cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Design of prodrug for stereoisomers of omapatrilat to cross the blood-brain barrier using docking, homology modeling, MD, and QM/MM methods
Creators: name: Sargolzaei, Mohsen
name: Nikoofard, Hossein
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Hematology
subject: Plant Biology

description: In this study, we designed a suitable ester prodrug for omapatrilat to penetrate the blood-brain barrier and treat CNS diseases. Based on the ADMET properties, the methyl carboxylate ester of omapatrilat was chosen from among several prodrug structures. Sixteen methyl carboxylate esters were constructed for omapatrilat. The structure of brain carboxylesterase was derived via homology modeling, and molecular docking was used to determine the most potent stereoisomers against brain carboxylesterase. The top three stereoisomer complexes, and the apo form of the protein, were then considered using molecular dynamics simulation and MM/GBSA analysis. Following the simulation, structural analysis was performed using RMSD, RMSF, Rg, and hydrogen bond analysis tools. Our data demonstrated that the prodrug of RSSR is a suitable structure for crossing the blood-brain barrier and binding to brain carboxylesterase. In addition, we found via QM/MM calculation that the catalytic reaction of the prodrug of RSSR against brain carboxylesterase occurs via two steps, including acylation and diacylation steps. Based on our findings, we propose a clinical trial of a methyl carboxylate ester prodrug of omapatrilat’s RSSR for the treatment of brain diseases. Communicated by Ramaswamy H. Sarma
Synthesis and characterizations of arsenic doped FeSe bulks
Creators: name: Singh, Priya
name: Manasa, Manasa
name: Azam, Mohammad
name: Zajarniuk, Tatiana
name: Kwatek, Konrad
name: Cetner, Tomasz
name: Morawski, Andrzej
name: Mizeracki, Jan
name: Singh, Shiv J.
Publisher: name: arXiv
Year: 2025
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: FeSe(11) family has a simple crystal structure belonging to iron-based superconductors (FBS) and has many stable phases including hexagonal and tetragonal structures, but only the tetragonal phase exhibits the superconductivity. In this study, we have investigated the effects of chemical pressure induced by As-doping at Se-sites in the FeSe system by preparing a series of FeSe1-xAsx (x = 0.005, 0.01, 0.02, 0.05, 0.1, and 0.2) bulks. A broad characterization has been performed on these samples using structural, microstructural, transport, and magnetic measurements. The obtained lattice parameters are increased by As-doping, which suggests the successful insertion of As at Se-sites into the tetragonal lattice for low doping contents up to 5%, whereas the higher As-substitution appears in the form of the FeAs impurity phase. The temperature dependence of the resistivity of all samples has similar behaviour and depicts the highest onset transition temperature of around 11.5 K, but the zero resistivity is not reached until the measured temperature of 7 K, which could be due to the presence of the impurity phases. Our study suggests that a dopant with a large ionic radius, i.e., Arsenic, promotes the formation of the hexagonal phase of the 11 family and is effective for a small amount of doping level for the superconducting properties, whereas higher As-doping levels reduce the superconducting properties.
description: 18 pages, 6 figures
Exploring the molecular interactions and binding affinity of resveratrol and calcitriol with RAGE and its intracellular proteins and kinases involved in colorectal cancer
Creators: name: Muthyalaiah, Yadav Sangeeta
name: Arockiasamy, Sumathy
name: A, Abhinand P.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Colorectal cancer (CRC) burden is progressively increasing in young population due to dietary and lifestyle pattern. Advanced glycation end products (AGEs), one of the dietary compounds, form complex aggregates with proteins, lipids, and nucleic acids distorting their structure and function. AGE’s pro-tumorigenic role is mediated through the receptor for AGEs (RAGE) triggering an array of signaling pathways. The current study aimed to target AGE-RAGE axis signaling proteins and kinases at multiple levels with calcitriol (CAL) and trans-resveratrol (RES) through in silico analysis using molecular docking (MD), molecular dynamic simulation(MDS), MM-PBSA analysis, and in vitro study. In silico analysis of CAL and RES showed significant binding affinity toward RAGE and its signaling proteins such as NF-kB, PI3K/AKT, ERK1/2, and PKC compared to its reference inhibitors through better hydrogen, hydrophobic, pi-pi stacking interactions. MD and MDS studies have revealed stable and compact protein-ligand complexes. Binding free energies of protein-ligand complex were estimated using MM/PBSA analysis thatprovided an assessment of overall interacting free energies of complexes and revealed the presence of low binding energy within the active site. Furthermore, in the in vitro study, methylglyoxal (MG), an AGE-precursor showed a proliferative effect on HCT116, however, CAL and RES showed an inhibitory effect against MG induced effect with an IC50 value of 51 nM and 110 µM respectively. Thus, the study suggests the possible target binding sites of AGE-RAGE signaling proteins and kinases with CAL and RES, thereby exploiting it for developing CAL with RES as adjuvant therapy along with chemo drug for CRC. Communicated by Ramaswamy H. Sarma
Predictive AI Models for Emergency Room Triage
Creators: name: Researchscholar
Publisher: name: Zenodo
Year: 2025

description: Emergency room (ER) triage is a critical process that prioritizes patients based on the severity of their conditions, aiming to ensure timely care in high-pressure environments. However, traditional triage methods are often subjective and may lead to delays in treatment, overcrowding, and suboptimal patient outcomes. This paper explores the role of predictive Artificial Intelligence (AI) models in enhancing ER triage by providing data-driven, real-time insights to optimize decision-making, improve patient prioritization, and streamline resource allocation. We examine various AI techniques, including machine learning (ML), deep learning (DL), and natural language processing (NLP), highlighting their application in analyzing structured and unstructured data such as electronic health records (EHRs), patient vital signs, medical imaging, and clinical notes. The paper also discusses the importance of data preprocessing, including handling missing values, data normalization, and feature selection, to ensure accurate model predictions. Through case studies and clinical implementations, we demonstrate how AI models have been successfully integrated into real-world ER settings to predict patient acuity, early deterioration, and patient outcomes. Ethical, legal, and practical considerations such as data privacy, algorithmic bias, and model transparency are also addressed. The paper concludes with a discussion on the future directions of AI in ER triage, including the integration of multimodal data, real-time monitoring, and personalized care. Predictive AI has the potential to significantly enhance ER efficiency and improve patient care, making it a valuable tool for modern healthcare systems.
