cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Experimental Demonstration of Discrete Modulation Formats for Continuous Variable Quantum Key Distribution
Creators: name: Roumestan, François
name: Ghazisaeidi, Amirhossein
name: Renaudier, Jérémie
name: Vidarte, Luis Trigo
name: Leverrier, Anthony
name: Diamanti, Eleni
name: Grangier, Philippe
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum key distribution (QKD) enables the establishment of secret keys between users connected via a channel vulnerable to eavesdropping, with information-theoretic security, that is, independently of the power of a malevolent party. QKD systems based on the encoding of the key information on continuous variables (CV), such as the values of the quadrature components of coherent states, present the major advantage that they only require standard telecommunication technology. However, the most general security proofs for CV-QKD required until now the use of Gaussian modulation by the transmitter, complicating practical implementations. Here, we experimentally implement a protocol that allows for arbitrary, Gaussian-like, discrete modulations, whose security is based on a theoretical proof that applies very generally to such situations. These modulation formats are compatible with the use of powerful tools of coherent optical telecommunication, allowing our system to reach a performance of tens of megabit per second secret key rates over 25 km.
description: 6 pages, 6 figures
Development of multi-epitope based subunit vaccine against Mycobacterium Tuberculosis using immunoinformatics approach
Creators: name: R, Savita Kumari
name: Sethi, Guneswar
name: Krishna, Ramadas
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
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
subject: Computational Biology

description: The etiological agent of tuberculosis (TB), Mycobacterium tuberculosis, is a deadly pathogen that adapts to thrive within the host. Since 2020, the COVID-19 pandemic has had colossal health, societal, and economic consequences, which have affected the reporting of new incidences and mortality cases of TB. As per the WHO 2022 report, 10.6 million people were diagnosed with TB, and 1.6 million died worldwide. The increase in resistant strains of tuberculosis is making it more burdensome to reach the End TB strategy. A reliable and efficient TB vaccine that may avert both primary infection and recurrence of latent TB in adults and adolescents is of the utmost importance. In this study, we used computational techniques to predict the ability of HLA molecules to display epitopes for six TB proteins (PPE68, PE_PGRS17, EspC, LDT4, RpfD, and RpfC) to design the multi-epitope subunit vaccine. From the aimed proteins, the potential B-cell, helper T lymphocyte (HTL), and cytotoxic T lymphocyte (CTL) epitopes were predicted and linked together with LPA adjuvant, and the vaccine was designed. The vaccine’s physicochemical analysis demonstrates that it is non-allergic, non-toxic, and antigenic. Then, the vaccine structure was predicted, improved, and verified to yield the optimal structure. The developed vaccine’s binding mechanism with distinct immunogenic receptors (Tlr2 and MHC-II) was assessed utilizing molecular docking. The molecular dynamic simulation and MMPBSA analysis were performed to comprehend the complexes’ dynamics and stability. The immune simulation was utilized to anticipate the vaccine’s immunogenic attributes. In silico cloning was employed to demonstrate the efficient expression of the designed vaccine in E. coli as a host. Moreover, in vitro and in vivo animal testing is required to determine the efficacy of the in silico developed vaccine. Communicated by Ramaswamy H. Sarma
Towards Domain-agnostic Depth Completion
Creators: name: Xu, Guangkai
name: Yin, Wei
name: Zhang, Jianming
name: Wang, Oliver
name: Niklaus, Simon
name: Chen, Simon
name: Bian, Jia-Wang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Existing depth completion methods are often targeted at a specific sparse depth type and generalize poorly across task domains. We present a method to complete sparse/semi-dense, noisy, and potentially low-resolution depth maps obtained by various range sensors, including those in modern mobile phones, or by multi-view reconstruction algorithms. Our method leverages a data-driven prior in the form of a single image depth prediction network trained on large-scale datasets, the output of which is used as an input to our model. We propose an effective training scheme where we simulate various sparsity patterns in typical task domains. In addition, we design two new benchmarks to evaluate the generalizability and the robustness of depth completion methods. Our simple method shows superior cross-domain generalization ability against state-of-the-art depth completion methods, introducing a practical solution to high-quality depth capture on a mobile device. The code is available at: https://github.com/YvanYin/FillDepth.
DDF operators in the Hybrid Formalism
Creators: name: Naderi, Kiarash
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: String theory with one unit of NS-NS flux on $\text{AdS}_3 \times \text{S}^3 \times \mathbb{T}^4$ has been recently realised to be the exact dual of the symmetric orbifold of $\mathbb{T}^4$. In the hybrid formalism of Berkovits, Vafa and Witten and using the free-field realisation of $\mathfrak{psu}(1,1|2)_1$, the DDF operators of the free bosons and the free fermions of $\mathbb{T}^4$ are constructed. It is shown that these DDF operators reproduce the whole spectrum of the space-time theory on the world-sheet and therefore provide a derivation of the dual spectrum from first-principles.
description: 32 pages, v2: agrees with the published version
Teaching Visual Accessibility in Introductory Data Science Classes with Multi-Modal Data Representations
Creators: name: Seo, JooYoung
name: Dogucu, Mine
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Computers and Society (cs.CY)
subject: Other Statistics (stat.OT)
subject: FOS: Computer and information sciences

