cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Machine-directed gravitational-wave counterpart discovery
Creators: name: Sravan, Niharika
name: Graham, Matthew J.
name: Coughlin, Michael W.
name: Ahumada, Tomas
name: Anand, Shreya
Publisher: name: arXiv
Year: 2023
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Joint observations in electromagnetic and gravitational waves shed light on the physics of objects and surrounding environments with extreme gravity that are otherwise unreachable via siloed observations in each messenger. However, such detections remain challenging due to the rapid and faint nature of counterparts. Protocols for discovery and inference still rely on human experts manually inspecting survey alert streams and intuiting optimal usage of limited follow-up resources. Strategizing an optimal follow-up program requires adaptive sequential decision-making given evolving light curve data that (i) maximizes a global objective despite incomplete information and (ii) is robust to stochasticity introduced by detectors/observing conditions. Reinforcement learning (RL) approaches allow agents to implicitly learn the physics/detector dynamics and the behavior policy that maximize a designated objective through experience. To demonstrate the utility of such an approach for the kilonova follow-up problem, we train a toy RL agent for the goal of maximizing follow-up photometry for the true kilonova among several contaminant transient light curves. In a simulated environment where the agent learns online, it achieves 3x higher accuracy compared to a random strategy. However, it is surpassed by human agents by up to a factor of 2. This is likely because our hypothesis function (Q that is linear in state-action features) is an insufficient representation of the optimal behavior policy. More complex agents could perform at par or surpass human experts. Agents like these could pave the way for machine-directed software infrastructure to efficiently respond to next generation detectors, for conducting science inference and optimally planning expensive follow-up observations, scalably and with demonstrable performance guarantees.
description: Accepted to the Astrophysical Journal; DOI: 10.3847/1538-4357/ad7257
Unified description of the dc conductivity of monolayer and bilayer graphene at finite densities based on resonant scatterers
Creators: name: Ferreira, A.
name: Gomes, J. Viana
name: Nilsson, Johan
name: Mucciolo, Eduardo R.
name: Peres, N. M. R.
name: Neto, A. H. Castro
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We show that a coherent picture of the dc conductivity of monolayer and bilayer graphene at finite electronic densities emerges upon considering that strong short-range potentials are the main source of scattering in these two systems. The origin of the strong short-range potentials may lie in adsorbed hydrocarbons at the surface of graphene. The equivalence among results based on the partial-wave description of scattering, the Lippmann-Schwinger equation, and the T-matrix approach is established. Scattering due to resonant impurities close to the neutrality point is investigated via a numerical computation of the Kubo formula using a kernel polynomial method. We find that relevant adsorbate species originate impurity bands in monolayer and bilayer graphene close to the Dirac point. In the midgap region, a plateau of minimum conductivity of about $e^2/h$ (per layer) is induced by the resonant disorder. In bilayer graphene, a large adsorbate concentration can develop an energy gap between midgap and high-energy states. As a consequence, the conductivity plateau is supressed near the edges and a "conductivity gap" takes place. Finally, a scattering formalism for electrons in biased bilayer graphene, taking into account the degeneracy of the spectrum, is developed and the dc conductivity of that system is studied.
description: 25 pages, 13 figures. published version: appendixes improved, references added, abstract and title slightly changed, plus other minor revisions
Electronic Supplementary Material from Collective motion diminishes, but variation between groups emerges, through time in fish shoals
Creators: name: MacGregor, Hannah E. A.
name: Ioannou, Christos C.
Publisher: name: The Royal Society
Year: 2021
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Supplementary materials and methods, Table S1, Table S2
Возможности развития современных 5G сетей передачи данных
Creators: name: Кернякевич П. С.
name: Кудабай Е. С.
name: Салих А. К.
name: Кривцун А. А.
name: Мосейчук В. А.
name: Сиренко П. С.
Publisher: name: Colloquium-journal
Year: 2019
Subjects: развитие сетей передачи данных пятого поколения 5G
возможности развития сетей передачи данных 5G
оценка возможностей существующих сетей передачи данных
экономические барьеры внедрения сотовой связи 5G.
development of data networks of the fifth generation 5G
opportunities for the development of data networks 5G
evaluation of the capabilities of existing data networks
economic barriers to the introduction of cellular communications 5G

description: Рассматривается важность развития современной российской мобильной связи. Дана оценка возможностям существующих сетей передачи данных, а так же сетей сотовой связи 5G. Приведены основные перспективные направления использования сетей передачи 5G. Сделан вывод о перспективности развития сетей передачи данных 5G и рассмотрены основные экономические барьеры, тормозящие внедрение сотовой связи пятого поколения.
description: The importance of the development of modern Russian mobile communications. Estimation is done of the capabilities of existing data networks, as well as fifth-generation cellular networks. The main promising directions for the applying of 5G data networks are presented. It is concluded that the development of 5G data transmission networks is promising and the main economic barriers hindering the implantation of the fifth generation cellular communications are considered.
