignani, Gianluca
name: Dannerbauer, Helmut
Publisher: name: Zenodo
Year: 2023

description: There is controversy in the literature regarding whether distant, massive, and dusty starbursts selected at (sub)millimeter wavelengths can trace galaxy overdensities. We thus performed the first systematic search for distant protoclusters around a homogeneously selected sample of 12 spectroscopically confirmed submillimeter galaxies (SMGs) at z ∼ 1.2 − 5.3, which we selected from the GOODS-N field. We applied the well-established Poisson probability method (PPM) to search for megaparsec-scale overdensities around these SMGs, using three different photometric redshift catalogs. We robustly detect galaxy overdensities for 11 out of the 12 SMGs (i.e., 92% ± 8%), distributed over eight large-scale protoclusters. We confirm all three previously discovered protoclusters, and we detect five new ones around the SMGs SMM J123634 (z = 1.225), ID.19 (z = 2.047), SMM J123607 (z = 2.487), SMM J123606 (z = 2.505), and GN10 (z = 5.303). A wavelet-based analysis of the protocluster fields shows that the SMGs are located in protocluster cores with a complex morphology (compact, filamentary, or clumpy) and an average size of ∼ (0.4 − 1) Mpc. By comparing the PPM results obtained using the three redshift catalogs independently, each of which trace different galaxy populations and redshift ranges, we speculate that we are possibly witnessing a transitioning phase at z ≳ 4 for the galaxy population of protoclusters. While z ≲ 4 protoclusters appear to be populated by dusty galaxies, those at the highest redshifts, z ∼ 5, are detected as overdensities of Lyman α emitters or Lyman break galaxies. Further investigation with larger samples is required to reach a definitive conclusion. We also find a good correlation between the molecular (H2) gas mass of the SMGs and the significance of the associated overdensity. To explain the overall phenomenology, we suggest that galaxy interactions in dense environments likely triggered the starburst and gas-rich phase of the SMGs. Altogether, our findings support the scenario that SMGs are excellent tracers of distant protoclusters. The ones presented in this work are excellent targets for the James Webb Space Telescope. Similarly, future surveys with forthcoming facilities (e.g., Euclid and LSST) can be tuned to detect even larger samples of distant protoclusters
Pancake bouncing on superhydrophobic surfaces
Creators: name: Liu, Yahua
name: Moevius, Lisa
name: Xu, Xinpeng
name: Qian, Tiezheng
name: Yeomans, Julia M
name: Wang, Zuankai
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Engineering surfaces that promote rapid drop detachment is of importance to a wide range of applications including anti-icing, dropwise condensation6, and self-cleaning. Here we show how superhydrophobic surfaces patterned with lattices of submillimetre-scale posts decorated with nano-textures can generate a counter-intuitive bouncing regime: drops spread on impact and then leave the surface in a flattened, pancake shape without retracting. This allows for a four-fold reduction in contact time compared to conventional complete rebound. We demonstrate that the pancake bouncing results from the rectification of capillary energy stored in the penetrated liquid into upward motion adequate to lift the drop. Moreover, the timescales for lateral drop spreading over the surface and for vertical motion must be comparable. In particular, by designing surfaces with tapered micro/nanotextures which behave as harmonic springs, the timescales become independent of the impact velocity, allowing the occurrence of pancake bouncing and rapid drop detachment over a wide range of impact velocities.
description: 11 pages, 4 figures, 31 references, + 5 pages of supplementary information
Upgrading the Export Logistics Network with Cyber-Physical Internet
Creators: name: Zhang, Hongtao
name: Pan, Shenle
name: Li, Ming
name: Zhong, Ray Y.
name: Huang, George Q.