description: Although there are various ways to represent data patterns and models, visualization has been primarily taught in many data science courses for its efficiency. Such vision-dependent output may cause critical barriers against those who are blind and visually impaired and people with learning disabilities. We argue that instructors need to teach multiple data representation methods so that all students can produce data products that are more accessible. In this paper, we argue that accessibility should be taught as early as the introductory course as part of the data science curriculum so that regardless of whether learners major in data science or not, they can have foundational exposure to accessibility. As data science educators who teach accessibility as part of our lower-division courses in two different institutions, we share specific examples that can be utilized by other data science instructors.
description: 17 pages, 6 figures
Additional file 1 of A WeChat applet-based national remote emergency system for malignant hyperthermia in China: a usability study
Creators: name: Yu, Hong
name: Tan, Lingcan
name: Zhu, Tao
name: Deng, Xiaoqian
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 1. Modified user-version of Mobile Application Rating Scale (uMARS).
Connecting Cosmic Inflation to Particle Physics with LiteBIRD, CMB-S4, EUCLID and SKA
Creators: name: Drewes, Marco
name: Ming, Lei
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We show that next generation Cosmic Microwave Background experiments will be capable of the first ever measurement of the inflaton coupling to other particles, opening a new window to probe the connection between cosmic inflation and particle physics.This sensitivity is based on the impact that the reheating phase after cosmic inflation has on the redshifting of cosmic perturbations. For our analysis we introduce a simple analytic method to estimate the sensitivity of future CMB observations to the reheating temperature and the inflaton coupling. Applying our method to LiteBIRD and CMB-S4 we find that, within a given model of inflation, these missions have the potential to impose both an upper and a lower bound on the inflaton coupling. Further improvement can be achieved if CMB data is combined with optical and 21cm surveys. Our results demonstrate the potential of future observations to constrain microphysical parameters that can provide an important clue to understand how a given model of inflation may be embedded in a more fundamental theory of nature.
description: 7 pages, 2 figures; matches version published in PRL
sj-pdf-1-pcr-10.1177_26323524231193038 – Supplemental material for Latino advanced cancer patients’ prognostic awareness and familial cultural influences on advance care planning engagement: a qualitative study
Creators: name: Torres Blasco, Normarie
name: Rosario, Lianel
name: Shen, Megan J.
Publisher: name: SAGE Journals
Year: 2023
Subjects: Aged Health Care

description: Supplemental material, sj-pdf-1-pcr-10.1177_26323524231193038 for Latino advanced cancer patients’ prognostic awareness and familial cultural influences on advance care planning engagement: a qualitative study by Normarie Torres Blasco, Lianel Rosario and Megan J. Shen in Palliative Care and Social Practice
COMPUTER VISION SYSTEMS FOR PRACTICAL APPLICATIONS IN PRECISION LIVESTOCK FARMING
Creators: name: Rao, Prajwal
Publisher: name: Purdue University Graduate School
Year: 2024
Subjects: classificationCode: 460304
subject: Computer vision
classificationCode: 409901
subject: Agricultural engineering
classificationCode: 461103
subject: Deep learning

description: The use of advanced imaging technology and algorithms for managing and monitoring livestock improves various aspects of livestock, such as health monitoring, behavioral analysis, early disease detection, feed management, and overall farming efficiency. Leveraging computer vision techniques such as keypoint detection, and depth estimation for these problems help to automate repeatable tasks, which in turn improves farming efficiency. In this thesis, we delve into two main aspects that are early disease detection, and feed management:Phenotyping Ducks using Keypoint Detection: A platform to measure duck phenotypes such as wingspan, back length, and hip width packaged in an online user interface for ease of use.Real-Time Cattle Intake Monitoring Using Computer Vision: A complete end-to-end real-time monitoring system to measure cattle feed intake using stereo cameras.Furthermore, considering the above implementations and their drawbacks, we propose a cost-effective simulation environment for feed estimation to conduct extensive experiments prior to real-world implementation. This approach allows us to test and refine the computer vision systems under controlled conditions, identify potential issues, and optimize performance without the high costs and risks associated with direct deployment on farms. By simulating various scenarios and conditions, we can gather valuable data, improve algorithm accuracy, and ensure the system's robustness. Ultimately, this preparatory step will facilitate a smoother transition to real-world applications, enhancing the reliability and effectiveness of computer vision in precision livestock farming.
sj-docx-1-psw-10.1177_14789299231193572 – Supplemental material for The Multiverse of Taiwan’s Future: Reconsidering the Independence–Unification (Tondu) Attitudes
Creators: name: Chen, Fang-Yu
name: Wang, Austin Horng-En
name: Wu, Charles KS
name: Yeh, Yao-Yuan
Publisher: name: SAGE Journals
Year: 2023
Subjects: International Relations