Stony Brook Summer Music Festival Press Release, June 13, 1955
Creators: name: Stony Brook Concert Community Concerts
Publisher: name: Unknown
Year: 1955
Subjects: Stony Brook
Concert halls
Concerts
Amphitheaters
Music festivals
Publicity

description: A press release announcing the commencement of the very first Summer Music Festival, listing many familiar names seen in other sources regarding the first concert. The release announces "to the name of Tanglewood, Aspen and Hollywood and Stony Brook, Long Island". It lists a capacity crowd of 2,000 expected. It describes Long Island as "culturally and geographically" being 'well suited for a major music festival... As one of the most important and fastest growing territories in the United States...with leaders in the arts and sciences." (Drafts of releases are housed in physical archive.)
DFT calculations of copper complexes mimicking superoxide dismutase and docking studies and molecular dynamics of the transition metal complex binding to serum albumin
Creators: name: da Silva, Talis Uelisson
name: Silva, Everton Tomaz
name: Albuquerque, Magaly Girão
name: da Silva Lima, Camilo Henrique
name: de Paula Machado, Sérgio
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Superoxide dismutase (SOD) is a metalloenzyme whose antioxidant activity is mimicked by some transition metal complexes, and such ability can be added in proteins such as the bovine serum albumin (BSA), creating a hybrid protein. In this work, density functional theory (DFT) calculations of three Cu(II)-complexes of general formula [CuL2phen] (phen = phenanthroline; C1, L = mefenamate; C2, L = tolfenamate; C3, L = flufenamate) with SOD-like activity, and docking and molecular dynamics (MD) simulations of these complexes with the BSA were performed. The DFT calculations revealed that the complex reduction involves Cu(II) → Cu(I) reduction, the theoretical electron affinity (EA) correlated with the SOD-like activity (IC50), and the contribution of the phenanthroline ligand and the metal in LUMO it’s related with the complex-protein interaction (KVS). The docking and MD simulations revealed the binding site of the complexes in BSA and the residues involved in the binding. The stability of the Cu(II) and Cu(I) forms of the complexes in the site indicated that the catalysis promoted by these complexes occurs in the same region of the BSA and that their mimetic activity can be incorporated into BSA, creating a hybrid protein (BSA with SOD activity) Communicated by Ramaswamy H. Sarma
Investigation of Insect Abundance near the Iona Island Wastewater Treatment Plant : Implications for Vancouver’s Aerial Insectivore Populations
Creators: name: Robinson-Leith, Emilie
name: Gooding, Grace
name: Peng, Shaoxuan
name: Ladki, Lana
name: Ni, Luke
Publisher: name: The University of British Columbia
Year: 2024

description: In response to the significant population decline of avian aerial insectivores in North America, we collaborated with Birds Canada to investigate trends in both aerial insectivores and their insect prey near the Iona Island Wastewater Treatment Plant (IIWWTP). The IIWWTP is located in Richmond, BC and is one of five wastewater treatment plants serving the Vancouver area. It is situated near the habitats of many aerial insectivore species and is near a stopover for millions of birds as they migrate along the Pacific Flyway. In 2022, Metro Vancouver approved plans to continue the expansion of the IIWWTP. In this study, insect biomass data were analyzed to investigate short-term seasonal changes in the insect community at two study sites (high-vegetation and low-vegetation) near the IIWWTP. Insect biomass was compared to precipitation, temperature, and vegetation level to assess for a correlation. Using eBird community science observation data, we investigated long-term trends in aerial insectivore populations in Iona Region (IR) and the Greater Metro Vancouver Area (GMVA). Daily average recorded individuals per checklist (RIC) was used as an indicator for aerial insectivore abundance. Linear regressions were performed on three bird species’ daily average RIC and insect biomass to test for a relationship between specific aerial insectivore species and their insect prey. Significantly higher insect biomass was found at the high-vegetation site near the IWWTP. Total collected insect biomass and precipitation were significantly negatively correlated across all nine bird groups, while total collected insect biomass and temperature were only significantly positively correlated in two. There were no significant declines in aerial insectivore populations near the IIWWTP from 2004-2023 suggesting that aerial insectivores in Vancouver, BC are not facing the same steep declines as populations elsewhere. There was an observed correlation between insects and aerial insectivores, suggesting a significant predator-prey relationship. Additionally, there was a statistically significant correlation between beetle (Coleoptera) biomass and Barn Swallows (Hirundo rustica). These results suggest that minimizing the disruption of insect communities during the IIWWTP expansion through maintenance of vegetation and aquatic habitats will help ensure the continued protection of the local avian population.