Ligand-based virtual screening, molecular dynamics, and biological evaluation of repurposed drugs as inhibitors of Trypanosoma cruzi proteasome
Creators: name: Gomes, Suzane Quintana
name: Federico, Leonardo Bruno
name: Silva, Guilherme Martins
name: Lopes, Carla Duque
name: de Albuquerque, Sérgio
name: da Silva, Carlos Henrique Tomich de Paula
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Chagas disease is a well-known Neglected Tropical Disease, mostly endemic in continental Latin America, but that has spread to North America and Europe. Unfortunately, current treatments against such disease are ineffective and produce known and undesirable side effects. To find novel effective drug candidates to treat Chagas disease, we uniquely explore the Trypanosoma cruzi proteasome as a recent biological target and, also, apply drug repurposing through different computational methodologies. For this, we initially applied protein homology modeling to build a robust model of proteasome β4/β5 subunits, since there is no crystallographic structure of this target. Then, we used it on a drug repurposing via a virtual screening campaign starting with more than 8,000 drugs and including the methodologies: ligand-based similarity, toxicity predictions, and molecular docking. Three drugs were selected concerning their favorable interactions at the protein binding site and subsequently submitted to molecular dynamics simulations, which allowed us to elucidate their behavior and compare such theoretical results with experimental ones, obtained in biological assays also described in this paper. Communicated by Ramaswamy H. Sarma
Ratings and rankings: Voodoo or Science?
Creators: name: Paruolo, Paolo
name: Saltelli, Andrea
name: Saisana, Michaela
Publisher: name: arXiv
Year: 2011
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: Composite indicators aggregate a set of variables using weights which are understood to reflect the variables' importance in the index. In this paper we propose to measure the importance of a given variable within existing composite indicators via Karl Pearson's `correlation ratio'; we call this measure `main effect'. Because socio-economic variables are heteroskedastic and correlated, (relative) nominal weights are hardly ever found to match (relative) main effects; we propose to summarize their discrepancy with a divergence measure. We further discuss to what extent the mapping from nominal weights to main effects can be inverted. This analysis is applied to five composite indicators, including the Human Development Index and two popular league tables of university performance. It is found that in many cases the declared importance of single indicators and their main effect are very different, and that the data correlation structure often prevents developers from obtaining the stated importance, even when modifying the nominal weights in the set of nonnegative numbers with unit sum.
description: 28 pages, 7 figures
Supplementary information from Anomalous invasion dynamics due to dispersal polymorphism and dispersal–reproduction trade-offs
Creators: name: Keenan, Vincent A.
name: Cornell, Stephen J.
Publisher: name: The Royal Society
Year: 2021
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Supporting methods information
Additional file 1 of The primary care COVID-19 integrated pathway: a rapid response to health and social impacts of COVID-19
Creators: name: Aghajafari, Fariba
name: Hansen, Brian
name: McBrien, Kerry
name: Leslie, Myles
name: Chiew, Alexandra
name: Ward, Rick
name: Li, Bing
name: Hu, Jia
Publisher: name: figshare
Year: 2023
Subjects: Medicine
Environmental Sciences not elsewhere classified
Cancer
Mental Health
Computational Biology

description: Additional file 1: Appendix A. COVID-19 Acute Care Use Supplementary Table 1. Proportion of COVID-19 hospitalizations in Canada by month, April-September 2020, based on total COVID-19 cases. Supplementary Table 2. Proportion of COVID-19 emergency department visits in Canada by month, April-September 2020, based on total COVID-19 cases. Supplementary Table 3. COVID-19 cases in Ontario between April-September 2020, by age group. Supplementary Table 4. COVID-19 cases in Alberta between April-September 2020, by age group. Supplementary Table 5. COVID-19 case severity between April-September 2020, by age group.
Supplementary information from Anomalous invasion dynamics due to dispersal polymorphism and dispersal–reproduction trade-offs
Creators: name: Keenan, Vincent A.
name: Cornell, Stephen J.