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Export logistics
Cyber-Physical internet
Logistics network
Digital internet; Multi-layer system

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: Given the complexity of the environment around export logistics, we look to apply physical internet to this case in order to increase effectiveness and save costs. In order to realize the interaction between diverse digital information at the cyber level and various physical entities in the logistics network, this article proposes the concept of the Cyber-Physical Internet(CPI), which focuses on installing routers in nodes for forwarding and routing. This research will examine how CPI establishes a multi-layer system to achieve vertical and horizontal interconnection of logistics network, using the digital Internet as an analogy, and attempt to determine the functional reality of each layer and the dependency between layers. Similar data packets and cargo units will be packaged or dismantled during this procedure, which will also be described in detail in Paper.
The complexity of unsupervised learning of lexicographic preferences
Creators: name: Fargier, Hélène
name: Gimenez, Pierre-François
name: Mengin, Jérôme
name: Nguyen, Bao Ngoc Le
Publisher: name: arXiv
Year: 2022
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Computational Complexity (cs.CC)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: This paper considers the task of learning users' preferences on a combinatorial set of alternatives, as generally used by online configurators, for example. In many settings, only a set of selected alternatives during past interactions is available to the learner. Fargier et al. [2018] propose an approach to learn, in such a setting, a model of the users' preferences that ranks previously chosen alternatives as high as possible; and an algorithm to learn, in this setting, a particular model of preferences: lexicographic preferences trees (LP-trees). In this paper, we study complexity-theoretical problems related to this approach. We give an upper bound on the sample complexity of learning an LP-tree, which is logarithmic in the number of attributes. We also prove that computing the LP tree that minimises the empirical risk can be done in polynomial time when restricted to the class of linear LP-trees.
Completion of continuity spaces with uniformly vanishing asymmetry
Creators: name: Chand, Alveen
name: Weiss, Ittay
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Topology (math.GN)
subject: FOS: Mathematics
subject: 54E35

description: The classical Cauchy completion of a metric space (by means of Cauchy sequences) as well as the completion of a uniform space (by means of Cauchy filters) are well-known to rely on the symmetry of the metric space or uniform space in question. For qausi-metric spaces and quasi-uniform spaces various non-equivalent completions exist, often defined on a certain subcategory of spaces that satisfy a key property required for the particular completion to exist. The classical filter completion of a uniform space can be adapted to yield a filter completion of a metric space. We show that this completion by filters generalizes to continuity spaces that satisfy a form of symmetry which we call uniformly vanishing asymmetry.
Unique Glycan Signatures Regulate Adeno-Associated Virus Tropism in the Developing Brain
Creators: name: Murlidharan, Giridhar
name: Ghashghaei, H. Troy
name: Corriher, Travis
name: Asokan, Aravind
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Adeno-associated viruses (AAV) are thought to spread through the central nervous system (CNS) by exploiting cerebrospinal fluid (CSF) flux and hijacking axonal transport pathways. The role of host receptors that mediate these processes is not well understood. In the current study, we utilized AAV serotype 4 (AAV4) as a model to evaluate whether ubiquitously expressed 2,3-linked sialic acid and the developmentally regulated marker 2,8-linked polysialic acid (PSA) regulate viral transport and tropism in the neonatal brain. Modulation of the levels of SA and PSA in cell culture studies using specific neuraminidases revealed possibly opposing roles of the two glycans in AAV4 transduction. Interestingly, upon intracranial injection into lateral ventricles of the neonatal mouse brain, a low-affinity AAV4 mutant (AAV4.18) displayed a striking shift in cellular tropism from 2,3-linked SA + ependymal lining to 2,8-linked PSA + migrating progenitors in the rostral migratory stream and olfactory bulb. In addition, this gain-of-function phenotype correlated with robust CNS spread of AAV4.18 through paravascular transport pathways. Consistent with these observations, altering glycan dynamics within the brain by coadministering SA- and PSA-specific neuraminidases resulted in striking changes to the cellular tropisms and transduction efficiencies of both parental and mutant vectors. We postulate that glycan signatures associated with host development can be exploited to redirect novel AAV vectors to specific cell types in the brain. IMPORTANCE Viruses invade the CNS through various mechanisms. In the current study, we utilized AAV as a model to study the dynamics of virus-carbohydrate interactions in the developing brain and their impact on viral tropism. Our findings suggest that carbohydrate content can be exploited to regulate viral transport and tropism in the brain.
