jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Lin Yue | Zengkui Lu | Tingting Guo | Bowen Chen | Jianbin Liu | Chao Yuan
Source: Animal Bioscience (article, 2025-09-30)
Field: Materials Science — Polymers and Plastics

Transcriptome and proteome combined analysis of wool fiber diameter regulation mechanism This study found that the triglyceride and energy metabolic pathways as significant factors influencing of wool fiber diameter, thus offering a theoretical basis for promoting wool industry through the refinement of wool diameter and quality. Wool ; Transcriptome ; Proteome ; Fiber ; Mechanism (biology) ; Metabolic pathway Textile materials and evaluations ; Molecular Biology Techniques and Applications ; Collagen: Extraction and Characterization
Authors: Daoyi Li | Maité Pérez | Xiaoqi Zhang | J. Li | Wen Jiang
Source: Acta Crystallographica Section D Structural Biology (article, 2025-08-21)
Field: Chemistry — Spectroscopy

Validation of helical symmetry parameters in the EMDB Helical symmetry is a structural feature of many biological assemblies, including cytoskeletons, viruses and pathological amyloid fibrils. The helical parameters twist and rise are unique metadata for helical structures. With the increasing number of helical structures being resolved through cryo-EM and deposited in the EMDB, there is a growing possibility of errors in the metadata associated with these entries. During our cryo-EM analysis of protein amyloids and the development of helical analysis tools, we realized that many deposited helical parameters appear to be inconsistent with the associated density maps. Here, we have developed a comprehensive validation process that examines the consistency of these parameters by combining high-throughput computational evaluation with manual verification. Multiple errors were identified and corrected for ∼14% of the total entries, including missing parameters, swapped twist and rise values, incorrect sign of twist angles, partial symmetries and bona fide errors. Our validation code, workflow and the validated parameters are publicly available. Twist ; Workflow ; Consistency (knowledge bases) ; Computer science ; Metadata ; Feature (linguistics) ; Symmetry (geometry) ; Algorithm ; Data mining ; Computational biology ; Artificial intelligence ; Mathematics ; Biology ; Geometry ; Database Advanced NMR Techniques and Applications ; Protein Structure and Dynamics ; Enzyme Structure and Function
Authors: Alyssa Rosenbloom | Kiran Edwardson | Grant Ongo | Nathaniel Robichaud | Narges Rashidi | Milad Dagher
Source: Regular and Young Investigator Award Abstracts (article, 2025-11-01)
Field: Chemistry — Spectroscopy

1231 A scalable, proteome-wide protein profiling platform with absolute quantification of 1000 proteins Profiling (computer programming) ; Quantitative proteomics ; Peptide mapping ; Quantitative analysis (chemistry) ; Proteomics Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Cell Image Analysis Techniques
Authors: Yaolan Tian | Guoxu Zhang | Yan Li | Mei Shen | Yufeng Xiong | Ting Li | Yunzheng Wang | Xian Zhao | Changbao Ma
Source: Materials (article, 2025-11-25)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Improvement of a Switchable Wide-Incident-Angle Perfect Absorber Incorporating Sb2S3 Active metasurfaces, whose optical properties can be tuned by an external stimulus such as electric or laser pulses, have attracted great research interest recently. The phase change material (PCM), antimony sulfide (Sb<sub>2</sub>S<sub>3</sub>), has been reported to modulate resonance wavelengths from the visible to the infrared. Here, we present a purely numerical study of an active and nonvolatile narrow-band perfect absorber in the infrared region based on a nanostructured metal-insulator-metal (MIM) metasurface incorporating Sb<sub>2</sub>S<sub>3</sub>. The proposed absorber exhibits a high quality factor and achieves near-unity absorption at resonance wavelengths. In addition, the absorption spectrum can be dynamically modulated by the phase transition of Sb<sub>2</sub>S<sub>3</sub>, with a modulation range approaching 1 μm. Moreover, the designed absorber shows insensitivity to the angle of incidence. This study offers a feasible strategy for developing Sb<sub>2</sub>S<sub>3</sub>-integrated metasurface perfect absorbers with potential applications in selective thermal emitters and bolometers. Resonance (particle physics) ; Absorption (acoustics) ; Phase modulation ; Infrared ; Laser ; Thermal ; Visible spectrum ; Wavelength ; Modulation (music) Metamaterials and Metasurfaces Applications ; Thermal Radiation and Cooling Technologies ; Phase-change materials and chalcogenides
Authors: Rui Peng | Shibo Fang | Pin Ho | Tong Zhou | Junwei Liu | Yee Sin Ang
Source: ArXiv.org (preprint, 2025-05-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Ferroelastic Altermagnetism Synergizing altermagnetism and other ferroic orders, such as ferroelectric switchable altermagnetism [Phys. Rev. Lett. 134, 106801 (2025) and ibid. 106802 (2025)], offers an effective route to achieve nonvolatile switching of altermagnetic spin splitting. In this work, by synergizing altermagnetism and ferroelasticity, we propose the concept of ferroelastic altermagnets in which the ferroelastic crystal reorientation can drive multistate nonvolatile switching of the altermagnetic spin splitting via altermagnetoelastic effect. Using monolayers RuF4 and CuF2 as material candidates, we demonstrate 2-state and 3-state altermagnetic spin splitting switching as driven by ferroelastic strain states. Transport calculation shows that multistate spin conductivities can be ferroelastically encoded in an ferroelastic altermagnet, thus suggesting the potential of ferroelastic altermagnetic as nonvolatile nanomechanical spin switches. The proposed concept of ferroelastic altermagnetism enriches the emerging landscape of multiferroic altermagnetism, paving a way towards altermagnetic-based straintronic device applications. Ferroelasticity ; Multiferroics ; Ferroelectricity ; Spin (aerodynamics) ; Non-volatile memory ; Monolayer ; Ferromagnetism Magnetic Properties and Applications ; Magnetic Properties of Alloys
Authors: Barry P. Sleckman | Bo-Ruei Chen
Source: PubMed (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