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Supporting methods information
Coulomb Drag of Massless Fermions in Graphene
Creators: name: Kim, Seyoung
name: Jo, Insun
name: Nah, Junghyo
name: Yao, Z.
name: Banerjee, S. K.
name: Tutuc, E.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Using a novel structure, consisting of two, independently contacted graphene single layers separated by an ultra-thin dielectric, we experimentally measure the Coulomb drag of massless fermions in graphene. At temperatures higher than 50 K, the Coulomb drag follows a temperature and carrier density dependence consistent with the Fermi liquid regime. As the temperature is reduced, the Coulomb drag exhibits giant fluctuations with an increasing amplitude, thanks to the interplay between coherent transport in the graphene layer and interaction between the two layers.
description: 5 pages, 5 figures
Virtual screening of bioactive anti-SARS-CoV natural products and identification of 3β,12-diacetoxyabieta-6,8,11,13-tetraene as a potential inhibitor of SARS-CoV-2 virus and its infection related pathways by MD simulation and network pharmacology
Creators: name: Huq, A.K.M. Moyeenul
name: Roney, Miah
name: Imran, Syahrul
name: Khan, Shafi Ullah
name: Uddin, Md. Nazim
name: Htar, Thet Thet
name: Baig, Atif Amin
name: Bhuiyan, Mohiuddin Ahmed
name: Zakaria, Zainul Amiruddin
name: Aluwi, Mohd Fadhlizil Fasihi Mohd
name: Tajuddin, Saiful Nizam
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Since the first prevalence of COVID-19 in 2019, it still remains the most devastating pandemic throughout the world. The current research aimed to find potential natural products to inhibit the novel coronavirus and associated infection by MD simulation and network pharmacology approach. Molecular docking was performed for 39 natural products having potent anti-SARS-CoV activity. Five natural products showed high binding interaction with the viral main protease for the SARS-CoV-2 virus, where 3β,12-diacetoxyabieta-6,8,11,13 tetraene showed stable binding in MD simulation until 100 ns. Both 3β,12-diacetoxyabieta-6,8,11,13 tetraene and tomentin A targeted 11 common genes that are related to COVID-19 and interact with each other. Gene ontology development analysis further showed that all these 11 genes are attached to various biological processes. The KEGG pathway analysis also showed that the proteins that are targeted by 3β,12-diacetoxyabieta-6,8,11,13 tetraene and tomentin A are associated with multiple pathways related to COVID-19 infection. Furthermore, the ADMET and MDS studies reveals 3β,12-diacetoxyabieta-6,8,11,13 as the best-suited compound for oral drug delivery. Communicated by Ramaswamy H. Sarma
Maximum likelihood estimation in log-linear models
Creators: name: Fienberg, Stephen E.
name: Rinaldo, Alessandro
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: We study maximum likelihood estimation in log-linear models under conditional Poisson sampling schemes. We derive necessary and sufficient conditions for existence of the maximum likelihood estimator (MLE) of the model parameters and investigate estimability of the natural and mean-value parameters under a nonexistent MLE. Our conditions focus on the role of sampling zeros in the observed table. We situate our results within the framework of extended exponential families, and we exploit the geometric properties of log-linear models. We propose algorithms for extended maximum likelihood estimation that improve and correct the existing algorithms for log-linear model analysis.
description: Published in at http://dx.doi.org/10.1214/12-AOS986 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Higher-Order Asynchronous Effects
Creators: name: Ahman, Danel
name: Pretnar, Matija
Publisher: name: arXiv
Year: 2023
Subjects: subject: Programming Languages (cs.PL)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: We explore asynchronous programming with algebraic effects. We complement their conventional synchronous treatment by showing how to naturally also accommodate asynchrony within them, namely, by decoupling the execution of operation calls into signalling that an operation's implementation needs to be executed, and interrupting a running computation with the operation's result, to which the computation can react by installing interrupt handlers. We formalise these ideas in a small core calculus and demonstrate its flexibility using examples ranging from a multi-party web application, to pre-emptive multi-threading, to (cancellable) remote function calls, to a parallel variant of runners of algebraic effects. In addition, the paper is accompanied by a formalisation of the calculus's type safety proofs in Agda, and a prototype implementation in OCaml.
description: Extended journal version of a POPL 2021 paper and thus substantial text overlap with arXiv:2003.02110
Complete solutions to the metric of spherically collapsing dust in an expanding spacetime with a cosmological constant
Creators: name: Valkenburg, Wessel
Publisher: name: arXiv
Year: 2011
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present semi-analytical solutions to the background equations describing the Lemaître-Tolman-Bondi (LTB) metric as well as the homogeneous Friedmann equations, in the presence of dust, curvature and a cosmological constant Lambda. For none of the presented solutions any numerical integration has to be performed. All presented solutions are given for expanding and collapsing phases, preserving continuity in time and radius. Hence, these solutions describe the complete space time of a collapsing spherical object in an expanding universe. In the appendix we present for completeness a solution of the Friedmann equations in the additional presence of radiation, only valid for the Robertson-Walker metric.
