jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Guanyu Liu | Weihong Huang | Yanping Li | Qiong Zhang | Jing Fu | Hongying Tang | Jia Huang | Zhongteng Zhang | Lei Zhang | Yu Wang | Jianzhong Hu
Source: Scientific Reports (article, 2025-04-21)
Field: Materials Science — Polymers and Plastics

A weakly-supervised follicle segmentation method in ultrasound images Accurate follicle segmentation in ultrasound images is crucial for monitoring follicle development, a key factor in fertility treatments. However, obtaining pixel-level annotations for fully supervised instance segmentation is often impractical due to time and workload constraints. This paper presents a weakly supervised instance segmentation method that leverages bounding boxes as approximate annotations, aiming to assist clinicians with automated tools for follicle development monitoring. We propose the Weakly Supervised Follicle Segmentation (WSFS) method, a novel one-stage weakly supervised segmentation technique model designed to enhance the ultrasound images of follicles, which incorporates a Convolutional Neural Network (CNN) backbone augmented with a Feature Pyramid Network (FPN) module for multi-scale feature representation, critical for capturing the diverse sizes and shapes of follicles. By leveraging Multiple Instance Learning (MIL), we formulated the learning process in a weakly supervised manner and developed an end-to-end trainable model that efficiently addresses the issue of annotation scarcity. Furthermore, the WSFS can be used as a prompt proposal to enhance the performance of the Segmentation Anything Model (SAM), a well-known pre-trained segmentation model utilizing few-shot learning strategies. In addition, this study introduces the Follicle Ultrasound Image Dataset (FUID), addressing the scarcity in reproductive health data and aiding future research in computer-aided diagnosis. The experimental results on both the public dataset USOVA3D and private dataset FUID showed that our method performs competitively with fully supervised methods. Our approach achieves performance with mAP of 0.957, IOU of 0.714 and Dice Score of 0.83, competitive to fully supervised methods that rely on pixel-level labeled masks, despite operating with less detailed annotations. Segmentation ; Ultrasound ; Computer science ; Artificial intelligence ; Follicle ; Pattern recognition (psychology) ; Computer vision ; Computational biology ; Medicine ; Biology ; Radiology ; Internal medicine Textile materials and evaluations
Authors: Eric Chung‐Yueh Yuan | Teresa Head‐Gordon
Source: arXiv (Cornell University) (preprint, 2025-09-17)
Field: Materials Science — Materials Chemistry