La Convenzione di Faro e la tradizione culturale italiana
Creators: name: Montella, Massimo
name: Petraroia, Pietro
name: Manacorda, Daniele
name: Di Macco, Michela
Publisher: name: M. Montella, P. Petraroia, D. Manacorda, e M. Di Macco. La Convenzione di Faro e la tradizione culturale italiana, «Il Capitale culturale», Supplementi 05, 2016, pp. 13-36
Year: 2016

description: Contributo in: La valorizzazione dell’eredità culturale in Italia Atti del convegno di studi in occasione del 5º anno della rivista (Macerata, 5-6 novembre 2015) a cura di Pierluigi Feliciati
Additional file 1 of Impact of prerelease methadone on mortality among people with HIV and opioid use disorder after prison release: results from a randomized and participant choice open-label trial in Malaysia
Creators: name: Bazazi, Alexander R.
name: Culbert, Gabriel J.
name: Wegman, Martin P.
name: Heimer, Robert
name: Kamarulzaman, Adeeba
name: Altice, Frederick L.
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Neuroscience
Cancer
Science Policy
Computational Biology

description: Additional file 1. Appendix. Detailed description of covariates, supplementary analyses not shown in main text, and raw data on cause of death classification.
Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding
Creators: name: Li, Siyu
name: Zandi, Roya
Publisher: name: arXiv
Year: 2022
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins: Envelope (E), Membrane (M), Nucleocapsid (N), and Spike (S), which self-assemble along with its RNA into the infectious virus by budding from intracellular lipid membranes. In this paper, we develop a model to explore the mechanisms of RNA condensation by structural proteins, protein oligomerization and cellular membrane-protein interactions that control the budding process and the ultimate virus structure. Using molecular dynamics simulations, we have deciphered how the positively charged N proteins interact and condense the very long genomic RNA resulting in its packaging by a lipid envelope decorated with structural proteins inside a host cell. Furthermore, considering the length of RNA and the size of the virus, we find that the intrinsic curvature of M proteins is essential for virus budding. While most current research has focused on the S protein, which is responsible for viral entry, and it has been motivated by the need to develop efficacious vaccines, the development of resistance through mutations in this crucial protein makes it essential to elucidate the details of the viral life cycle to identify other drug targets for future therapy. Our simulations will provide insight into the viral life cycle through the assembly of viral particles de novo and potentially identify therapeutic targets for future drug development.
What Is the Reservoir of Emergent Human Norovirus Strains?
Creators: name: Baric, Ralph S.
name: Karst, Stephanie M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Since 1996, there have been at least six human norovirus pandemics. All of the pandemic strains are genetically related, segregating in the genogroup II, genotype 4 (GII.4) cluster within the Norovirus genus. Evidence indicates that these strains are closely related but antigenically distinct, supporting immune-driven viral evolution. Thus, norovirus vaccines will likely require periodic reformulation to protect from newly emergent strains. A major obstacle is that the reservoir of emergent strains is unknown. Noroviruses display tight species specificity and there is no evidence supporting zoonotic transmission, so an animal reservoir is considered unlikely. Moreover, available data indicate minimal viral diversity in most natural human infections. In this Gem, we discuss the widely speculated idea that chronically infected immunocompromised individuals are norovirus reservoirs and provide a rationale for the theory that elderly and malnourished hosts may also represent norovirus reservoirs.