description: Supplemental material, sj-docx-1-psw-10.1177_14789299231193572 for The Multiverse of Taiwan’s Future: Reconsidering the Independence–Unification (Tondu) Attitudes by Fang-Yu Chen, Austin Horng-En Wang, Charles KS Wu and Yao-Yuan Yeh in Political Studies Review
General coefficient-vanishing results associated with theta series
Creators: name: Chern, Shane
name: Tang, Dazhao
Publisher: name: arXiv
Year: 2022
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11F27, 11B65, 11J13, 11J20

description: There are a number of sporadic coefficient-vanishing results associated with theta series, which suggest certain underlying patterns. By expanding theta powers as linear combinations of products of theta functions, we present two strategies that will provide a unified treatment. Our approaches rely on studying the behavior of products of two theta series under the action of the huffing operator. For this purpose, some explicit criteria are given. We may use the presented methods to not only verify experimentally discovered coefficient-vanishing results, but also to produce a series of general phenomena.
description: 72 pages
Inquest for the interaction of canonical and non-canonical DNA/RNA bases with ternary based 2D Si2BN and doped Si2BN for biosensing applications
Creators: name: Muralidharan, Akilesh
name: Subramani, Mohanapriya
name: Subramani, Divyakaaviri
name: Ramasamy, Shankar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Computational Biology

description: Density functional theory (DFT) is invoked to investigate the interaction between the canonical (CN) and non-canonical (NC) bases with pristine Si2BN (Si2BN) and Phosphorous-doped Si2BN (P-dop-Si2BN) sheets. Inquest for the better sensing substrate is decided through the adsorption energy calculation which reveals that doping of phosphorous atom enhances the adsorption strength of AT (-83.74 kcal/mol) AU (-82.77 kcal/mol) and GC (-96.36 kcal/mol) base pairs. The CN and NC bases have higher adsorption energy than the previous reported values which concludes that the P-dop-Si2BN sheet will be optimal substrate to sense the bases. Meanwhile, the selected CN and NC (except hypoxanthine) bases interact with sheet in parallel manner which infers the π-π interaction with Si2BN and P-dop-Si2BN sheets. The energy gap variation (ΔEg%) of the P-dop-Si2BN complexes has a noticeable change, ranging from −24.75 to −197.28% which thrust the sensitivity of the P-dop-Si2BN sheet over the detection of CN and NC bases. The natural population analysis (NPA) and electron density difference map (EDDM) confirms that charges are transferred from CN and NC bases to Si2BN and P-dop-Si2BN sheet. The optical property of the P-dop-Si2BN complexes reveals that the noticeable red and blue shift in the visible and near-infrared regions (778 nm to 1143 nm) has been observed. Therefore, the above results conclude that the P-dop-Si2BN sheet plays a potential candidate to detect the CN and NC bases which contribute to the development of biosensors and DNA/RNA sequencing devices. Communicated by Ramaswamy H. Sarma
title: Intelligent Self-Correction Feedback System (ASCQ): Enhancing AI Response Accuracy through Human-Driven Evaluation Loops
title: نظام التصحيح الذكي المعتمد على التغذية الراجعة البشرية
titleType: AlternativeTitle
Creators: name: alshraiedeh, Mahmoud
Publisher: name: Zenodo
Year: 2025
Subjects: Feedback
Ai
System
human-in-the-loop
error correction
machine learning
real-time learning

description: This research introduces the "Intelligent Self-Correction Feedback System (ASCQ)," a novel concept designed to enhance the performance and reliability of AI-generated outputs by integrating real-time human feedback into the correction loop. The system identifies common patterns of mistakes made by AI models and dynamically updates response behavior based on contextual human corrections, aiming to increase precision, credibility, and adaptability over time. This paper lays the groundwork for future implementations in educational, medical, and customer service applications.
description: AI, self-correction, feedback system, artificial intelligence, human-in-the-loop, machine learning, error detection
Additional file 2 of A WeChat applet-based national remote emergency system for malignant hyperthermia in China: a usability study
Creators: name: Yu, Hong
name: Tan, Lingcan
name: Zhu, Tao
name: Deng, Xiaoqian
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 2. Post-Study System Usability Questionnaire (PSSUQ).
Identification of novel dual acting ligands targeting the adenosine A2A and serotonin 5-HT1A receptors
Creators: name: Touati, Iman
name: Abdalla, Mohnad
name: Boulaamane, Yassir
name: Al-Hoshani, Nawal
name: Alouffi, Abdulaziz
name: Britel, Mohammed Reda
name: Maurady, Amal
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biochemistry
Medicine
Molecular Biology
Neuroscience
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Mental Health