Teachers that teach the irrelevant: Pre-training machine learned interaction potentials with classical force fields for robust molecular dynamics simulations Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics simulations using MLIPs exhibit numerical instabilities due to underlying data insufficiencies when encountering new regions of the potential energy surface. Here we propose a pre-training learning scheme that uses low-quality, practically free, single-molecule non-reactive force field data while all intermolecular interactions and reactive properties are learned at a fine-tuning stage with a small amount of computationally more expensive labels. We show that the force field pre-training approach followed by data efficient ab initio fine tuning allows for stable and accurate molecular dynamics and metadynamics simulations of gas phase molecules, liquid water, and hydrogen combustion reactions compared to models trained from scratch. Metadynamics ; Molecular dynamics ; Force field (fiction) ; Field (mathematics) ; Potential energy ; Intermolecular force ; Work (physics) ; Scheme (mathematics) ; Range (aeronautics) Machine Learning in Materials Science ; Topic Modeling
Authors: Bárbara F. Farias | Miller Santos Ferreira | Domingo Chinea Miranda | Thiago Cunha Nunes | Natália Pereira | Patrícia Ferreira Espuri | Jaqueline Pereira Januário | Fábio Antônio Colombo | Marcos José Marques | João L. B. Zanin | Marisi G. Soares | Thiago Belarmino de Souza | Diogo Teixeira Carvalho | Daniela Aparecida Chagas‐Paula | Danielle Ferreira Dias
Source: Journal of the Brazilian Chemical Society (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Computational Modeling and Biological Evaluation of Benzophenone Derivatives as Antileishmanial Agents Leishmaniasis is a neglected tropical disease with limited therapeutic options characterized by high toxicity, adverse side effects, and growing resistance to existing treatments. In this study, machine learning (ML) methods were employed to design and evaluate benzophenone and xanthone derivatives as potential antileishmanial agents. A dataset of 73 compounds was curated, and Quantitative Structure-Activity Relationship (QSAR) models were developed using artificial neural networks (ANN), Random Forest (RF), and J48 decision tree classifiers. The ANN model achieved the highest accuracy (86.2%) in predicting antileishmanial activity, validated through in vitro assays. Among 14 newly synthesized benzophenones, compounds 5 and 7 demonstrated significant biological activity with inhibitory concentration 50 (IC50) values of 10.19 and 14.35 μM, respectively, and favorable selectivity indices compared to reference drugs pentamidine and amphotericin B. Structural analysis highlighted the importance of thiosemicarbazone and 4-methyl groups, alongside electronegative substituents at position 11, in enhancing activity. This study underscores the potential of computational tools to streamline the discovery of novel, effective, and selective antileishmanial agents. Benzophenone ; Chemistry ; Combinatorial chemistry ; Biochemical engineering ; Computer science ; Engineering ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds
Authors: Larbi Elmchichi | Marwa Alaqarbeh | Mohammed Bouachrin
Source: Current Chemistry Letters (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Rational in silico design and synthetic route elaboration for anti-RCC benzimidazole candidates Benzimidazole continues to be an intriguing scaffold in recent drug discovery, owing to its broad spectrum of pharmacological effects. In recent years, a variety of its derivatives, which included chalcone imines, hydrazones, and thiosemicarbazones, were actively investigated for their antitumor potential. In the search for new agents capable of treating kidney cancer, an analysis of a small series of 2-substituted benzimidazoles (45) using 3D-QSAR modelling was performed to determine the antiproliferative activities against cancer cell lines A-498. The biological activity was sufficient to establish a meaningful structure–activity relationship, providing a foundation for the design of more potent compounds. The activity-favouring and activity-disfavoring structural regions were clearly revealed using contour maps generated by the models. The CoMSIA/SHD model was one of the best developed, and its high statistical robustness (q2 = 0.751) and predictive power (R2 pred = 0.924) indicated its reliability. We designed five new derivatives of benzimidazole based on the QSAR results, which demonstrated potent inhibitory potential. Molecular docking studies were performed in order to investigate in detail their interaction modes with the aromatic receptor, and stable binding conformations at the active site have been found. The in silico pharmacokinetic studies suggested that these compounds have a favourable ADMET and bioavailability profile, reinforcing their suitability for in vitro testing. Two leads, L15 and L22, with better PKs properties and high-predicted activities, were subjected to a 100-ns MD simulation in complex with the aromatase target to investigate their stability. We also conducted a retrosynthetic analysis for L15 and L22, suggesting potential synthetic routes for experimental validation. Overall, these findings suggest that benzimidazole analogues could be promising candidates for treating RCC and possibly for blocking aromatase. In silico ; Benzimidazole ; Chalcone ; Quantitative structure–activity relationship ; Docking (animal) ; Rational design ; Robustness (evolution) Synthesis of Tetrazole Derivatives ; Synthesis and properties of polymers ; Medical Imaging Techniques and Applications
Authors: Aastha Sharma | Balasubramanian Narasimhan | Rakesh Kumar Marwaha
Source: ChemistrySelect (article, 2025-08-01)
Field: Chemistry — Organic Chemistry

Advances in Quinoxaline Derivatives: Multi‐Target Anticancer Potential and Nanocatalyst‐Driven Synthesis Abstract Cancer remains one of the most formidable pathological conditions, necessitating early diagnosis and the development of effective therapeutic strategies. Quinoxaline derivatives have emerged as promising candidates among nitrogen‐containing heterocyclic compounds due to their diverse pharmacological profile. This review critically examines the anticancer potential of quinoxaline scaffolds through their ability to modulate multiple oncogenic pathways simultaneously. Notably, these compounds demonstrate potent inhibitory effects against critical targets such as tubulin polymerization, c‐Met kinase, topoisomerase II, and EGFR kinase, while also inducing apoptosis, arresting cell cycle progression, and inhibiting FLT3, JAK2, VEGFR2, SIRT1, and PI3Kα signaling pathways. This review highlights recent advancements in the synthesis of quinoxaline derivatives, with a particular focus on nanocatalyst‐based approaches and the use of nano‐carriers. The integration of nanocatalyst‐based synthetic approaches represents a significant advancement over conventional methods, providing eco‐friendly, efficient, and high‐yield processes. Furthermore, structure–activity relationship analysis provides critical insights for rational drug design, revealing key molecular determinants that enhance potency and selectivity against specific cancer targets. By bridging nanotechnology with medicinal chemistry, this review demonstrates how quinoxaline derivatives can be strategically modified to overcome challenges in targeted cancer therapy, offering promising directions for developing next‐generation anticancer agents with improved efficacy and reduced toxicity profiles. Quinoxaline ; Combinatorial chemistry ; Chemistry ; Nanotechnology ; Computational biology ; Pharmacology ; Materials science ; Biology ; Organic chemistry Synthesis and Biological Evaluation ; Synthesis and biological activity ; Bioactive Compounds and Antitumor Agents
Authors: Rachid Bouzammit | Soumia Ait Assou | M. Er-rajy | Noura Aflak | Lahoucine Bahsis | Mohammed Chalkha | Mohammed El Hassouni | Mohammed Lachkar | Taïbi Ben Hadda | Daryn Benson | Abdullah A. Alyousef | Mourad A. M. Aboul-Soud | John P. Giesy | Ghali Al Houari
Source: Frontiers in Chemistry (article, 2025-12-29)
Field: Chemistry — Organic Chemistry