description: 23 pages, one figure. Numerical module for evaluation of the solutions released at http://web.physik.rwth-aachen.de/download/valkenburg/ColLambda/ Matches published version, published under Open Access. Note change of title
Triad pyrazole–thiazole–coumarin heterocyclic core effectively inhibit HSP and drive cancer cells to apoptosis
Creators: name: Gümüş, Mehmet
name: Koca, İrfan
name: Sert, Yusuf
name: Dişli, Ali
name: Tunoğlu, Ezgi Nurdan Yenilmez
name: Tutar, Lütfi
name: Tutar, Yusuf
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Intensive studies on hepatocellular carcinoma (HCC), which is spreading rapidly around the world and has a high mortality rate, is due to the lack of adequate preventive or curative treatment methods. Treating patients with HCC has become very challenging because of the heterogeneity in the patient population lead activation of different signaling pathways, and pathway crosstalk for patients. Therefore, understanding these molecular mechanisms and combining drugs with molecular therapies to overcome these drawbacks has become an area of utmost importance. In this study, the biological activities of the designed and characterized triad Pyrazole–Thiazol–Coumarin (PTC) compounds were determined by performing cell viability, qPCR array, apoptosis and cell cycle assays. One of the compounds (PTC10) implicitly suppresses multiple pathways (RAS/MAP kinase and PI3K-AKT) simultaneously. This action is provided by (i) arresting cancer cells at G2 phase, (ii) driving cancer cells to apoptosis and (iii) inhibiting HSP network. Remarkably, HSP is an apoptotic factor and help cancer cell to survive. HSP90 also coordinates with Cdk4/Cdc37, therefore inhibiting HSP both drives cells to arrest and apoptosis. ATP hydrolysis and aggregation assay further displayed specific HSP inhibition. Therefore, PTC provides a unique drug template for HCC treatment. Communicated by Ramaswamy H. Sarma
Fast computing of scattering maps of nanostructures using graphical processing units
Creators: name: Favre-Nicolin, Vincent
name: Coraux, Johann
name: Richard, Marie-Ingrid
name: Renevier, Hubert
Publisher: name: arXiv
Year: 2010
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Scattering maps from strained or disordered nano-structures around a Bragg reflection can either be computed quickly using approximations and a (Fast) Fourier transform, or using individual atomic positions. In this article we show that it is possible to compute up to 4.10^10 $reflections.atoms/s using a single graphic card, and we evaluate how this speed depends on number of atoms and points in reciprocal space. An open-source software library (PyNX) allowing easy scattering computations (including grazing incidence conditions) in the Python language is described, with examples of scattering from non-ideal nanostructures.
description: 7 pages, 4 figures
Meta-hallucinator: Towards Few-Shot Cross-Modality Cardiac Image Segmentation
Creators: name: Zhao, Ziyuan
name: Zhou, Fangcheng
name: Zeng, Zeng
name: Guan, Cuntai
name: Zhou, S. Kevin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Image and Video Processing (eess.IV)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Domain shift and label scarcity heavily limit deep learning applications to various medical image analysis tasks. Unsupervised domain adaptation (UDA) techniques have recently achieved promising cross-modality medical image segmentation by transferring knowledge from a label-rich source domain to an unlabeled target domain. However, it is also difficult to collect annotations from the source domain in many clinical applications, rendering most prior works suboptimal with the label-scarce source domain, particularly for few-shot scenarios, where only a few source labels are accessible. To achieve efficient few-shot cross-modality segmentation, we propose a novel transformation-consistent meta-hallucination framework, meta-hallucinator, with the goal of learning to diversify data distributions and generate useful examples for enhancing cross-modality performance. In our framework, hallucination and segmentation models are jointly trained with the gradient-based meta-learning strategy to synthesize examples that lead to good segmentation performance on the target domain. To further facilitate data hallucination and cross-domain knowledge transfer, we develop a self-ensembling model with a hallucination-consistent property. Our meta-hallucinator can seamlessly collaborate with the meta-segmenter for learning to hallucinate with mutual benefits from a combined view of meta-learning and self-ensembling learning. Extensive studies on MM-WHS 2017 dataset for cross-modality cardiac segmentation demonstrate that our method performs favorably against various approaches by a lot in the few-shot UDA scenario.