description: GPCRs are a family of transmembrane receptors that are profoundly linked to various neurological disorders, among which is Parkinson’s disease (PD). PD is the second most ubiquitous neurological disorder after Alzheimer’s disease, characterized by the depletion of dopamine in the central nervous system due to the impairment of dopaminergic neurons, leading to involuntary movements or dyskinesia. The current standard of care for PD is Levodopa, a dopamine precursor, yet the chronic use of this agent can exacerbate motor symptoms. Recent studies have investigated the effects of combining A2AR antagonist and 5-HT1A agonist on dyskinesia and motor complications in animal models of PD. It has been proved that the drug combination has significantly improved involuntary movements while maintaining motor activity, highlighting as a result new lines of therapy for PD treatments, through the regulation of both receptors. Using a combination of ligand-based pharmacophore modelling, virtual screening, and molecular dynamics simulation, this study intends on identifying potential dual-target compounds from IBScreen. Results showed that the selected models displayed good enrichment metrics with a near perfect receiver operator characteristic (ROC) and Area under the accumulation curve (AUAC) values, signifying that the models are both specific and sensitive. Molecular docking and ADMET analysis revealed that STOCK2N-00171 could be potentially active against A2AR and 5-HT1A. Post-MD analysis confirmed that the ligand exhibits a stable behavior throughout the simulation while maintaining crucial interactions. These results imply that STOCK2N-00171 can serve as a blueprint for the design of novel and effective dual-acting ligands targeting A2AR and 5-HT1A. Communicated by Ramaswamy H. Sarma
Identification of novel small molecule inhibitors for solute carrier SGLT1; a computational exploration
Creators: name: Haider, Sajjad
name: Mushtaq, Mamona
name: Nur-e-Alam, Mohammad
name: Ahmed, Aftab
name: Ul-Haq, Zaheer
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Medicine
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: Diabetes results in substantial disabilities, diminished quality of life, and mortality that imposes a huge economic burden on societies and governments worldwide. Despite the absence of specific oral therapies at present, there exists an urgent requirement to develop a novel drug for the treatment of diabetes mellitus. The membrane protein sodium glucose co-transporters (SGLT1) present a captivating therapeutic target for diabetes, given its pivotal role in facilitating glucose absorption in the small intestine, offering immense promise for potential therapeutic intervention. In this connection, the present study is aimed at identifying potential inhibitors of SGLT1 from a small molecule database, including compounds from both natural as well as synthetic origins. A comprehensive approach was employed, by integrating homology modeling, ligand-based pharmacophore modeling, virtual screening, and molecular docking simulation. The process resulted in the identification of 16 new compounds, featuring similar attributes as observed for the documented actives. In a systematic screening procedure, five potential virtual hits were selected for simulation studies followed by subsequent binding free energy calculations, providing deeper insight into the time-dependent behavior of protein-ligand complexes in a dynamic state. In conclusion, our findings demonstrated that the identified compounds, particularly compounds 81 and 91, exhibit enhanced stability and favorable binding affinities with the target protein, marking them promising candidates for further investigations. Communicated by Ramaswamy H. Sarma
Additional file 3 of A WeChat applet-based national remote emergency system for malignant hyperthermia in China: a usability study
Creators: name: Yu, Hong
name: Tan, Lingcan
name: Zhu, Tao
name: Deng, Xiaoqian
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 3. The System Usability Scale (SUS).
Synthesis, crystal structure, spectroscopic characterization, DFT calculations, Hirshfeld surface analysis, molecular docking, and molecular dynamics simulation investigations of novel pyrazolopyranopyrimidine derivatives
Creators: name: Elmachkouri, Younesse Ait
name: Irrou, Ezaddine
name: Thiruvalluvar, Aravazhi Amalan
name: Anouar, El Hassane
name: Varadharajan, Venkatramanan
name: Ouachtak, Hassan
name: Mague, Joel T.
name: Sebbar, Nada Kheira
name: Essassi, El Mokhtar
name: Taha, Mohamed Labd