THE GID COMPLEX REGULATES DNA END PROCESSING DURING DNA DOUBLE-STRAND BREAK REPAIR BY NONHOMOLOGOUS END JOINING. Genome instability is a hallmark of cancer, allowing for clonal evolution and improved tumor fitness. The mis-repair of DNA double-strand breaks (DSBs) is a major source of genome instability. DNA DSBs are normally repaired by homologous recombination (HR) and nonhomologous end joining (NHEJ). The nucleolytic resection of broken DNA ends generates single-stranded DNA (ssDNA) overhangs that are required for HR, but inhibitory to NHEJ. DNA end resection must be prevented in nondividing cells where NHEJ is the only active DSB repair pathway. Using a novel whole genome gRNA CRISPR/Cas9 screen, we identified the GID complex as functioning to protect DNA ends from nucleolytic resection. The GID complex contains multiple E3 ubiquitin ligase subunits and regulates the expression and function of pro-resection machinery. Thus, by antagonizing DNA end resection GID may prevent homology-mediated joining leading to aberrant DSB repair and genome instability in normal and cancerous nondividing cells. Non-homologous end joining ; DNA ; DNA repair ; Double strand ; End-to-end principle ; Computer science ; Genetics ; Biology ; Computational biology ; Cell biology ; Molecular biology ; Artificial intelligence Metal Alloys Wear and Properties ; High Temperature Alloys and Creep ; Surface Treatment and Coatings
Authors: Jianbo Jian | Chunhai Chen | Xiaodong Fang | Christopher T. Workman | Thomas Ostenfeld Larsen | Yuhang Li | Eva C. Sonnenschein
Source: DNA Research (article, 2025-12-12)
Field: Materials Science — Biomaterials

The genome of <i>Pleurosigma</i> provides insights into the evolutionary adaptations of pelagic diatoms The diatom Pleurosigma pacificum is a newly described tropical pelagic species from the Western Pacific Ocean with one of largest genome size among published diatom genomes, making it an ideal candidate for studying adaptation to tropical open ocean environments and diatom evolution. We employed HiFi long-read sequencing to construct a high-quality and contaminant-free genome. The assembled genome is 1.357 Gb in size and consists of 821 contigs with a contig N50 of 3.23 Mb. The GC content is 38.6%, which is much lower than that of other published diatom genomes. The genome contains 27,408 predicted genes, 540 of which were implicated in environmental adaptation. Gene features and gene family comparisons suggest that the primary driver of genome expansion and functional diversification is long terminal repeats (LTR) retrotransposons and tandem duplications. The phylogenetic analysis revealed that the clade of P. pacificum is closely associated with other members of Naviculales. The expansion of chlorophyll a/c proteins might facilitate the adaptation of P. pacificum to high-light conditions in pelagic environments. The percentage of approximately 3.2% horizontal gene transfer (HGT) events is observed in the P. pacificum genome. HGTs are a prevalent phenomenon in diatoms and serve as a common mechanism to enhance their adaptive capabilities. In conclusion, the P. pacificum genome provides important understanding into the development of large genome size and evolutionary adaptations of pelagic diatoms. Pelagic zone ; Genome ; Adaptation (eye) ; Diatom ; Genome size ; Phylogenetic tree ; Gene ; Clade ; Genomics Diatoms and Algae Research ; Genomics and Phylogenetic Studies ; Algal biology and biofuel production
Authors: Amy R. Johnson | Nathaniel Robichaud | Samantha I. Liang | Grant Ongo | Enjun Yang | Kiran Edwardson | Jiamin Huang | Andy Lee | Eric D. Miller | Narges Rashidi | Jeffrey D. Munzar | John E. Connolly | Milad Dagher
Source: Regular and Young Investigator Award Abstracts (article, 2025-11-01)
Field: Chemistry — Spectroscopy