description: Accepted by MICCAI 2022 (top 13% paper; early accept)
Leveraging developer discussions to improve design accessibility
Creators: name: Viviani, Giovanni
Publisher: name: University of British Columbia
Year: 2022

description: Since the inception of software engineering, the design of a software system has been recognized as one of its most important attributes. A software system’s design determines many of its properties, such as maintainability and performance. One might expect that there is a common and well-established understanding about what software design is and is not. Such an understanding is not evident in the literature, where design has been described in many ways such as large-scale architecture and low-level design patterns, to name just a few. At the same time, an understanding of design is also needed to maintain system properties as changes to the system are made. When developers lose track of the overall design, the system may not conform to its intended properties. Unfortunately, many systems do not have up-to-date design documentation and approaches to recover design often focus on how a system works by extracting structural and behavioural information rather than why it was designed to work like that. In this thesis, we propose an automated approach to extract design information from written discussions between developers. The aim is to make this information accessible to developers, helping them understand the design of a system and make better design decisions. First, we present an interview study we conducted to understand what researchers and practitioners consider as software design. These interviews revealed five recurring topics that can help inform what software design truly represents. We then introduce a classifier able to locate paragraphs in discussions, which we call design points, that pertain to design. Results show that this classifier is able to locate design information with high accuracy even in systems that it was not trained on. We describe a study conducted with software developers that shows that newcomers to a project, when provided with design points relevant to a programming task, are able to interpret and use the design information to consider additional design alternatives. We finally discuss an early exploration into the use of semantic frames to identify useful design points.
Targeting Olokizumab-Interleukin 6 interaction interface to discover novel IL-6 inhibitors
Creators: name: Tran, Que-Huong
name: Cao, Hoang-Nhi
name: Nguyen, Dac-Nhan
name: Tran, Thi-Thuy-Nga
name: Le, Minh-Tri
name: Nguyen, Quoc-Thai
name: Tran, Van-Thanh
name: Tran, Viet-Hung
name: Thai, Khac-Minh
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: The IL-6/IL-6R or IL-6/GP130 protein-protein interactions play a significant role in controlling the development of chronic inflammatory diseases, such as rheumatoid arthritis, Castleman disease, psoriasis, and, most recently, COVID-19. Modulating or antagonizing protein-protein interactions of IL6 binding to its receptors by oral drugs promises similar efficacy to biological therapy in patients, namely monoclonal antibodies. In this study, we used a crystal structure of the Fab part of olokizumab in a complex with IL-6 (PDB ID: 4CNI) to uncover starting points for small molecule IL-6 antagonist discovery. Firstly, a structure‑based pharmacophore model of the protein active site cavity was generated to identify possible candidates, followed by virtual screening with a significant database Drugbank. After the docking protocol validation, a virtual screening by molecular docking was carried out and a total of 11 top hits were reported. Detailed analysis of the best scoring molecules was performed with ADME/T analysis and molecular dynamics simulation. Furthermore, the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) technique has been utilized to evaluate the free binding energy. Based on the finding, one newly obtained compound in this study, namely DB15187, may serve as a lead compound for the discovery of IL-6 inhibitors. Communicated by Ramaswamy H. Sarma
Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies
Creators: name: Afshinpour, Maral
name: Mahdiuni, Hamid
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Metabolic and signaling mechanisms in mammalian cells are facilitated by the transportation of L-arginine (Arg) across the plasma membrane through cationic amino acid transporter (CAT) proteins. Due to a lack of argininosuccinate synthase (ASS) activity in various tumor cells such as acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia, these tumor entities are arginine-auxotrophic and therefore depend on the uptake of the amino acid arginine. Cationic amino acid transporter-1 (CAT-1) is the leading arginine importer expressed in the aforementioned tumor entities. Hence, in the present study, to investigate the transportation mechanism of arginine in CAT-1, we performed molecular dynamics (MD) simulation methods on the modeled human CAT-1. The MM-PBSA approach was conducted to determine the critical residues interacting with arginine within the corresponding binding site of CAT-1. In addition, we found out that the water molecules have the leading role in forming the transportation channel within CAT-1. The conductive structure of CAT-1 was formed only when the water molecules were continuously distributed across the channel. Steered molecular dynamics (SMD) simulation approach showed various energy barriers against arginine transportation through CAT-1, especially while crossing the bottlenecks of the related channel. These findings at the molecular level might shed light on identifying the crucial amino acids in the binding of arginine to eukaryotic CATs and also provide fundamental insights into the arginine transportation mechanisms through CAT-1. Understanding the transportation mechanism of arginine is essential to developing CAT-1 blockers, which can be potential medications for some types of cancers. Communicated by Ramaswamy H. Sarma