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: A series of new pyrazolopyranopyrimidine derivatives (3-9) were synthesized from 5-amino-2,4-dihydro-3-methyl-4-phenylpyrano-[2,3-c]pyrazole-5-carbonitrile (2) by multicomponent reactions (MCR) involving malononitrile, benzaldehyde, and pyrazolone under refluxing ethanol in the presence of piperidine. Compound (2) was then converted to 2-acetylpyrazolopyranopyrimidine (3) through a reaction with acetic anhydride. The deprotection of 3 using ammonium hydroxide in ethanol, leads to 4. Subsequent chlorination of 4 by phosphorus oxychloride affords 5 which was alkylated using methyl iodide and ethyl bromoacetate in DMF, leading to regioisomers 6-9. The products were characterized by spectroscopic techniques (1H and 13C NMR) and confirmed by single crystal X-ray diffraction (XRD) studies for 2, 5, 6, and 9. Moreover, the geometrical parameters, molecular orbital calculations, and spectral data of 2, 5, 6, and 9 were compared by DFT at the B3LYP/6-311G(d,p) level of theory. There is good agreement between the calculated results and the experimental data. The intermolecular contacts for 2, 5, 6, and 9 were studied by Hirshfeld surface analysis. In addition, the molecular docky study was conducted to investigate the binding patterns of 2, 5, 6, and 9 within the binding site of cyclin-dependent kinase 2 (CDK2) and penicillin-binding protein 1 A. After the docking process, molecular dynamics (MD) simulations for 100 ns were performed on CDK2 and PBP 1 A proteins in the complex with 5. Communicated by Ramaswamy H. Sarma
Finding and Exploring Promising Search Space for the 0-1 Multidimensional Knapsack Problem
Creators: name: Xu, Jitao
name: Li, Hongbo
name: Yin, Minghao
Publisher: name: arXiv
Year: 2022
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: The 0-1 Multidimensional Knapsack Problem (MKP) is a classical NP-hard combinatorial optimization problem with many engineering applications. In this paper, we propose a novel algorithm combining evolutionary computation with the exact algorithm to solve the 0-1 MKP. It maintains a set of solutions and utilizes the information from the population to extract good partial assignments. To find high-quality solutions, an exact algorithm is applied to explore the promising search space specified by the good partial assignments. The new solutions are used to update the population. Thus, the good partial assignments evolve towards a better direction with the improvement of the population. Extensive experimentation with commonly used benchmark sets shows that our algorithm outperforms the state-of-the-art heuristic algorithms, TPTEA and DQPSO, as well as the commercial solver CPlex. It finds better solutions than the existing algorithms and provides new lower bounds for 10 large and hard instances.
Exploring the dark side of tertiary and quaternary structure dynamics in MtbFBPaseII
Creators: name: Greco, Gabriel Luís Cardoso
name: Segretti, Natanael
name: Abad-Zapatero, Celerino
name: Movahedzadeh, Farahnaz
name: Hirata, Mario Hiroyuki
name: Ferreira, Elizabeth Igne
name: Ferreira, Glaucio Monteiro
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Tuberculosis (TB) is a major global cause of mortality, primarily stemming from latent tuberculosis infection (LTBI). Failure to fully treat LTBI can result in drug-resistant forms of TB. Therefore, it is essential to develop novel drugs with unique mechanisms of action to combat TB effectively. One crucial metabolic pathway in Mycobacterium tuberculosis (Mtb), which contributes to TB infection and persistence, is gluconeogenesis. Within this pathway, the enzyme fructose bisphosphatase (FBPase) plays a significant role and is considered a promising target for drug development. By targeting MtbFBPaseII, a specific class of FBPase, researchers have employed molecular dynamics simulations to identify regions capable of binding new drugs, thereby inhibiting the enzyme’s activity and potentially paving the way for the development of effective treatments. Communicated by Ramaswamy H. Sarma
Quantum Fibrations: quantum computation on an arbitrary topological space
Creators: name: Ikeda, Kazuki
Publisher: name: arXiv
Year: 2022
Subjects: subject: Operator Algebras (math.OA)
subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: Using von Neumann algebras, we extend the theory of quantum computation on a graph to a theory of computation on an arbitrary topological space.
Guide for Researchers to Implement FAIR Workflows
Creators: name: Chen, Xiaoli
name: Cousijn, Helena
name: Stathis, Kelly
Publisher: name: Zenodo
Year: 2024