Cheminformatics bioprospection of selected medicinal plants metabolites against trypsin cleaved VP4 (spike protein) of rotavirus A
Creators: name: Lanrewaju, Adedayo Ayodeji
name: Enitan-Folami, Abimbola Motunrayo
name: Nyaga, Martin M.
name: Sabiu, Saheed
name: Swalaha, Feroz Mahomed
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
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: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Rotaviruses have continued to be the primary cause of acute dehydrating diarrhoea in children under five years of age despite the global introduction of four World Health Organization (WHO) prequalified oral vaccines in over 106 countries. Currently, no medication is approved by the Food and Drug Administration (FDA) specifically for treating rotavirus A-induced diarrhoea. Consequently, it is important to focus on developing prophylactic and curative therapeutics to combat rotaviral infections. For the first time, this study computationally screened and identified metabolites from Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum as potential novel inhibitors with broad-spectrum activity against VP5* and VP8* (spike protein) of rotavirus A (RVA). The initial top 20 metabolites identified through molecular docking were further filtered using drug-likeness and pharmacokinetics parameters. The molecular properties of the resulting top-ranked compounds were predicted by conducting density functional theory (DFT) calculations, while molecular dynamics (MD) simulation revealed their thermodynamic compatibility with a significant affinity towards VP8* than VP5*. Except for ellagic acid (−11.78 kcal/mol), the lead compounds had higher binding free energy than the reference standard (VP5* (−11.81 kcal/mol), VP8* (−14.12 kcal/mol)) with 2SG (−20.98 kcal/mol) and apigenin-4'-glucoside (−23.56 kcal/mol) having the highest affinity towards VP5* and VP8*, respectively. Of all the top-ranked compounds, better broad-spectrum affinities for both VP5* and VP8* than tizoxanide were observed in 2SG (VP5* (−20.98 kcal/mol), VP8* (−20.13 kcal/mol)) and sericetin (VP5* (−20.46 kcal/mol), VP8* (−18.31 kcal/mol)). While the identified leads could be regarded as potential modulators of the investigated therapeutic targets for effective management of rotaviral infection, additional in vitro and in vivo evaluation is strongly recommended, and efforts are on-going in this regard. Communicated by Ramaswamy H. Sarma
Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein
Creators: name: Verma, Jigyasa
name: Kaushal, Neha
name: Manish, Manish
name: Subbarao, Naidu
name: Shakirova, Venera
name: Martynova, Ekaterina
name: Liu, Rongzeng
name: Hamza, Shaimaa
name: Rizvanov, Albert A.
name: Khaiboullina, Svetlana F.