Bioactive plantaricins as potent anti-cancer drug candidates: double docking, molecular dynamics simulation and in vitro cytotoxicity analysis
Creators: name: Chakrobarty, Soumyadip
name: Garai, Swarnava
name: Ghosh, Arabinda
name: Mukerjee, Nobendu
name: Das, Deeplina
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: The medical community is desperate for a reliable source of medications to alleviate the severity of conventional cancer treatments and prevent secondary microbial infections in oncological patients. In this regard, plantaricins from lactic acid bacteria were explored as prospective drug candidates against known anti-cancer drug targets. Three plantaricins, JLA-9, GZ1-27 and BN, have a binding affinity of −8.8, −8.6 and −7.2 kcal/mol, respectively, with squalene synthase (SQS), a key molecule in lung cancer metastasis. All three plantaricins displayed analogous binding patterns as SQS inhibitors and generated hydrogen and hydrophobic interactions with ARG 47, ARG 188, PHE24, LEU183 and PRO292. Structural stability of docked complexes was validated using molecular dynamics simulation derived parameters such as RMSD, RMSF and radius of gyration. Based on MD simulation results, conformational changes and stabilities of docked SQS/plantaricin complexes with respect to the time frame were evaluated using machine learning (logistic regression algorithm). Double docking with SQS/matrix metalloproteinase MMP1 and PCA analysis revealed the potential of plantaricin JLA-9 as a multi-substrate inhibitor. Further, plantaricin JLA-9 induced a significant cytotoxic response against the lung carcinoma cell line (A549) in a dose and time dependent manner with inhibition concentration (IC50) of 0.082 µg/ml after 48 h. However, plantaricin JLA-9 did not induce cytotoxicity in normal lung cells (L-132), as the IC50 value was not obtained even at a higher dose of 0.8 µg/ml. In silico pharmacokinetic (ADMET) profile implies that plantaricin JLA-9 could be developed as new age anti-cancer therapeutic with a preference for parenteral administration. Communicated by Ramaswamy H. Sarma
“Máquinas y autómatas : retratos de la mujer amazónica y su relación con la naturaleza en la literatura del auge de la extracción del caucho (1879-1914)”
Creators: name: Moscoso-Garay, Marcos
Publisher: name: University of British Columbia
Year: 2022

description: My research examines the representation of women during the Amazon Rubber Boom in the work of novelists and filmmakers. Portrayals of the Amazon in Latin American literature tend to fixate upon gender and nature (and the relationship between them). They demonstrate the stereotyped and idealized way in which Amazonian women and nature have been understood. I consider that the character of the Amazonian women has not been studied enough. I show that the female character has been simplified to a kind of machine object (automaton) by the artists who intend to criticize the system created at the time of extraction of rubber in the Amazon. I study eleven novels written across the twentieth and twenty-first centuries, emphasizing one in each chapter: Páginas bárbaras (1914), Los Shiringeros (1965) and Manaos (1973). These works take the reader back to the time of rubber exploitation from different perspectives, demonstrating a literary system created in relation to long-lasting stereotypes. These novels also highlight the ambivalence of these stereotypes about women and nature, both of which are portrayed as beautiful and sensual, but also dangerous and wild. In some cases (Mendoza, for instance), writers try to re-evaluate Amazonian cultures, re-articulating these stereotypes in positive fashion. In other cases (Rivera and Vargas Llosa), women and nature are simply condemned to ever-lasting ambivalence. My purpose is to show the ways in which industrial modernization and the modes and relations of capitalist production helped to perpetuate stereotypes of gender in the Amazon. More specifically, I investigate how these artists under study—like Jaime Mendoza, Lino La Rosa Olazábal and Alberto Vázquez Figueroa—react to, problematize, and criticize the discourse of progress, the hope in capital, the systematic process of death, torture and slavery against indigenous women at the time of rubber extraction. However, that attempted criticism of the system does not manage to be effective because it is mediated by a discourse of modernity that keeps stereotyping Amazonian women by using the metaphor of the automaton woman.
Laboratório de Alimentos e Bebidas: Carne Bovina
Creators: name: De Lemos, Vanessa Maria Braga
name: De Souza Lima, Adriana
Publisher: name: Zenodo
Year: 2022
Subjects: laboratório de alimentos e bebidas
hotelaria
restaurante
food service
carne bovina

description: Esta apresentação em slide foi realizada pela monitora Vanessa Maria Braga de Lemos e sua orientadora Adriana de Souza Lima, para a aula de Carnes Bovinas ser apresentada na matéria de Laboratório de Alimentos e Bebidas (A&B), do Curso Superior de Tecnologia em Hotelaria da Universidade Federal Fluminense (UFF).