description: Conventional research practice tends to focus on research articles and withhold the procedural documents, supporting datasets, and other relevant materials generated during the research process. However, the limitations of this approach have become increasingly apparent due to phenomena such as 'publish or perish,' the reproducibility crisis, and instances of academic fraud. In response, the research community is advocating for greater accountability, transparency, and openness. This call is being met by various initiatives across disciplinary domains, all aimed at making research data and supporting resources FAIR: findable, accessible, interoperable, and reusable. In this guide, we outline steps researchers can take to share all their research outputs with PIDs and metadata to make their research process and practices FAIR.
Supplementary information: the genetic architecture of polygenic local adaptation and its role in shaping barriers to gene flow
Creators: name: zwaenepoel, arthur
name: Sachdeva, Himani
name: Fraïsse, Christelle
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310403
subject: Biological adaptation
classificationCode: 310412
subject: Speciation and extinction
classificationCode: 310499
subject: Evolutionary biology not elsewhere classified
classificationCode: 310510
subject: Molecular evolution
classificationCode: 310599
subject: Genetics not elsewhere classified

description: Theoretical and numerical investigation in how the genetic architecture of polygenic local adaptation shapes barriers to gene flow between populations.
Additional file 1 of Infectious disease control: from health security strengthening to health systems improvement at global level
Creators: name: Zhang, Xiao-Xi
name: Jin, Yin-Zi
name: Lu, Yi-Han
name: Huang, Lu-Lu
name: Wu, Chuang-Xin
name: Lv, Shan
name: Chen, Zhuo
name: Xiang, Hao
name: Zhou, Xiao-Nong
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Environmental Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Representative works in global health governance.
Gibbs Sampling of Continuous Potentials on a Quantum Computer
Creators: name: Motamedi, Arsalan
name: Ronagh, Pooya
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Data Structures and Algorithms (cs.DS)
subject: Optimization and Control (math.OC)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Gibbs sampling from continuous real-valued functions is a challenging problem of interest in machine learning. Here we leverage quantum Fourier transforms to build a quantum algorithm for this task when the function is periodic. We use the quantum algorithms for solving linear ordinary differential equations to solve the Fokker--Planck equation and prepare a quantum state encoding the Gibbs distribution. We show that the efficiency of interpolation and differentiation of these functions on a quantum computer depends on the rate of decay of the Fourier coefficients of the Fourier transform of the function. We view this property as a concentration of measure in the Fourier domain, and also provide functional analytic conditions for it. Our algorithm makes zeroeth order queries to a quantum oracle of the function. Despite suffering from an exponentially long mixing time, this algorithm allows for exponentially improved precision in sampling, and polynomial quantum speedups in mean estimation in the general case, and particularly under geometric conditions we identify for the critical points of the energy function.
description: 50 pages, version accepted in ICML 2024 / PMLR
Entropy spectrum of Lyapunov exponents for typical cocycles
Creators: name: Mohammadpour, Reza
Publisher: name: arXiv
Year: 2022
Subjects: subject: Dynamical Systems (math.DS)
subject: Mathematical Physics (math-ph)
subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 28A80, 28D20, 37D35, 37H15

description: In this paper, we study the size of the level sets of all Lyapunov exponents. For typical cocycles, we establish a variational relation between the topological entropy of the level sets of Lyapunov exponents and the topological pressure of the generalized singular value function.
description: Some minor changes. Accepted for publication in the Journal of Dynamics and Differential Equations
Additional file 2 of Infectious disease control: from health security strengthening to health systems improvement at global level
Creators: name: Zhang, Xiao-Xi
name: Jin, Yin-Zi
name: Lu, Yi-Han
name: Huang, Lu-Lu
name: Wu, Chuang-Xin
name: Lv, Shan
name: Chen, Zhuo
name: Xiang, Hao
name: Zhou, Xiao-Nong
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Environmental Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 2: Selected evaluation frameworks and tools for global health research and practice.
Targeting of HPV E6 at the binding sites to the host-cell E6AP, p53, and the endoplasmic reticulum-resident chaperone, GRP78
Creators: name: Elfiky, Abdo A.
name: Saied, Hazem R.
name: Ali, Maha A.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Background: Human papillomavirus (HPV) represents an etiological factor for many cancer types, especially cervical cancer. Its oncoprotein E6 sheds drug designers who aim to stop its cellular protein associations, such as p53 and E6AP. Recently, it was discovered that the host-cell chaperone glucose-regulated protein 78 (GRP78) plays a crucial function in HPV infectivity by association with the viral E6 and E7 proteins. Therefore, we aimed to test small molecules inhibitor that could contradict the association between E6 and cellular factors E6AP, GRP78, and p53. Methods: In this study, molecular docking protocol was elaborated to test 115 small molecule compounds against the three binding sites of HPV E6 to the host-cell proteins; E6AP, p53, and GRP78. After that, molecular dynamics simulation and free energy calculations were performed on the best three complexes. Results: The results reveal the potency of 18 compounds against the HPV E6 at different binding sites, which give lower free energies than paclitaxel (positive control). The best two compounds, hypericin, and anabsinthin, could bind effectively and stably during the 100 ns MD simulation period to HPV E6. The calculated average free energies for hypericin and anabsinthin are −18.76 and −14.40 kcal/mol, respectively. They formed stable complexes with the three binding sites by forming hydrophobic contacts. The key residues that stabilize the two ligands in HPV E6 binding sites are V31, Y32, V62, and Y70 (E6AP), P13, C16, T22, I23 and A46 (p53), and M1, V31, L50, L67, and Q107 (GRP78). Conclusions: The best two compounds, hypericin, and anabsinthin, are potential candidates against HPV E6 at the host-cell factors binding sites, hence could block the oncoprotein activity of E6 in infected cells. Further experimental validation is yet to be performed and suggested as future work. Communicated by Ramaswamy H. Sarma
Identifying therapeutic antibacterial peptides against Vibrio cholerae to inhibit the function of Na(+)-translocating NADH-quinone reductase
Creators: name: Baothman, Othman A. S.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Vibrio cholerae is the bacteria responsible for cholera, which is a significant threat to many nations. Curing and treating this infection requires identification of the critical protein and development of a drug to inhibit its function. In this context, Na(+)-translocating NADH-quinone reductase was considered a potential therapeutic target. A library of antibacterial peptides with residue lengths of 50 was screened using a docking method, and the five most potent peptides were selected on the basis of a weighted score derived from solvent accessible surface area and docking score. To investigate the stability of the protein–peptide complex, a 100-ns molecular dynamics simulation was performed. These peptides targeted the native dimeric binding interface of Na(+)-transporting NADH-quinone reductase. This study evaluated the binding affinity and conformational stability of these peptides with the protein using different post-simulation metrics. A peptide, CCL28, exhibited steady RMSD characteristics; nonetheless, it modified the docked conformation but stabilized in the new conformation. This peptide also demonstrated the best performance in addressing the protein’s native binding interface. It demonstrated a binding free energy of −120 kcal/mol with the protein. Principal component analysis (PCA) revealed that the first PC had the lowest conformational variation and the greatest coverage. Eventually, these peptides were also evaluated using steered molecular dynamics, and it was discovered that CCL28 had a greater maximum force than the other five peptides, at 1139.08 kJ/mol/nm. Targeting the native binding interface, we present a CCL28 peptide with a strong potential to block the biological activity of Vibrio cholerae’s Na(+)-translocating NADH-quinone reductase. Communicated by Ramaswamy H. Sarma
The effects of temperature, moisture content, and cricket frass on gas emissions and survival rates in cricket farming at Honghee Village, Kalasin Province, Thailand
Creators: name: Sopa Cansee
name: Siripuk Suraporn
name: Adisak Pattiya
name: Sarawut Saenkham
Publisher: name: Faculty of Engineering, Khon Kaen University
Year: 2024
Subjects: Ammonia
Carbon dioxide
Cricket frass
Cricket survival
Thailand