Automating Capacity Pre-Booking at Warehouse Nodes of the Physical Internet
Creators: name: Zavitsas, Kostas
name: Kouloumpis, Makis
name: Sen, Juan Manuel
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Predictive modelling
Inventory replenishment theory
Warehouse PI node

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: The Physical Internet envisages the automation of the capacity booking process through the introduction of smart contracts. This requires the use of predictive models to determine what is a reasonable quantity to book, which are not well integrated into the decision making process. Currently, most warehouse operators book capacity only one day ahead when more concrete bookings’ data are available. The Paper proposes the integration of a pre-booking decision support tool to enhance the implementation of the predictive model outputs into smart contracts. Each delivery route is assumed to have a pricing structure that spans from ten days ahead to the day of delivery and contains early booking and cancellation fees. The aim of the tool is, considering the prediction quantity and pricing structure to determine an optimal strategy for issuing smart contract orders.
Activation of Apoptosis by Cytoplasmic Microinjection of Cytochrome c
Creators: name: Deshmukh, Mohanish
name: Kole, Adam J.
name: Knight, Elizabeth R.W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Apoptosis, or programmed cell death, is a conserved and highly regulated pathway by which cells die1. Apoptosis can be triggered when cells encounter a wide range of cytotoxic stresses. These insults initiate signaling cascades that ultimately cause the release of cytochrome c from the mitochondrial intermembrane space to the cytoplasm2. The release of cytochrome c from mitochondria is a key event that triggers the rapid activation of caspases, the key cellular proteases which ultimately execute cell death3-4.
Formulation of Diblock Polymeric Nanoparticles through Nanoprecipitation Technique
Creators: name: Wang, Edina C.
name: Cummings, Natalie D.
name: Karve, Shrirang
name: Werner, Michael E.
name: Zhang, Ying-Ao
name: Wang, Andrew Z.
name: Sukumar, Rohit
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Nanotechnology is a relatively new branch of science that involves harnessing the unique properties of particles that are nanometers in scale (nanoparticles). Nanoparticles can be engineered in a precise fashion where their size, composition and surface chemistry can be carefully controlled. This enables unprecedented freedom to modify some of the fundamental properties of their cargo, such as solubility, diffusivity, biodistribution, release characteristics and immunogenicity. Since their inception, nanoparticles have been utilized in many areas of science and medicine, including drug delivery, imaging, and cell biology1-4. However, it has not been fully utilized outside of "nanotechnology laboratories" due to perceived technical barrier. In this article, we describe a simple method to synthesize a polymer based nanoparticle platform that has a wide range of potential applications.
IMPOVING WRITING SKILLS IN TEACHING ENGLISH LANGUAGE
Creators: name: Abdumajitova, Ra'no
Publisher: name: Zenodo
Year: 2023

description: This article explores effective strategies to improve writing skills in English language teaching. It emphasizes the importance of creating a supportive and engaging learning environment where students can develop their writing abilities. The article highlights the significance of authentic writing tasks, process writing, vocabulary development, grammar instruction, and critical thinking skills. It also discusses the value of incorporating technology tools, peer collaboration, and independent writing projects. Additionally, the article emphasizes the need for reflection, goal-setting, and celebrating students' writing achievements. By implementing these strategies, educators can guide students towards becoming proficient and confident writers in the English language.
MKID, an energy sensitive superconducting detector for the next generation of XAO
Creators: name: Magniez, Aurelie
name: Bardou, Lisa
name: Morris, Tim
name: O'Brien, Kieran
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Selected for the next generation of adaptive optics (AO) systems, the pyramid wavefront sensor (PWFS) is recognised for its closed AO loop performance. As new technologies are emerging, it is necessary to explore new methods to improve it. Microwave Kinetic Inductance Detectors (MKID) are photon-counting devices that measure the arrival time and energy of each incident photon, providing new capabilities over existing detectors and significant AO performance benefits. After developing a multi-wavelength PWFS simulation, we study the benefits of using an energy sensitive detector, analyse the PWFS performance according to wavelength and explore the possibility of using fainter natural guide stars by widening the bandpass of the wavefront sensor.
description: Proceeding going with presentation done at SPIE 2022, 8 figures, 12 pages
Enhancing Energy Efficiency and Dynamic Carbon Footprint Calculation at Container Terminals
Creators: name: Benítez, Ignacio
name: Giménez, José A.