129 nELISA high-throughput protein profiling applied to the RADIOHEAD cohort: insights from the largest plasma proteomics study of patients receiving checkpoint inhibitor therapy Proteomics ; Profiling (computer programming) ; Antibody therapy ; Antibody ; Gene expression profiling ; Cancer therapy Advanced Proteomics Techniques and Applications ; Cancer Immunotherapy and Biomarkers ; Radiopharmaceutical Chemistry and Applications
Authors: Zengqi Wen | Haizhen Long
Source: Scientia Sinica Vitae (article, 2025-05-21)
Field: Chemistry — Organic Chemistry

Subnucleosome&amp;mdash;where does it come from? 真核生物的基因组以染色质形式紧密包装于细胞核内，核小体则构成了染色质的基本结构单元。在细胞中，核小体并非静态存在，其结构具有高度动态性，并与染色质的结构调控与功能执行密切相关。近年来，随着研究技术的不断进步，越来越多的证据表明，在核小体结构的动态变化与调控过程中，能够形成多种多样的亚核小体结构，进而参与染色质的构象调控与生物学功能调节。作为一种新兴的表观遗传特征，亚核小体正受到日益广泛的关注。本文将综述近年来利用单分子技术、原子力显微镜、冷冻电镜及高通量测序等方法在亚核小体结构研究方面的最新进展，重点探讨亚核小体结构的动态特性，以及其在染色质重塑、转录和DNA复制等过程中形成的分子机制。 History Fullerene Chemistry and Applications
Authors: Liz Hernández | Théo Paris | Maria Demou | Catherine Birck | Christina Begon‐Pescia | J.F. Rodriguez-Vidal | Sylwia D. Tyrkalska | Charlotte Bureau | Catherine Gonzalez | Juliette Gracia | Etienne Lelièvre | Víctoriano Mulero | Mai Nguyen‐Chi | Laure Yatime
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-06-14)
Field: Materials Science — Biomaterials

Teleost-specific ictacalcins exhibit similar structural organization, cation-dependent activation and transcriptional regulation as human S100 proteins Abstract S100 proteins are highly versatile calcium-binding proteins from vertebrates. Following extracellular release, they become instrumental in immune and antimicrobial defenses, initiating the inflammatory response through receptor signaling and providing direct control of bacterial invaders via nutritional immunity. While mammalian S100s have been extensively studied, very little is known about the more recently discovered S100 proteins from teleost fish, including those with no strict orthologs in mammals. Comparable functioning between both clades would allow to expand their study into the highly popular zebrafish model, particularly suited for live imaging and mechanistic exploration of immune and inflammatory processes. To fill the gap of knowledge on teleost S100s, we here provide a detailed structural and biochemical characterization of S100i1 and S100i2 from Danio rerio , two teleost-specific S100s absent in mammals. We demonstrate that they nevertheless share conserved tertiary and quaternary organization with mammalian S100s. In addition, they exhibit comparable calcium binding properties and undergo a similar calcium-dependent activation mechanism. Furthermore, they display analogous expression pattern, being enriched in tissues highly exposed to the environment like gills and skin, the latter constituting an important reservoir of S100 proteins in mammals. Finally, our results show, for the very first time, that s100i2 / i2 gene expression is differentially modulated in sterile disease conditions associated with sustained inflammation or high hypoxic state. Altogether, these findings underline the strong parallelism existing between mammalian and teleost-specific S100 proteins despite their divergent evolution, opening up new avenues to explore their biology in the zebrafish model. Cell biology ; Transcriptional regulation ; Chemistry ; Biology ; Biochemistry ; Transcription factor ; Gene Silk-based biomaterials and applications ; Physiological and biochemical adaptations ; S100 Proteins and Annexins
Authors: Baojun Tang | Xinyu Ren | Zhiguo Dong | Hanfeng Zheng | Yujia Liu | Tao Wei
Source: Preprints.org (preprint, 2025-04-27)
Field: Chemistry — Physical and Theoretical Chemistry