name: Baranwal, Manoj
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The emergence of the new SARS-CoV-2 variants has led to major concern regarding the efficacy of approved vaccines. Nucleocapsid is a conserved structural protein essential for replication of the virus. This study focuses on identifying conserved epitopes on the nucleocapsid (N) protein of SARS-CoV-2. Using 510 unique amino acid sequences of SARS-CoV-2 N protein, two peptides (193 and 215 aa) with 90% conservancy were selected for T cell epitope prediction. Three immunogenic peptides containing multiple T cell epitopes were identified which were devoid of autoimmune and allergic immune response. These peptides were also conserved (100%) in recent Omicron variants reported in Jan-August 2023. HLA analysis reveals that these peptides are predicted as binding to large number of HLA alleles and 71–90% population coverage in six continents. Identified peptides displayed good binding score with both HLA class I and HLA class II molecules in the docking study. Also, a vaccine construct docked with TLR-4 receptor displays strong interaction with 20 hydrogen bonds and molecular simulation analysis reveals that docked complex are stable. Additionally, the immunogenicity of these N protein peptides was confirmed using SARS-CoV-2 convalescent serum samples. We conclude that the identified N protein peptides contain highly conserved and antigenic epitopes which could be used as a target for the future vaccine development against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
Problématique de la production et de la consommation des safous dans le village Sese Mulutu, groupement Mangungu, Territoire de Bulungu (Kwilu) en République Démocratique du Congo
Creators: name: MUKOKO L'AMBEM Willy
name: AGUGA KWAKENDA Tony
name: MAKASHINGA MUDILA Crispin
name: PINDO KULONGESA Eustache
name: MUZEYA KISENZELE Florent
name: KAMIZELO KIMEYA Macaire
name: GALONJI MUBANDA Martin
name: MBIDIKA FUMUNEZMBA Alvaro
name: KAMBINZU MBEDI Eric
Publisher: name: Zenodo
Year: 2025

description: Cet article explore les enjeux liés à la production et à la consommation des safous dans le village Sese Mulutu dans le secteur Kipuka, territoire de Bulungu au Sud-ouest de la République Démocratique du Congo.  Bien que ce fruit soit nutritif et prisé pour sa saveur, sa culture fait face à plusieurs défis dans ce village. Le changement climatique impacte la saisonnalité et la qualité des récoltes, tandis que les pratiques agricoles traditionnelles limitent la productivité. Il faut joindre à ces défis les maladies et les ravageurs ainsi que les difficultés liées à la question de transport et de conditionnement des fruits. Les producteurs manquent d'accès à des semences de qualité et à des outils modernes, ce qui entrave l'augmentation de la production. De plus, l'absence d'infrastructures adéquates pour le stockage constitue un autre défi. Côté consommation, des facteurs culturels et économiques poussent certains ménages à privilégier la vente. L'article suggère des solutions pour améliorer la situation, telles que la formation des agriculteurs aux techniques modernes et la sensibilisation des consommateurs aux bienfaits nutritionnels du safou. En renforçant les chaînes de valeur locales et en s’intéressant à la culture de safoutier, Sese Mulutu pourrait non seulement améliorer son système alimentaire, mais aussi améliorer les moyens financiers dans la vente des safous et soutenir l’économie d’une population qui vit dans la paupérisation.
Activity of comet 7P/Pons-Winnecke during the 2021 apparition
Creators: name: Mariblanca-Escalona, Irene
name: Lara, Luisa M.
name: Moreno, Fernando
name: Gutiérrez, Pedro J.
name: Evangelista-Santana, Marçal
Publisher: name: arXiv
Year: 2025
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Comet 7P/Pons-Winnecke was observed from the Calar Alto Observatory (Spain) for four months during the 2021 inbound apparition. Broad-band visible images were taken between 1.71 and 1.25 AU pre-perihelion, while long-slit spectrophotometric data were taken at $\sim$ 1.25 AU pre-perihelion. This dataset has been complemented with three $r$-Sloan images observed from Zwicky Transient Facility (ZTF) to model the physical properties and loss rate of the dust with a forward Monte Carlo dust tail code. The model fits the observed isophotes well for most observations. The peak dust production rate was measured at 83 kg s$^{-1}$, 15 days after perihelion. The particle terminal speed ranges from 3 m s$^{-1}$ for 0.1 m particles to 23 m s$^{-1}$ for 5 $μ$m particles. Regarding the gas production from spectra, CN and C$_2$ show asymmetric emission between the sunward and antisunward directions beyond the data uncertainties and error propagation, while a clear asymmetry for C$_3$ cannot be definitively claimed. Average production rates for CN, C$_2$, and C$_3$ near 2021 perihelion are 1.15 $\times 10^{24}$, 2.32$\times 10^{24}$, and 1.69$\times 10^{23}$ s$^{-1}$, respectively. The dust-to-gas mass ratio value is estimated to be around 2, suggesting a dust-rich composition. Based on the gas composition and the $Afρ$ value, we classify 7P/Pons-Winnecke as having a typical composition for Jupiter Family comets, with some C$_3$ depletion. Given the limited previous knowledge, our work contributes to expanding the understanding of the activity and characteristics of 7P/Pons-Winnecke.
description: 10 pages, 9 figures
Mind the Gap: Detecting Black-box Adversarial Attacks in the Making through Query Update Analysis
Creators: name: Park, Jeonghwan
name: McLaughlin, Niall
name: Alouani, Ihsen
Publisher: name: arXiv
Year: 2025
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Adversarial attacks remain a significant threat that can jeopardize the integrity of Machine Learning (ML) models. In particular, query-based black-box attacks can generate malicious noise without having access to the victim model's architecture, making them practical in real-world contexts. The community has proposed several defenses against adversarial attacks, only to be broken by more advanced and adaptive attack strategies. In this paper, we propose a framework that detects if an adversarial noise instance is being generated. Unlike existing stateful defenses that detect adversarial noise generation by monitoring the input space, our approach learns adversarial patterns in the input update similarity space. In fact, we propose to observe a new metric called Delta Similarity (DS), which we show it captures more efficiently the adversarial behavior. We evaluate our approach against 8 state-of-the-art attacks, including adaptive attacks, where the adversary is aware of the defense and tries to evade detection. We find that our approach is significantly more robust than existing defenses both in terms of specificity and sensitivity.