name: Blanquer, Francisco
name: Martínez, Ángel
Publisher: name: Georgia Institute of Technology
Year: 2023
Subjects: Port container terminals
Process standardization
IoT
Big data
Carbon footprint
Key performance indicators
Energy efficiency

description: Presented at the 9th International Physical Internet Conference (IPIC 2023) 13-15 June 2023, Athens, Greece
description: The Paper presents the results of the proof of concept (PoC) developed in the scope of the iTerminals 4.0 Project, to achieve a real-time calculation of the carbon footprint generated in port container terminals. iTerminals 4.0 is an innovation project co-funded by the Connecting Europe Facility Program (CEF) of the European Commission, with the objective of deploying and implementing the necessary concepts, tools, and systems to enable digital transformation of the port container industry, thus achieving the paradigm of ‘container terminal 4.0’ based on the integration of Industry 4.0 principles. The iTerminals 4.0 project comprises a study with pilot deployments in real operations at European port-container terminals, focused on digitization of port operations and adoption of Industry 4.0 technologies within the container-handling sector. A wide range of transversal benefits is expected from the digital transformation of container port operations, like operational efficiency increase, safety and (cyber) security improvement, costs reduction and carbon footprint decrease, to name only a few.
Rex Iudaeorum. Citare in giudizio un titolo regale?
Creators: name: Biazzo, Letizia
Publisher: name: La Rivista di Engramma
Year: 2023
Subjects: Titulus crucis
trilingual inscription
cross of Christ
christian iconography

description: This essay examines the artistic representations and inscriptions associated with the crucifixion of Jesus Christ. It discusses the discovery of a wooden relic with three inscriptions in Hebrew, Greek, and Latin, resembling the trilingual title of Jesus on the Cross. The artifact, found during restoration work of the Basilica of the Holy Cross in Jerusalem, in Rome, inspired artists and influenced the iconography of Jesus in crucifixion scenes. The study analyzes the artistic renditions of the inscriptions and their variations in different works of art. It also compares the Gospel accounts of the inscription, emphasizing the variations in wording and language. Through philological and art historical research, the author contributes to the understanding of the visual representation and cultural significance of the titulus crucis in art from the Middle Ages to the early modern period.
Charging/discharging mechanism in Mg3Bi2 anode for Mg-ion batteries; The role of the spin-orbit coupling
Creators: name: Assadi, M. Hussein N.
name: Kirkham, Christopher J.
name: Hamada, Ikutaro
name: Hanaor, Dorian A. H.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Computational Physics (physics.comp-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Using density functional calculations, we examine insertion/extraction of Mg ions in Mg3Bi2, an interesting Mg-ion battery anode. We found that a (1 1 0) facet is the most stable termination. Vacating a Mg2+ ion from the octahedral site is more favourable for both surface and bulk regions of the material. However, the diffusion barriers among the tetrahedral sites are around 3 times smaller than those among octahedral sites. Consequently, during the magnesiation/demagnesiation process, Mg ions first vacate the octahedral sites and then diffuse through the tetrahedral sites. The spin-orbit interaction lowers Mg's vacancy formation energy but has a minor effect on diffusion barriers.
Hyperuniformity and phase separation in biased ensembles of trajectories for diffusive systems
Creators: name: Jack, Robert L.
name: Thompson, Ian R.
name: Sollich, Peter
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We analyse biased ensembles of trajectories for diffusive systems. In trajectories biased either by the total activity or the total current, we use fluctuating hydrodynamics to show that these systems exhibit phase transtions into `hyperuniform' states, where large-wavelength density fluctuations are strongly suppressed. We illustrate this behaviour numerically for a system of hard particles in one dimension and we discuss how it appears in simple exclusion processes. We argue that these diffusive systems generically respond very strongly to any non-zero bias, so that homogeneous states with "normal" fluctuations (finite compressibility) exist only when the bias is very weak.