Regioselective synthesis of novel spiro-isoxazolines congeners as antimicrobial agents: in vitro and in-silico assessments Two spiroisoxazolines, defined as <b>3b</b> and <b>c</b>, showed notable antimicrobial activity, producing inhibition zones between 8.33 ± 0.57 and 14.00 ± 2.00 mm. Compound <b>3b</b> was active against all tested strains and demonstrated ampicillin-comparable MIC values of 10 μg/mL against <i>E. coli</i>, <i>P. brasiliensis</i>, and <i>B. subtilis</i>. It showed moderate to weak activity against S. aureus (90 μg/mL) and C. albicans (300 μg/mL). Compound <b>3c</b> displayed selective activity toward Gram-positive bacteria with MIC values of 50 and 500 μg/mL against <i>B. subtilis</i> and <i>S. aureus</i>, respectively. Molecular docking studies confirmed the high binding affinities of <b>3b</b> and <b>3c</b> toward the active sites of the targeted proteins, in agreement with the antimicrobial results. POM analyses further indicated the coexistence of antifungal (O1δ--O2δ-) and antiviral (O1δ--N1δ-) pharmacophoric sites, although steric constraints introduced by two methyl substituents may limit their optimal interaction. The calculations also confirmed favorable bioavailability and the absence of predicted toxicity for all compounds. Overall, this combined experimental -theoretical study highlights the mechanistic basis and biological relevance of these spiroisoxazolines, underscoring their potential as promising scaffolds for the rational design of antiviral drug candidates. Antimicrobial ; Docking (animal) ; Candida albicans ; Steric effects ; In vitro ; Drug ; Bioavailability ; Antifungal ; Bacteria Synthesis of heterocyclic compounds ; Multicomponent Synthesis of Heterocycles ; Synthesis and Characterization of Pyrroles
Authors: Nadia Hanafy Metwally | Galal H. Elgemeie | A. S. Abdel‐Razek | Salwa Magdy Eldaly
Source: BMC Chemistry (article, 2025-01-31)
Field: Chemistry — Organic Chemistry

Synthesis, antibacterial evaluation and in silico studies of novel 2-(benzo[d]thiazol-2-yl)-N-arylacetamides and their derivatives as potential DHFR inhibitors Novel N-arylacetamides 2a-f were synthesized based on benzo[d]thiazole scaffold. The compounds 2a-c underwent Knoevenagel condensation through green synthetic method with different aromatic aldehydes and pyrazole-7-carbaldehydes delivered the respective arylidenes with efficient yields. Arylidenes 4 reacted with malononitrile affording the corresponding N-arylpyridones 11a-i. Moreover, the reaction of 2a-c with each of salicylaldehyde and 5-arylazo salicylaldehydes afforded the unexpected coumarins rather than quinolin-5-ones. The structure of coumarin 8 was confirmed by density functional theory (DFT) calculations using basis set B3LYP/6-311 G + + (d,p) to obtain the suitable geometrical structure with molecular orbitals` energies revealing its planar structure and its agreement with experimental data. Besides, the antibacterial activity was tested against different bacterial strains revealing potent activity especially Gram-negative bacteria with excellent minimum inhibition concentration (MIC) value ranging from 31.25 to 250 µg/L. Additionally, compounds 2c and 4m showed enzyme inhibition against dihydrofolate reductase in Escherichia coli with greater potency (IC<sub>50</sub> for 2c = 3.796 µM, IC<sub>50</sub> for 4m = 2.442 µM) than the standard antibiotic trimethoprim (IC<sub>50</sub> = 8.706 µM). Investigation of the physicochemical properties of the newly compounds exhibited their better ADME properties that can be developed for the discovery of new antibacterial agents. In silico ; Chemistry ; Stereochemistry ; Toxicology ; Pharmacology ; Biology ; Biochemistry ; Gene Synthesis and biological activity ; Sulfur-Based Synthesis Techniques ; Phenothiazines and Benzothiazines Synthesis and Activities
Authors: Violina T. Angelova | Rositsa Mihaylova | Zvetanka Zhivkova | Nikolay Vassilev | Boris Shivachev | Irini Doytchinova
Source: Pharmaceuticals (article, 2025-08-20)
Field: Chemistry — Organic Chemistry