Herschel-ATLAS: First data release of the Science Demonstration Phase source catalogues
Creators: name: Rigby, E. E.
name: Maddox, S. J.
name: Dunne, L.
name: Negrello, M.
name: Smith, D. J. B.
name: González-Nuevo, J.
name: Herranz, D.
name: López-Caniego, M.
name: Auld, R.
name: Baes, M.
name: Buttiglione, S.
name: Cava, A.
name: Cooray, A.
name: Clements, D. L.
name: Dariush, A.
name: De Zotti, G.
name: Dye, S.
name: Eales, S.
name: Frayer, D.
name: Fritz, J.
name: Hopwood, R.
name: Ibar, E.
name: Ivison, R. J.
name: Jarvis, M.
name: Panuzzo, P.
name: Pascale, E.
name: Pohlen, M.
name: Rodighiero, G.
name: Serjeant, S.
name: Temi, P.
name: Thompson, M. A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The Herschel-ATLAS is a survey of 550 square degrees with the Herschel Space Observatory in five far--infrared and submillimetre bands. The first data for the survey, observations of a field 4x4 sq. degrees in size, were taken during the Science Demonstration Phase, and reach a 5 sigma noise level of 33 mJy/beam at 250 microns. This paper describes the source extraction methods used to create the corresponding Science Demonstration Phase catalogue, which contains 6876 sources, selected at 250 microns, within ~14 sq. degrees. SPIRE sources are extracted using a new method specifically developed for Herschel data; PACS counterparts of these sources are identified using circular apertures placed at the SPIRE positions. Aperture flux densities are measured for sources identified as extended after matching to optical wavelengths. The reliability of this catalogue is also discussed, using full simulated maps at the three SPIRE bands. These show that a significant number of sources at 350 and 500 microns have undergone flux density enhancements of up to a factor of ~2, due mainly to source confusion. Correction factors are determined for these effects. The SDP dataset and corresponding catalogue will be available from http://www.h-atlas.org/.
description: 15 pages, MNRAS accepted, Minor changes to text to address referee's comments
Investigating the antibacterial mechanism of Ampelopsis cantoniensis extracts against methicillin-resistant Staphylococcus aureus via in vitro and in silico analysis
Creators: name: Bich, Van Ngo Thai
name: Nguyen, Tan Khanh
name: Thu, Thao Dao Thi
name: Tran, Linh Thuy Thi
name: Nguyen, Sa Vo Duong
name: Le Han, Ho
name: Pham, Long-Hung Dinh
name: Thanh, Trung Hoang
name: Duong, Van Hoa
name: Trieu, Tuan Anh
name: Tran, Manh Hung
name: Pham, Phu Tran Vinh
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Methicillin-resistant Staphylococcus aureus (MRSA) is a critical pathogen responsible for a wide variety of serious infectious diseases in humans. The accelerated phenomena of drug tolerance, drug resistance, and dysbacteriosis provoked by antibiotic misuse are impeding the effectiveness of contemporary antibiotic therapies primarily used to treat this common worldwide pathogen. In this study, the antibacterial activity of 70% ethanol extract and multiple polar solvents of Ampelopsis cantoniensis were measured against the clinical MRSA isolate. The agar diffusion technique was employed to determine the zone of inhibition (ZOI), accompanied by the use of a microdilution series to identify the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). Our results revealed that the ethyl acetate fraction exhibited the most significant antibacterial activity, which was determined to be bacteriostatic based on the MBC/MIC ratio 8. A list of compounds isolated from A. cantoniensis was computationally studied to further investigate the mechanism of action with the bacterial membrane protein PBP2a. The combination of molecular docking and molecular dynamics methods showed that the main compound, dihydromyricetin (DHM), is expected to bind to PBP2a at allosteric site. In addition, DHM was identified as the major compound of ethyl acetate fraction, which accounts for 77.03 ± 2.44% by high performance liquid chromatography (HPLC) analysis. As a concluding remark, our study addressed the antibacterial mechanism and suggested the prioritization of natural products derived from A. cantoniensis as a potential therapy for MRSA. Communicated by Ramaswamy H. Sarma
Characterization of the coupling mechanism of scorpion β-neurotoxins on the voltage-gated sodium channel hNav1.6
Creators: name: Montero-Dominguez, Pavel Andrei
name: Corzo, Gerardo
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified

description: Scorpion β-neurotoxins represent a pharmacological group that affects voltage-gated sodium channels (Nav). Despite knowing the electrophysiological effect of these toxins on Nav channels, the molecular mechanism by which the union is carried out is still undetermined. In this study, computational techniques such as modeling, docking and molecular dynamics were used to elucidate the mechanism of interaction between scorpion β-neurotoxins using the neurotoxin nCssII and its recombinant variant CssII-RCR, which bind to the site-4, an extracellular receptor, of the human sodium channel hNav1.6. Different modes of interaction were observed for both toxins, where the main distinguishing feature was the interaction generated by the residue E15 on such site-4; that is, E15 in nCssII exhibits an interaction with the voltage-sensing domain II, and the same residue E15 of CssII-RCR exhibits an interaction with domain III. Despite this difference in interaction by E15, it is seen that both neurotoxins interact with similar regions of the voltage sensing domain such as the S3-S4 connecting loop (L834-E838) of the hNav1.6. Our simulations present a first approach to the mode of interaction of scorpion beta-neurotoxins in toxin-receptor complexes, being able to explain at the molecular level the phenomenon of voltage sensor entrapment generated by these toxins. Communicated by Ramaswamy H. Sarma
New characterization of Robertson-Walker geometries involving a single timelike curve
Creators: name: Mars, Marc
name: Vera, Raül
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Our aim in this paper is two-fold. We establish a novel geometric characterization of the Roberson-Walker (RW) spacetime and, along the process, we find a canonical form of the RW metric associated to an arbitrary timelike curve and an arbitrary space frame. A known characterization establishes that a spacetime foliated by constant curvature leaves whose orthogonal flow (the cosmological flow) is geodesic, shear-free, and with constant expansion on each leaf, is RW. We generalize this characterization by relaxing the condition on the expansion. We show it suffices to demand that the spatial gradient and Laplacian of the expansion on a single arbitrary timelike curve vanish. In General Relativity these local conditions are equivalent to demanding that the energy flux measured by the cosmological flow, as well as its divergence, are zero on a single arbitrary timelike curve. The proof allows us to construct canonically adapted coordinates to the arbitrary curve, thus well-fitted to an observer with an arbitrary motion with respect to the cosmological flow.
description: 29 pages, no figures. Added references and included some further discussion on the result. Version matches the published version
Coherent control of the cooperative branching ratio for nuclear x-ray pumping
Creators: name: Pálffy, Adriana
name: Keitel, Christoph H.
name: Evers, Jörg
Publisher: name: arXiv
Year: 2010
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Coherent control of nuclear pumping in a three level system driven by x-ray light is investigated. In single nuclei, the pumping performance is determined by the branching ratio of the excited state populated by the x-ray pulse. Our results are based on the observation that in ensembles of nuclei, cooperative excitation and decay leads to a greatly modified nuclear dynamics, which we characterize by a time-dependent cooperative branching ratio. We discuss prospects of steering the x-ray pumping by coherently controlling the cooperative decay. First, we study an ideal case with purely superradiant decay and perfect control of the cooperative emission. A numerical analysis of x-ray pumping in nuclear forward scattering with coherent control of the cooperative decay via externally applied magnetic fields is presented. Next, we provide an extended survey of nuclei suitable for our scheme, and propose proof-of-principle implementations already possible with typical Mössbauer nuclear systems such as $^{57}\mathrm{Fe}$. Finally, we discuss the application of such control techniques to the population or depletion of long-lived nuclear states.
description: 11 pages, 8 figures; updated to the published version
Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies
Creators: name: Sultana, Razia
name: Ali, Asghar
name: Twala, Charmy
name: Mehandi, Rabiya
name: Rana, Manish
name: Yameen, Daraksha
name: Abid, Mohammad
name: Rahisuddin
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: We have synthesized the pyrazole-bearing Schiff base derivatives (5a–5e) and (6a–6h) then the structural confirmation was supported by various spectral analyses. The antibacterial activity of all analogs was screened against bacterial strains Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumonieae and Pseudomonas aeruginosa. In comparison to the reference drug ciprofloxacin, the lead analogs 5c and 6c showed potent activity, with MIC values of 64 µg/mL against E. coli and B. subtilis. Compound 5c showed a moderate effect with a MIC value of 128 µg/mL against B. subtilis, P. aeruginosa and K. pneumonieae, while compound 6c was against E. coli and P. aeruginosa. Furthermore, the compounds 5c and 6c displayed groove binding mode towards CT-DNA by absorption, emission, competitive fluorescence studies using EtBr, CD and time-resolved fluorescence studies. Thermodynamic parameters of analogs 5c and 6c with CT-DNA were also calculated at 298, 303 and 308K temperatures by UV–visible spectroscopy. The molecular docking studies give the docking score for all compounds with PDB codes: 1BNA and 2XCT. The MD simulation study of analogs 5c and 6c was also carried out. The pharmacokinetic and ADME properties were calculated for all of the synthesized analogs (5a–5e) and (6a–6h). Communicated by Ramaswamy H. Sarma