Metabolic and Immune Response of Juvenile &lt;i&gt;Babylonia areolate&lt;/i&gt; to Hypoxia Stress As an important aquaculture species, the marine snail Babylonia areolate is frequently subjected to fluctuation in dissolved oxygen concentration during farming and transportation processes. In the present study, we measured the oxygen consumption rate, ammonia excretion rate, metabolic enzyme activities, immune enzyme activities, as well as changes in gene expression of these enzymes under long-term stress (144 hours) on B. areolate at two hypoxia levels (2.0 and 0.5 mg O2/L). The findings indicated that the mortality rate of juvenile B. areolate was higher in the 0.5 mg O2/L group compared to the 2 mg O2/L group. During the hypoxic stress period, both oxygen consumption and ammonia excretion rates were observed to be lower in juvenile B. areolate than those in the control group. The group exposed to 0.5 mg O2/L exhibited lower oxygen consumption and ammonia excretion rates compared to the group exposed to 2 mg O2/L at most measurement time points. As stress duration prolonged, juvenile B. areolate demonstrated significantly elevated activities of PK and ACP, alongside reduced activities of LDH, ACP, and SOD. The expression levels of PK and LDH genes in juvenile B. areolate were significantly reduced during the early stages of hypoxic stress; however, a significant increase was observed in the later stages. The expression levels of ACP and AKP genes were significantly downregulated, while juvenile B. areolate exhibited elevated SOD gene expression levels under 0.5 mg O2/L. The results indicated that B. areolate may respond to hypoxic stress by reducing its metabolic rate and modulating the expression of metabolism-related enzymes. Furthermore, hypoxic stress was found to significantly impact the antioxidant capacity and immune function of B. areolate. Notably, the mortality rate of B. areolate can be substantially decreased by ensuring that transportation time does not exceed 48 hours. Hypoxia (environmental) ; Immune system ; Juvenile ; Fight-or-flight response ; Medicine ; Biology ; Chemistry ; Immunology ; Biochemistry ; Oxygen ; Genetics ; Gene thermodynamics and calorimetric analyses ; Metabolomics and Mass Spectrometry Studies ; Biochemical Acid Research Studies
Authors: Malikussaid | Hilal Hudan Nuha | Isman Kurniawan
Source:  (article, 2025-12-15)
Field: Materials Science — Materials Chemistry

Bridging the Plausibility-Validity Gap by Fine-Tuning a Reasoning-Enhanced LLM for Chemical Synthesis and Discovery Large Language Models frequently generate outputs that appear scientifically reasonable yet violate fundamental principles—a phenomenon we characterize as the “plausibility-validity gap.” This challenge proves especially acute in chemistry, where superficial correctness masks deeper errors in molecular structure, reaction mechanisms, and synthetic pathways. We present a systematic approach combining a reasoning-centric model architecture (Magistral Small) with Low-Rank Adaptation fine-tuning on a dual-domain dataset covering molecular properties and chemical transformations. Evaluation reveals substantial improvements: the fine-tuned system achieves 96.3 % format adherence, 97.4 % chemical validity, and 74.4 % synthesis feasibility. Comparative analysis shows our approach outperforms specialized translation models like MolT5 (97.4 % vs 77.2 % validity) while achieving performance comparable to complex tool-augmented systems like ChemCrow (9.0/10 vs 9.24/10 expert rating) through a more transparent, efficient methodology. Results demonstrate a learning hierarchy where syntactic correctness develops before chemical understanding, which precedes synthetic planning capability. This work establishes a reproducible framework for transforming generalist language models into dependable scientific tools while identifying critical areas including stereochemical precision, knowledge currency, and computational accessibility as key challenges for future advancement. Bridging (networking) ; Correctness ; Hierarchy ; Key (lock) ; Translation (biology) ; Workflow Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Asymmetric Hydrogenation and Catalysis
Authors: Md Foysal Rabbi | Gijsje H. Koenderink | Yuval Mulla | Taeyoon Kim
Source: Acta Biomaterialia (article, 2025-06-03)
Field: Materials Science — Biomaterials