Novel Indole-Based Sulfonylhydrazones as Potential Anti-Breast Cancer Agents: Synthesis, In Vitro Evaluation, ADME, and QSAR Studies <b>Background</b>: Breast cancer continues to pose a significant global health challenge despite advances in early detection and targeted therapies. The development of novel chemotherapeutic agents remains crucial, particularly those with selective cytotoxicity toward specific breast cancer subtypes. <b>Methods</b>: A series of ten hybrid indolyl-methylidene phenylsulfonylhydrazones and one bis-indole derivative were designed, synthesized, and structurally characterized using NMR and high-resolution mass spectrometry (HRMS). Prior to synthesis, in silico screening was performed to assess drug likeness and ADME-related properties. Single-crystal X-ray diffraction was conducted for compound <b>3e</b>. The cytotoxic potential of the synthesized compounds was evaluated using the MTT assay against MCF-7 (ER-α⁺) and MDA-MB-231 (triple-negative) breast cancer cell lines. Additionally, quantitative structure-activity relationship (QSAR) analysis was conducted to identify key structural features contributing to activity. <b>Results</b>: Most compounds exhibited selective cytotoxicity against MCF-7 cells. Notably, compound <b>3b</b> demonstrated the highest potency with an IC<sub>50</sub> of 4.0 μM and a selectivity index (SI) of 20.975. Compound <b>3f</b> showed strong activity against MDA-MB-231 cells (IC<sub>50</sub> = 4.7 μM). QSAR analysis revealed that the presence of a non-substituted phenyl ring and specific indolyl substituents (5-methoxy, 1-acetyl, 5-chloro) significantly contributed to enhanced cytotoxic activity and ligand efficiency. <b>Conclusion</b>: The synthesized phenylsulfonylhydrazone hybrids exhibit promising and selective cytotoxicity, particularly against ER-α⁺ breast cancer cells. Structural insights from QSAR analysis provide a valuable foundation for the further optimization of this scaffold as a potential source of selective anticancer agents. ADME ; Quantitative structure–activity relationship ; Cytotoxicity ; Chemistry ; Indole test ; Stereochemistry ; MTT assay ; Breast cancer ; In silico ; In vitro ; Pharmacology ; Cancer ; Biochemistry ; Medicine ; Internal medicine Synthesis and biological activity ; Click Chemistry and Applications ; Computational Drug Discovery Methods
Authors: Francesco Zaccaria | Andrea Pucciarelli | Roberta Cipullo | Vincenzo Busico
Source: Polymers (article, 2025-05-07)
Field: Materials Science — Polymers and Plastics

A Straightforward Methodology for the Quantification of Long Chain Branches in Polyethylene by 13C NMR Spectroscopy Formation of long chain branches (LCB) in polyethylene (PE), via incorporation of in situ generated vinyl macromonomers, is known to affect material properties dramatically, making their detection and quantification of primary importance. <sup>13</sup>C NMR spectroscopy is the archetypal technique for the analysis of polymer microstructure, yet it suffers from major limitations in the analysis of LCB in polyethylene, primarily in terms of resolution. Herein, we propose a simple and effective methodology for detecting and quantifying LCB based on the analysis of C atoms in β-position with respect to the branching point. By analyzing model ethylene/α-olefin copolymers bearing methyl, ethyl, butyl, hexyl or tetradecyl chain branches, we show how the C<sub>β</sub> resonances can be used to discriminate between shorter or longer branches. Importantly, the proposed method allows the most critical discrimination between hexyl-type branches and LCB, with an up to three-fold detection enhancement with respect to previously proposed procedures based on the analysis of the methine carbons. The proposed approach is then tested on a representative industrial sample of HDPE, proving that it is suitable to detect very small amounts of LCB. Polyethylene ; Branching (polymer chemistry) ; Materials science ; Polymer ; Ethylene ; Olefin fiber ; Nuclear magnetic resonance spectroscopy ; Carbon-13 NMR ; Polymer chemistry ; Chemistry ; Organic chemistry ; Composite material Polymer crystallization and properties ; Mass Spectrometry Techniques and Applications ; Protein Structure and Dynamics
Authors: Lian Ojotule Abah | Samuel Attah Egu | Aminu Omale | Simon sani Ocholi | Jamila Audu Omale | Andrew Omachoko Onoja | Suleiman Kazeem | Abdullahi Abdulrazak | Clifford B. Okpanachi | Emmanuel Amlabu
Source: Discover Chemistry. (article, 2025-08-08)
Field: Chemistry — Organic Chemistry