description: Engineering and Applied Science Research, 51, 5, 588-596
sj-pdf-1-cep-10.1177_03331024231206375 - Supplemental material for An exploratory analysis of clinical and sociodemographic factors in CGRP-induced migraine attacks: A REFORM study
Creators: name: Al-Khazali, Haidar M.
name: Ashina, Håkan
name: Christensen, Rune Häckert
name: Wiggers, Astrid
name: Rose, Kathrine
name: Iljazi, Afrim
name: Schytz, Henrik W.
name: Amin, Faisal Mohammad
name: Ashina, Messoud
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: Endocrinology
subject: Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: Psychology not elsewhere classified
subject: Psychiatry (incl. Psychotherapy)
subject: Neuroscience

description: Supplemental material, sj-pdf-1-cep-10.1177_03331024231206375 for An exploratory analysis of clinical and sociodemographic factors in CGRP-induced migraine attacks: A REFORM study by Haidar M. Al-Khazali, Håkan Ashina, Rune Häckert Christensen, Astrid Wiggers, Kathrine Rose, Afrim Iljazi, Henrik W. Schytz, Faisal Mohammad Amin and Messoud Ashina in Cephalalgia
Identification of novel dual acting ligands targeting the adenosine A2A and serotonin 5-HT1A receptors
Creators: name: Touati, Iman
name: Abdalla, Mohnad
name: Boulaamane, Yassir
name: Al-Hoshani, Nawal
name: Alouffi, Abdulaziz
name: Britel, Mohammed Reda
name: Maurady, Amal
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Medicine
Molecular Biology
Neuroscience
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Mental Health

description: GPCRs are a family of transmembrane receptors that are profoundly linked to various neurological disorders, among which is Parkinson’s disease (PD). PD is the second most ubiquitous neurological disorder after Alzheimer’s disease, characterized by the depletion of dopamine in the central nervous system due to the impairment of dopaminergic neurons, leading to involuntary movements or dyskinesia. The current standard of care for PD is Levodopa, a dopamine precursor, yet the chronic use of this agent can exacerbate motor symptoms. Recent studies have investigated the effects of combining A2AR antagonist and 5-HT1A agonist on dyskinesia and motor complications in animal models of PD. It has been proved that the drug combination has significantly improved involuntary movements while maintaining motor activity, highlighting as a result new lines of therapy for PD treatments, through the regulation of both receptors. Using a combination of ligand-based pharmacophore modelling, virtual screening, and molecular dynamics simulation, this study intends on identifying potential dual-target compounds from IBScreen. Results showed that the selected models displayed good enrichment metrics with a near perfect receiver operator characteristic (ROC) and Area under the accumulation curve (AUAC) values, signifying that the models are both specific and sensitive. Molecular docking and ADMET analysis revealed that STOCK2N-00171 could be potentially active against A2AR and 5-HT1A. Post-MD analysis confirmed that the ligand exhibits a stable behavior throughout the simulation while maintaining crucial interactions. These results imply that STOCK2N-00171 can serve as a blueprint for the design of novel and effective dual-acting ligands targeting A2AR and 5-HT1A. Communicated by Ramaswamy H. Sarma
A computational investigation of action selection in the basal ganglia – role of the GPe
Creators: name: Shreyas M. Suryanarayana
name: Kotaleski, Jeanette Hellgren
name: Gurney, Kevin
name: Grillner, Sten
Publisher: name: F1000 Research Limited
Year: 2018