Fine-tuning of material properties by catch bonds Materials science ; Composite material ; Bond ; Business Calcium Carbonate Crystallization and Inhibition ; Advanced Theoretical and Applied Studies in Material Sciences and Geometry ; Tribology and Wear Analysis
Authors: Yueqing Zhang | Wentao Liu | Yan Zhang | Danyang Xiong | Jihang Zhai | Hao Hao | Yeonsang Gu | Haibo Yang | Shuanhu Gao | Lianrui Hu | Aimin Zhou | Xiao He
Source: ArXiv.org (preprint, 2025-07-02)
Field: Materials Science — Materials Chemistry

A Large Language Model for Chemistry and Retrosynthesis Predictions Large language models (LLM) have achieved impressive progress across a broad range of general-purpose tasks, but their effectiveness in chemistry remains limited due to scarce domain-specific datasets and the demand for precise symbolic and structural reasoning. Here we introduce ECNU-ChemGPT(name after East China Normal University), a chemistry-specialized LLM engineered for deep chemical knowledge understanding and accurate retrosynthetic route planning. Our approach is distinguished by four key strategies: structured prompt-based knowledge distillation from authoritative chemistry textbooks to construct a high-quality question-answering dataset; domain-specific prompt engineering using curated chemical keywords, combined with LLMs APIs for data derivation and knowledge distillation; large-scale fine-tuning on a meticulously cleaned and enriched Pistachio reaction dataset to enhance retrosynthesis prediction accuracy; and integration of BrainGPT, a dynamic multi-model scheduling framework that enables task-specific invocation of multiple specialized models trained for diverse chemistry-related tasks. ECNU-ChemGPT exhibits superior performance on chemistry question-answering and retrosynthetic planning benchmarks, outperforming leading general-purpose models-including Deepseek-R1, Qwen-2.5, and GPT-4o. In retrosynthesis, it achieves a Top-1 accuracy of 68.3% on the USPTO_50K dataset and successfully reconstructed 13 complete experimental pathways for real-world drug molecules from medicinal chemistry journals. These results underscore the effectiveness of domain-adapted fine-tuning combined with dynamic multi-model task scheduling, providing a scalable and robust solution for chemical knowledge question answering and retrosynthetic planning. Retrosynthetic analysis ; Construct (python library) ; Heuristics ; Scalability ; Range (aeronautics) ; Expert system ; Language model ; Key (lock) Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Advanced Graph Neural Networks
Authors: Lu Tie | Ran Lei | Dandan Xi
Source: Advances in Colloid and Interface Science (article, 2025-12-26)
Field: Materials Science — Surfaces, Coatings and Films

Programming superlyophobic interfaces via fine-tuning surface chemistry: From controllable fabrication to intelligent manipulation Fabrication ; Interface (matter) ; Surface (topology) ; Rational design ; Mechanism (biology) Surface Modification and Superhydrophobicity ; Pickering emulsions and particle stabilization ; Nanopore and Nanochannel Transport Studies
Authors: Seungki Jo | Jeong Min Park | Linh Vu Ba | Haeum Park | Sejin Jung | Jinhee Bae | Jong Min Park | Jungho Choe | Kyung Tae Kim
Source: Ceramics International (article, 2025-08-27)
Field: Materials Science — Materials Chemistry

Hot isostatic pressing-driven fine-tuning of electrical properties in p- and n-type (Bi,Sb)2Te3 thermoelectric materials Hot isostatic pressing (HIP) is generally used for densification of powders in thermoelectric materials, yet its potential for tuning electrical properties remains underexplored. Herein, we employ hot isostatic pressing as a post-processing for fine-tuning the electrical properties of sintered p - and n -type (Bi,Sb) 2 Te 3 compounds through simultaneous modulation of point defects and microstructure. The HIP process effectively optimizes carrier concentrations via the preferential formation of Sb Te and Bi Te antisite defects, while concurrently improving carrier mobility through grain growth. Based on this synergistic effect, the power factor increases by 11 % and 15 % for p - and n -type samples, respectively. Consequently, owing to the fine-tuned electronic transport properties the calculated device ZT of both p - and n -type samples increased across all tested temperature differences. Materials science ; Thermoelectric effect ; Hot isostatic pressing ; Thermoelectric materials ; Pressing ; Composite material ; Hot pressing ; Metallurgy ; Sintering ; Thermal conductivity ; Thermodynamics Advanced Thermoelectric Materials and Devices ; Thermal properties of materials ; Advanced Thermodynamics and Statistical Mechanics