Highlights of the chemistry and pharmacological potential of 8-hydroxyquinoline: a review Abstract Fundamental heterocyclic molecules, quinolone and its analogs, especially 8-hydroxyquinoline, play a significant role in chemical synthesis. It has become clear that 8-hydroxyquinoline derivatives are incredibly adaptable molecules with a wide range of uses in industrial and medical chemistry. Quinoline has undergone significant modification since it was first synthesized in the 1980s, yielding derivatives with notable biological activities, such as antibacterial, antioxidant, and antidiabetic characteristics. The major discussions of this review are the synthetic techniques and modifications in the structure of 8-hydroxyquinoline and its nitro, amino, and halogenated derivatives. This review also includes information on forming various 8-hydroxyquinoline derivatives and their biological activities. This review discusses traditional and modern synthetic pathways, emphasizing the quinoline core and changes to functional groups that affect yield and reactivity. Chemists looking forward to investigating the various reactivity patterns of quinoline-based compounds and enhancing synthetic procedures will observe significant value in the insights provided in this review. 8-Hydroxyquinoline ; Environmental chemistry ; Chemistry ; Organic chemistry Click Chemistry and Applications ; Synthesis and Biological Evaluation ; Synthesis and biological activity
Authors: Haroon Rashid | Sher Wali Khan | Abdul Latif | Saira Nayab | Muhammad Umar | Sana Fatima | Abdul Bari Shah | Muhammad Zahoor | Riaz Ullah | Essam A. Ali
Source: Future Medicinal Chemistry (article, 2025-03-17)
Field: Chemistry — Organic Chemistry

Synthesis, <i>in vitro</i> and <i>in-silico</i> evaluation of amide derivatives as prospective antimicrobial and antileishmanial agents This study focused on the synthesis, antimicrobial, and antileishmanial evaluation of seven amide derivatives (<b>AL-1</b> to <b>AL-7</b>). The target compounds were synthesized from <i>L-</i>cysteine methyl ester and various substituted aromatic and aliphatic carboxylic acids. The final products were characterized using physical and spectro-analytical techniques (FT-IR, <sup>1</sup>H NMR). The derivatives were evaluated for their antimicrobial activity at various concentrations. Experimental studies revealed that compounds <b>AL-5</b> and <b>AL-6</b> were the most potent against <i>Staphylococcus aureus</i> and <i>Escherichia coli</i>, exhibiting 18 mm and 21 mm inhibition zones, respectively, at a concentration of 2000 µg/mL. Additionally, <b>AL-5</b> and <b>AL-6</b> showed significant activity against <i>Candida albicans</i>, with 20 mm and 23 mm inhibition zones, respectively, at a concentration of 1000 µg/mL. The compounds also exhibited moderate to good activity against <i>Leishmania tropica</i>. Compounds <b>AL-2, AL-4, AL-5</b>, and <b>AL-6</b> demonstrated good activity, with IC<sub>50</sub> values of 0.68 ± 0.09, 0.68 ± 0.16, 0.66 ± 0.08, and 0.68 ± 0.12 µg/mL, respectively. Molecular docking, <i>in silico</i> Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis, and Density Functional Theory (DFT) studies were conducted on the most potent compounds (<b>AL-5</b> and <b>AL-6</b>) to validate and support their experimental antimicrobial and antileishmanial potential. Antimicrobial ; In silico ; In vitro ; Chemistry ; Amide ; Pharmacology ; Combinatorial chemistry ; Biology ; Biochemistry ; Organic chemistry Synthesis and biological activity ; Research on Leishmaniasis Studies ; Phenothiazines and Benzothiazines Synthesis and Activities