description: We use a hypothesis driven systems level model of the basal ganglia to investigate the role of the GPe and its newly discovered neuronal subpopulations in action selection.
The Effect of Group Music Therapy on Patient Satisfaction in a Behavioral Health Setting
Creators: name: LaPrade, Madelyn L.
Publisher: name: University of Kentucky Libraries
Year: 2018

description: Abstract:
Patient satisfaction has become increasingly important to medical facilities as a result of reimbursement rates being tied to patient satisfaction scores. Music therapy’s potential to enhance patient satisfaction scores has been explored and several studies exist examining its impact in the medical setting. No studies exist, however, examining how music therapy contributes to patient satisfaction scores in the behavioral health setting. Therefore, the purpose of this study was to compare overall patient satisfaction scores of inpatient psychiatric patients who received group music therapy services with those at the same facility who did not receive group music therapy services.
Participants who attended music therapy group (n=14) received an anonymous, voluntary survey with 10 questions based on the facility’s satisfaction survey and the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey. Participants who did not attend music therapy group (n=15) received the same survey.
Results showed that patients who attended music therapy group reported overall satisfaction scores that were on average 3.02 points higher than participants who did not attend music therapy group. Age correlation and gender differences which may affect patient satisfaction scores are described. The implications for future research and current clinical practice are also discussed.
Copyright: © Madelyn Lindsley LaPrade 2018
Nonlocal optical conductivity of Fermi surface nesting materials
Creators: name: Huang, Xiamin
name: Jiang, Xiao
name: Huang, Bing
name: Li, Zhou
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We investigate the nonlocal optical conductivity of Fermi surface nesting materials which support charge density waves or spin density waves. The nonlocal optical conductivity contains information of correlations in electron fluids which could not be accessed by standard optical probes. Half metal emerges from doping a charge density wave and similarly spin-valley half metal emerges from doping a spin density wave. Based on the parabolic band approximation, we find the Drude peak is shifted to higher frequency and splits into two peaks in the nonlocal optical conductivity. We attribute this to the two Fermi velocities in the half-metal or spin-valley half metal states.
description: 16 pages, 12 figures, to appear on Science China Physics, Mechanics & Astronomy
Voting on Cyclic Orders, Group Theory, and Ballots
Creators: name: Crisman, Karl-Dieter
name: Holleran, Abraham
name: Martin, Micah
name: Noonan, Josephine
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Representation Theory (math.RT)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: 91B12 (Primary) 91B14, 20C05 (Secondary)

description: A cyclic order may be thought of informally as a way to seat people around a table, perhaps for a game of chance or for dinner. Given a set of agents such as $\{A,B,C\}$, we can formalize this by defining a cyclic order as a permutation or linear order on this finite set, under the equivalence relation where $A\succ B\succ C$ is identified with both $B\succ C\succ A$ and $C\succ A\succ B$. As with other collections of sets with some structure, we might want to aggregate preferences of a (possibly different) set of voters on the set of possible ways to choose a cyclic order.
 However, given the combinatorial explosion of the number of full rankings of cyclic orders, one may not wish to use the usual voting machinery. This raises the question of what sort of ballots may be appropriate; a single cyclic order, a set of them, or some other ballot type? Further, there is a natural action of the group of permutations on the set of agents. A reasonable requirement for a choice procedure would be to respect this symmetry (the equivalent of neutrality in normal voting theory).
 In this paper we will exploit the representation theory of the symmetric group to analyze several natural types of ballots for voting on cyclic orders, and points-based procedures using such ballots. We provide a full characterization of such procedures for two quite different ballot types for $n=4$, along with the most important observations for $n=5$.
description: 29 pages, to be published in conference proceedings from AMS Special Session on The Mathematics of Decisions, Elections and Games, 2022
vaginal microbiome of pregnant women affected by vulvovaginal candidiasis
Creators: name: 张红琴(Hongqing Zhang)
Publisher: name: CNGB
Year: 2024
Subjects: Raw sequence reads
Environment

description: This study aims to characterize the vaginal microbiome in pregnant women with vulvovaginal candidiasis and its impact on their offspring's meconium microbiome.