description: 9 pages, 3 figures
In Vivo Canine Muscle Function Assay
Creators: name: Childers, Martin K.
name: Kornegay, Joe N.
name: Grange, Robert W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: We describe a minimally-invasive and reproducible method to measure canine pelvic limb muscle strength and muscle response to repeated eccentric contractions. The pelvic limb of an anesthetized dog is immobilized in a stereotactic frame to align the tibia at a right angle to the femur. Adhesive wrap affixes the paw to a pedal mounted on the shaft of a servomotor to measure torque. Percutaneous nerve stimulation activates pelvic limb muscles of the paw to either push (extend) or pull (flex) against the pedal to generate isometric torque. Percutaneous tibial nerve stimulation activates tibiotarsal extensor muscles. Repeated eccentric (lengthening) contractions are induced in the tibiotarsal flexor muscles by percutaneous peroneal nerve stimulation. The eccentric protocol consists of an initial isometric contraction followed by a forced stretch imposed by the servomotor. The rotation effectively lengthens the muscle while it contracts, e.g., an eccentric contraction. During stimulation flexor muscles are subjected to an 800 msec isometric and 200 msec eccentric contraction. This procedure is repeated every 5 sec. To avoid fatigue, 4 min rest follows every 10 contractions with a total of 30 contractions performed.
Affinity Precipitation of Active Rho-GEFs Using a GST-tagged Mutant Rho Protein (GST-RhoA(G17A)) from Epithelial Cell Lysates
Creators: name: Dan, Qinghong
name: Szaszi, Katalin
name: Garcia-Mata, Rafael
name: Waheed, Faiza
name: Speight, Pamela
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Proteins of the Rho family of small GTPases are central regulators of the cytoskeleton, and control a large variety of cellular processes, including cell migration, gene expression, cell cycle progression and cell adhesion 1. Rho proteins are molecular switches that are active in GTP-bound and inactive in GDP-bound state. Their activation is mediated by a family of Guanine-nucleotide Exchange Factor (GEF) proteins. Rho-GEFs constitute a large family, with overlapping specificities 2. Although a lot of progress has been made in identifying the GEFs activated by specific signals, there are still many questions remaining regarding the pathway-specific regulation of these proteins. The number of Rho-GEFs exceeds 70, and each cell expresses more than one GEF protein. In addition, many of these proteins activate not only Rho, but other members of the family, contributing further to the complexity of the regulatory networks. Importantly, exploring how GEFs are regulated requires a method to follow the active pool of individual GEFs in cells activated by different stimuli. Here we provide a step-by-step protocol for a method used to assess and quantify the available active Rho-specific GEFs using an affinity precipitation assay. This assay was developed a few years ago in the Burridge lab 3,4 and we have used it in kidney tubular cell lines 5,6,7. The assay takes advantage of a "nucleotide free" mutant RhoA, with a high affinity for active GEFs. The mutation (G17A) renders the protein unable to bind GDP or GTP and this state mimics the intermediate state that is bound to the GEF. A GST-tagged version of this mutant protein is expressed and purified from E. coli, bound to glutathione sepharose beads and used to precipitate active GEFs from lysates of untreated and stimulated cells. As most GEFs are activated via posttranslational modifications or release from inhibitory bindings, their active state is preserved in cell lysates, and they can be detected by this assay8. Captured proteins can be probed for known GEFs by detection with specific antibodies using Western blotting, or analyzed by Mass Spectrometry to identify unknown GEFs activated by certain stimuli.