description: 14 pages
Probing the interaction and aggregation of lysozyme in presence of organophosphate pesticides: a comprehensive spectroscopic, calorimetric, and in-silico investigation
Creators: name: Dudure, Rushali
name: Joshi, Ritika
name: Pritam, Pulak
name: Panda, Alok Kumar
name: Jadhao, Manojkumar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer

description: Organophosphorus pesticides (OPs) are widely used in agriculture and may contaminate food or water, leading to potential health risks. However, there are few reports on the effect of OPs on protein conformation and aggregation. Hence, in this paper, we have characterized the impact of two OPs, chlorpyrifos (CPF) and methyl parathion (Para), on the model protein HEWL using biophysical and computational methods. The steady-state and time-resolved spectroscopy, Circular dichroism (CD), molecular dynamics simulation, and isothermal titration calorimetry were employed to investigate the binding interactions between HEWL and OPs. The steady-state and time-resolved fluorescence spectroscopy confirm the presence of both static and dynamic quenching between OPs and proteins. Based on fluorescence, MD, and CD results, it was found that the OPs not only show strong binding but also destabilize the protein structure and alter the secondary and tertiary structure of the protein. The molecular docking results showed that OPs entered the binding pocket of the HEWL molecule and interacted through hydrophobic and hydrogen bond interactions. The thermodynamic studies indicated that the binding was spontaneous and OPs have shown an effect on the aggregation process of HEWL. Finally, the protein aggregation process was studied using fluorescence and SDS-PAGE studies in the presence of both the OPs and found to enhance the aggregation process in the presence of OPs. These results provide insights into the potential health risks associated with OPs and highlight the importance of understanding their interactions with biological macromolecules. Communicated by Ramaswamy H. Sarma The graphical abstract presents the thermodynamic stability of the complex formed between lysozyme and organopesticides and its influence on lysozyme aggregation.
title: Sauce :
title: Directrices para la ejecución del examen de la distinción, la homogeneidad y la estabilidad.
titleType: Subtitle
Creators: name: International Union For The Protection Of New Varieties Of Plants..,
Publisher: name: International Union for the Protection of New Varieties of Plants
Year: 0
Subjects: New Varieties of Plants
Willow
Group identity.

description: La finalidad de estas directrices (“directrices de examen”) es elaborar los principios que figuran en la Introducción General (documento TG/1/3) y sus documentos TGP conexos, con objeto de que sirvan de orientación práctica y detallada para el examen armonizado de la distinción, homogeneidad y estabilidad (DHE) y en particular, para identificar los caracteres apropiados para el examen DHE y producir descripciones armonizadas de variedades.
Automatic Drywall Analysis for Progress Tracking and Quality Control in Construction
Creators: name: Trzeciakiewicz, Mariusz
name: Barreiro, Aleixo Cambeiro
name: Gard, Niklas
name: Hilsmann, Anna
name: Eisert, Peter
Publisher: name: arXiv
Year: 2025
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Digitalization in the construction industry has become essential, enabling centralized, easy access to all relevant information of a building. Automated systems can facilitate the timely and resource-efficient documentation of changes, which is crucial for key processes such as progress tracking and quality control. This paper presents a method for image-based automated drywall analysis enabling construction progress and quality assessment through on-site camera systems. Our proposed solution integrates a deep learning-based instance segmentation model to detect and classify various drywall elements with an analysis module to cluster individual wall segments, estimate camera perspective distortions, and apply the corresponding corrections. This system extracts valuable information from images, enabling more accurate progress tracking and quality assessment on construction sites. Our main contributions include a fully automated pipeline for drywall analysis, improving instance segmentation accuracy through architecture modifications and targeted data augmentation, and a novel algorithm to extract important information from the segmentation results. Our modified model, enhanced with data augmentation, achieves significantly higher accuracy compared to other architectures, offering more detailed and precise information than existing approaches. Combined with the proposed drywall analysis steps, it enables the reliable automation of construction progress and quality assessment.
Evaluation of Rapanone and Nectandrin B as novel inhibitors for targeting the metastatic regulator protein BACH1 using breast cancer cell line Mcf-7
Creators: name: Arunachalam, Abirami
name: Sankar, Muthumanickam
name: Pandi, Boomi
name: Paul, Soumi
name: Thilagar, Sivasudha
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Cancer formation is defined as the unrestrained proliferation of cells due to various factors acting as a causing agent. A limited number of over-expressed transcription factors are contributed to the development of numerous types of cancer. The metastatic regulator protein BTB And CNC Homology 1 (BACH1) is Cap ‘N’ Collar (CNC) and it belongs to a basic region leucine zipper (bZIP) family. The presence of the least level concentration of intracellular heme BACH1 forms heterodimers with musculo aponeurotic fibrosarcoma (sMAF) proteins and inhibits or induces the target gene expression. Based on the previous studies, BACH1 plays a critical player in the conditions of senescence and oxidative stress, cycling of cell life, heme degradation pathway and cancer, especially in metastasis. Discovering new anti-cancer drugs (identification of bioactive compounds) stages finally needs to inhibit the target protein. This present study is aimed to screen and identify stability, binding affinity and analysis of pharmacokinetics of selected compounds through structural screening, ADMET, DFT and MESP. From this study, it is revealed that Rapanone and Nectandrin B have the potential to alter the degree of gene expression via binding with the BACH1 allosteric region which will further change the degree of expression of BACH1 downstream target genes involved in the regulation of cancer progression particularly in metastasis. The two plant origin compounds Rapanone and Nectandrin B might be novel candidates for developing anti-cancer drugs. The predicted compounds were further validated through in-vitro experimental approaches. Communicated by Ramaswamy H. Sarma.
Intrinsic and Extrinsic Factor Disentanglement for Recommendation in Various Context Scenarios
Creators: name: Su, Yixin
name: Jiang, Wei
name: Lin, Fangquan
name: Yang, Cheng
name: Erfani, Sarah M.
name: Gan, Junhao
name: Zhao, Yunxiang
name: Li, Ruixuan
name: Zhang, Rui
Publisher: name: arXiv
Year: 2025
Subjects: subject: Information Retrieval (cs.IR)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: In recommender systems, the patterns of user behaviors (e.g., purchase, click) may vary greatly in different contexts (e.g., time and location). This is because user behavior is jointly determined by two types of factors: intrinsic factors, which reflect consistent user preference, and extrinsic factors, which reflect external incentives that may vary in different contexts. Differentiating between intrinsic and extrinsic factors helps learn user behaviors better. However, existing studies have only considered differentiating them from a single, pre-defined context (e.g., time or location), ignoring the fact that a user's extrinsic factors may be influenced by the interplay of various contexts at the same time. In this paper, we propose the Intrinsic-Extrinsic Disentangled Recommendation (IEDR) model, a generic framework that differentiates intrinsic from extrinsic factors considering various contexts simultaneously, enabling more accurate differentiation of factors and hence the improvement of recommendation accuracy. IEDR contains a context-invariant contrastive learning component to capture intrinsic factors, and a disentanglement component to extract extrinsic factors under the interplay of various contexts. The two components work together to achieve effective factor learning. Extensive experiments on real-world datasets demonstrate IEDR's effectiveness in learning disentangled factors and significantly improving recommendation accuracy by up to 4% in NDCG.
description: 32 pages, 13 figures, 11 tables. Published on Transactions of Information Systems
The binding mechanism of failed, in processing and succeed inhibitors target SARS-CoV-2 main protease
Creators: name: Hongyu, Hu
name: Wu, Tong
name: He, Fengming
name: Chao, Ma
name: Huang, Junjie
name: Wang, Xiaofeng
name: Niu, Zhangming
name: Tang, Bowen
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Since the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), several variants have caused a persistent pandemic. Consequently, it is crucial to develop new potential anti-SARS-CoV-2 drugs with specificity. To minimize potential failures and preserve valuable clinical resources for the development of other useful drugs, researchers must enhance their understanding of the interactions between drugs and SARS-CoV-2. While numerous crystal structures of the SARS-CoV-2 main protease (SCM) and its inhibitors have been reported, they provide only static snapshots and fail to capture the dynamic nature of SCM/inhibitor interactions. Herein, we conducted molecular dynamics simulations for five SCM complexes: ritonavir (SCM/RTV), lopinavir (SCM/LPV), the identified inhibitor N3 (SCM/N3), the approved inhibitor ensitrelvir (SCM/ESV), and the approved drug nirmatrelvir (SCM/NMV). Additionally, we explored the potential for covalent bond formation in the N3 and NMV inhibitors through QM/MM calculations using Umbrella sampling. The results show that the binding site is highly flexible to fit those five different inhibitors and each compound has its unique binding mode at the same binding site. Moreover, the binding affinities of positive and negative inhibitors to SCM exhibit significant differences. By gaining insights into the dynamics, we can potentially elucidate why lopinavir/ritonavir, initially considered promising, failed to effectively treat COVID-19. Furthermore, understanding the mechanistic aspects of N3 and NMV inhibition on SCM not only contributes to rational drug discovery against COVID-19 but also aids future studies on the catalytic mechanisms of main proteases in other novel coronaviruses. Communicated by Ramaswamy H. Sarma
Comparing the Carbon Impacts of Retrofit versus Redevelopment Options for the Alder Bay Housing Co-op in False Creek, Vancouver, British Columbia
Creators: name: Zhu, Bellie
name: Zhu, Corrine
name: Lai, Hayley
name: Wu, Reta
Publisher: name: The University of British Columbia
Year: 2024

description: This research, conducted by a team of students in ENVR400 at the University of British Columbia, investigates the carbon emissions of retrofit versus redevelopment options for the Alder Bay Housing Co-op in False Creek South Neighborhood, Vancouver. The study emerges from an urgent need for low carbon urban planning solutions, particularly in light of upcoming lease expirations, the housing crisis, and Vancouver’s push towards net-zero carbon developments (City of Vancouver, 2024).