Ultra-fast photo-carrier relaxation in Mott insulators with short-range spin correlations
Creators: name: Eckstein, Martin
name: Werner, Philipp
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We compute the time-resolved photoemission spectrum after photo-doping in a two-dimensional Mott-Hubbard insulator. We find that the relaxation rate of high-energy photo-doped electrons in the paramagnetic phase scales with the strength of the nearest-neighbor spin correlations, which implies a pronounced increase of the relaxation times with temperature and excitation density. Finite doping, in contrast, opens additional scattering channels and leads to a faster relaxation. To obtain our results we have implemented a nonequilibrium version of the dynamical cluster approximation (DCA), which, in contrast to single-site dynamical mean-field theory, captures the effect of short-range correlations.
description: 5 pages, 5 figures
Additional file 1 of Distinctive alterations in the functional anatomy of the cerebral cortex in pain-sensitized osteoarthritis and fibromyalgia patients
Creators: name: Pujol, Jesus
name: Blanco-Hinojo, Laura
name: Doreste, Andrea
name: Ojeda, Fabiola
name: Martínez-Vilavella, Gerard
name: Pérez-Sola, Víctor
name: Deus, Joan
name: Monfort, Jordi
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Supplementary Material. Description of data: Supplementary Methods. Supplementary Figures. Supplementary Tables.
Small-scale Properties of Atomic Gas in Extended Disks of Galaxies
Creators: name: Borthakur, Sanchayeeta
name: Momjian, Emmanuel
name: Heckman, Timothy M.
name: York, Donald G.
name: Bowen, David V.
name: Yun, Min S.
name: Tripp, Todd M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present high-resolution HI 21 cm observations with the Karl G. Jansky Very Large Array (VLA) for three HI rich galaxies in absorption against radio quasars. Our sample contains six sightlines with impact parameters from 2.6 to 32.4 kpc. We detected a narrow HI absorber of FWHM 1.1 km/s at 444.5 km/s towards J122106.854+454852.16 probing the dwarf galaxy UCG 7408 at an impact parameter of 2.8 kpc. The absorption feature was barely resolved and its width corresponds to a maximum kinetic temperature, $\rm T_k \approx 26~K$. We estimate a limiting peak optical depth of 1.37 and a column density of $\rm 6\times 10^{19}~cm^{-2}$. The physical extent of the absorber is $\rm 0.04~kpc^2$ and covers $\sim$25-30\% of the background source. A comparison between the emission and absorption strengths suggests the cold-to-total HI column density in the absorber is ~30%. Folding in the covering fraction, the cold-to-total HI mass is ~10%. This suggest that condensation of warm HI ($\rm T_s\sim 1000~K$) to cold phase ($\rm T_s < 100~K$) is suppressed in UGC 7408. The unusually low temperature of the HI absorber also indicates inefficiency in condensation of atomic gas into molecular gas. The suppression in condensation is likely to be the result of low-metal content in this galaxy. The same process might explain the low efficiency of star formation in dwarf galaxies despite their huge of gas reservoirs. We also report the non-detection of HI in absorption in five other sightlines. This indicates that either the cold gas distribution is highly patchy or the gas is much warmer ($\rm T_s~>1000~K$) towards these sightlines.
description: Accepted for publication in The Astrophysical Journal. 11 pages, 6 figures, 5 pages
A Wilderness Therapy Intervention for Violent, Gang-Involved Latino Adolescents
Creators: name: Gill, Andrew
Publisher: name: Unknown
Year: 2006

description: Wilderness programs offer a nontraditional treatment option for adolescents with a variety of problems. Unfortunately, many of these programs appear to be directed at White adolescents from high-income families. This article presents a wilderness intervention that could be appropriate for Latino adolescents from lower- and middle-income families. This wilderness intervention is based on an evidence-based search and literature review as outlined by Leonard Gibbs (2003). This article illustrates Gibbs’s techniques for researching and identifying evidence-based practice methods and outlines a possible wilderness therapy intervention for gang-involved Latino adolescents.
Additional file 1 of Trawling through time: reconstructing a late nineteenth century beam trawl for scientific inshore fishery investigations
Creators: name: Hunt, Georgina L.
name: Engelhard, Georg H.
name: Pinnegar, John K.
name: Wigham, Benjamin D.
name: Polunin, Nicholas V. C.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Supplementary file1 (DOCX 1604 kb)