Supplementary document for Free-space creation of a perfect vortex beam with fractional topological charge - 6204327.pdf
Creators: name: Wang, Guanxue
name: weng, xiaoyu
name: Kang, Xiangyu
name: Li, Ziyan
name: Chen, Keyu
name: Gao, Xiumin
name: zhuang, songlin
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Classical and Physical Optics

description: Supplemental Document
Towards a Study of Low Energy Antiproton Annihilations on Nuclei
Creators: name: Kraxberger, Viktoria
name: Bumbar, Marcus
name: Gligorova, Angela
name: Amsler, Claude
name: Bayo, Matias
name: Breuker, Horst
name: Cerwenka, Matti
name: Costantini, Giovanni
name: Ferragut, Rafael
name: Giammarchi, Marco
name: Gosta, Giulia
name: Higaki, Hiroyuki
name: Hunter, Eric D.
name: Killian, Carina
name: Kuroda, Naofumi
name: Leali, Marco
name: Maero, Giancarlo
name: Malbrunot, Chloe
name: Mascagna, Valerio
name: Matsuda, Yasuyuki
name: Migliorati, Stefano
name: Murtagh, Daniel
name: Nanda, Amit
name: Nowak, Lilian
name: Romé, Massimiliano
name: Simon, Martin C.
name: Tajima, Minori
name: Toso, Valerio
name: Ulmer, Stefan
name: Venturelli, Luca
name: Weiser, Alina
name: Widmann, Eberhard
name: Yamazaki, Yasunori
Publisher: name: arXiv
Year: 2025
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: A study of antiproton annihilations at rest on thin solid targets is underway at the ASACUSA facility, which now features a dedicated beam line for slow extraction at 250 eV. The experiment will employ new technologies, such as the Timepix4 ASICs coupled to silicon sensors, to measure the total multiplicity, energy, and angular distribution of various prongs produced in thin solid targets. A detection system consisting of seven Timepix4, covering most of the solid angle, is being constructed. A 3D annihilation vertex reconstruction algorithm from particle tracks in the single-plane detectors has been developed using Monte Carlo simulations. The measurements will enable a study of pbar-nucleus interactions, their dependence on nucleus mass and branching ratios. The results will be used to assess and potentially improve various simulation models.
description: Submitted to PoS, Proceedings for the International Conference on Exotic Atoms and Related Topics and Conference on Low Energy Antiprotons, EXA/LEAP2024
The News about the News : Exploring the Impact of Meta’s Social Media News Ban on the Quality and Quantity of Online News in Canada
Creators: name: Waatainen, Henry
Publisher: name: The University of British Columbia
Year: 2024

description: Little has been written about the effects that social media news bans (SMNBs) have on journalism and, as a potential consequence, democracy. This paper provides an initial assessment of whether SMNBs—in particular, those that are isolated to specific countries and social media platforms—incentivize online news organizations to shift their publication patterns in ways that could be detrimental to citizen participation in democracy. More specifically, an original dataset of Canadian newspaper headlines from before and after Meta’s 2023 SMNB is analyzed for correlations between the existence of an SMNB and the amount of sensationalized and foreign news published. The results indicate no observable effect on either outcome. Therefore, this study does not find that SMNBs pose significant consequences for the quality and quantity of domestic journalism in the sample examined. However, further research is necessary in order to determine what broader impact such bans may have on individuals’ capacity to make informed democratic decisions.
Insight into the corrosion inhibiting potential and anticancer activity of 1-(4-methoxyphenyl)-5-methyl-N’-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide via computational approaches
Creators: name: Oyeneyin, Oluwatoba Emmanuel
name: Ibrahim, Abdulwasiu
name: Ipinloju, Nureni
name: Ademoyegun, Adeniyi John
name: Ojo, Nathanael Damilare
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
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: Cancer is a major health concern globally. Orthodox and traditional medicine have actively been explored to manage this disease. Also, corrosion is a natural catastrophe that weakens and deteriorates metallic structures and their alloys causing major structural failures and severe economic implications. Designing and exploring multi-functional materials are beneficial since they are adaptive to different fields including engineering and pharmaceutics. In this study, we examined the anti-corrosion and anti-cancer potentials of 1-(4-methoxyphenyl)-5-methyl-N’-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide (MAC) using computational approaches. The molecular reactivity descriptors and charge distribution parameters of MAC were studied in gas and water at density functional theory (DFT) at B3LYP/6-311++G(d,p) theory level. The binding and mechanism of interaction between MAC and iron surface was studied using Monte Carlo (MC) and molecular dynamics (MD) simulation in hydrochloric acid medium. From the DFT, MC, and MD simulations, it was observed that MAC interacted spontaneously with iron surface essentially via van der Waal and electrostatic interactions. The near-parallel alignment of the corrosion inhibitor on iron plane facilitates its adsorption and isolation of the metal surface from the acidic solution. Further, the compound was docked in the binding pocket of anaplastic lymphoma kinase (ALK: 4FNZ) protein to assess its anti-cancer potential. The binding score, pharmacokinetics, and drug-likeness of MAC were compared with the reference drug (Crizotinib). The MAC displayed binding scores of −5.729 kcal/mol while Crizotinib has −3.904 kcal/mol. MD simulation of the complexes revealed that MAC is more stable and exhibits more favourable hydrogen bonding with the ALK receptor’s active site than Crizotinib. Communicated by Ramaswamy H. Sarma
Improving Merge Sort and Quick Sort Performance by Utilizing Alphadev's Sorting Networks as Base Cases
Creators: name: Aly, Anas Gamal
name: Jensen, Anders E.
name: ElAarag, Hala
Publisher: name: arXiv
Year: 2025
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: Computational Complexity (cs.CC)
subject: FOS: Computer and information sciences

description: Recent work by Google DeepMind introduced assembly-optimized sorting networks that achieve faster performance for small fixed-size arrays (3-8). In this research, we investigate the integration of these networks as base cases in classical divide-and-conquer sorting algorithms, specifically Merge Sort and Quick Sort, to leverage these efficient sorting networks for small subarrays generated during the recursive process. We conducted benchmarks with 11 different optimization configurations and compared them to classical Merge Sort and Quick Sort. We tested the configurations with random, sorted and nearly sorted arrays.
 Our optimized Merge Sort, using a configuration of three sorting networks (sizes 6, 7, and 8), achieves at least 1.5x speedup for random and nearly sorted arrays, and at least 2x speedup for sorted arrays, in comparison to classical Merge Sort. This optimized Merge Sort surpasses both classical Quick Sort and similarly optimized Quick Sort variants when sorting random arrays of size 10,000 and larger.
 When comparing our optimized Quick Sort to classical Quick Sort, we observe a 1.5x speedup using the 3-to-5 configuration on sorted arrays of size 10,000. The 6-to-8 configuration maintains a consistent 1.5x improvement across sorted arrays from 25,000 to 1 million elements. Our findings demonstrate the potential of integrating AI-optimized sorting networks to enhance the performance of classical sorting algorithms.
description: \copyright{} Anas Gamal Aly, Anders E. Jensen, and Hala ElAarag, 2025. This is the authors' version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record will be published in Proceedings of the 2025 ACM Southeast Conference (ACMSE 2025)
Exploring natural products as multi-target-directed drugs for Parkinson’s disease: an in-silico approach integrating QSAR, pharmacophore modeling, and molecular dynamics simulations
Creators: name: Boulaamane, Yassir
name: Touati, Iman
name: Goyal, Nainee
name: Chandra, Anshuman
name: Kori, Lokesh
name: Ibrahim, Mahmoud A. A.
name: Britel, Mohammed Reda
name: Maurady, Amal
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
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: Information Systems not elsewhere classified
subject: Cancer

description: Parkinson’s disease is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the midbrain. Current treatments provide limited symptomatic relief without halting disease progression. A multi-targeting approach has shown potential benefits in treating neurodegenerative diseases. In this study, we employed in silico approaches to explore the COCONUT natural products database and identify novel drug candidates with multi-target potential against relevant Parkinson’s disease targets. QSAR models were developed to screen for potential bioactive molecules, followed by a hybrid virtual screening approach involving pharmacophore modeling and molecular docking against MAO-B, AA2AR, and NMDAR. ADME evaluation was performed to assess drug-like properties. Our findings revealed 22 candidates that exhibited the desired pharmacophoric features. Particularly, two compounds: CNP0121426 and CNP0242698 exhibited remarkable binding affinities, with energies lower than −10 kcal/mol and promising interaction profiles with the chosen targets. Furthermore, all the ligands displayed desirable pharmacokinetic properties for brain-targeted drugs. Lastly, molecular dynamics simulations were conducted on the lead candidates, belonging to the dihydrochalcone and curcuminoid class, to evaluate their stability over a 100 ns timeframe and compare their dynamics with reference complexes. Our findings revealed the curcuminoid CNP0242698 to have an overall better stability with the three targets compared to the dihydrochalcone, despite the high ligand RMSD, the curcuminoid CNP0242698 showed better protein stability, implying ligand exploration of different orientations. Similarly, AA2AR exhibited higher stability with CNP0242698 compared to the reference complex, despite the high initial ligand RMSD due to the bulkier active site. In NMDAR, CNP0242698 displayed good stability and less fluctuations implying a more restricted conformation within the smaller active site of NMDAR. These results may serve as lead compounds for the development and optimization of natural products as multi-target disease-modifying natural remedies for Parkinson’s disease patients. However, experimental assays remain necessary to validate these findings. Communicated by Ramaswamy H. Sarma.