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BioChemCite

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Recently, we introduced the TCOSA method (Thermodynamics-based COfactor Swapping Analysis) and used it to analyze the optimality of the NAD(P)(H) specificity of redox reactions in E. coli with respect to network-wide thermodynamic driving forces [CITATION] .	10.1038/s41467-023-40297-8	Network-wide thermodynamic constraints shape NAD (P) H cofactor specificity of biochemical reactions	PMC13279740	dq0000	cc by
AlphaFold2 [CITATION] -predicted 3D protein structures and subsequent alignment revealed that substantial homology existed between B.ovatus, B.xylanisolvens, and E.	10.1038/s41586-021-03819-2	Highly accurate protein structure prediction with AlphaFold	PMC13248909	dq0001	cc by
It holds extensive applications in metabolic engineering, minimal cell assembly, recombinant protein production, and the development of in vitro diagnostic biosensors [CITATION] .	10.1016/j.csbj.2023.05.003	Advancing synthetic biology through cell-free protein synthesis	PMC13217924	dq0002	cc by
Microbial natural products exhibit a broad spectrum of potent bioactivities, spanning antimicrobial, antiviral and anticancer properties, underscoring their immense potential in drug development. As indispensable sources of pharmaceutical leads and aproved drugs, these metabolites hold a prominent position in innovativ...	10.1016/s1875-5364(20)60024-3	Chemical ecology-driven discovery of bioactive marine natural products as potential drug leads	PMC13144596	dq0003	cc by
Targeted drug delivery therapy represents a precision medicine approach, the core of which is to concentrate drugs in targeted tissues, thereby improving symptoms while reducing the impact on healthy tissues [CITATION] .	10.1021/acs.chemrev.7b00013	Ligand-targeted drug delivery	PMC13162546	dq0004	cc by
Comparative benchmarking of transcriptional regulatory network inference methods has shown that ICA-based methods perform strongly in recovering known gene modules [CITATION] .	10.1038/s41467-018-03424-4	A comprehensive evaluation of module detection methods for gene expression data	PMC13316221	dq0005	cc by
Such successes highlight the potential of SynCom to address the complexity of plant-pathogen interactions. The microbial community induces plant ethylene reactions to control certain stages of lateral root development [CITATION] .	10.1073/pnas.2301054120	Plant microbiota controls an alternative root branching regulatory mechanism in plants	PMC13265649	dq0006	cc by
CD8⁺ T-cell neutralization in wild-type mice resulted in tumor sizes comparable to those observed in 5-LO-deficient mice, supporting a protective role for CD8⁺ T cells in tumor suppression. [CITATION]	10.4049/jimmunol.1501648	Deletion of 5-Lipoxygenase in the Tumor Microenvironment Promotes Lung Cancer Progression and Metastasis through Regulating T Cell Recruitment	PMC13313223	dq0007	cc by
An early implementation employing the Cas9 DNA endonuclease, RNA presynthesized in vitro, and a single-strand DNA template successfully achieved site-specific deletions and insertions [CITATION] .	10.3389/fmicb.2018.01157	Efficient CRISPR-Cas9 Gene Disruption System in Edible-Medicinal Mushroom Cordyceps militaris	PMC13197704	dq0008	cc by
Although lavender essential oil has traditionally been considered the main source of biological activity, increasing evidence suggests that nonvolatile constituents may contribute to the broader biological activity profile of lavender-derived preparations, particularly in relation to antioxidant, antimicrobial, anti-in...	10.3389/fphar.2017.00280	Exploring Pharmacological Mechanisms of Lavender (Lavandula angustifolia) Essential Oil on Central Nervous System Targets	PMC13244516	dq0009	cc by
We previously showed that HC7 efficiently cleaves only mucins with Tn and T O-glycans. [CITATION] Note that the apparent high cleavage of reporters displayed on cells with complex O-glycans is likely due to incomplete sialylation of the mucin reporters on cells resulting in single/low cleavage events and signal loss.	10.1371/journal.pone.0030287	A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes	PMC13003899	dq0010	cc by
Identified loci include genes involved in transcription (E2F4, IRF2BPL), Alu-mediated gene expression regulation (MIR205HG), neuronal function (HTT, ATXN2), and chromatin remodelling (SMARCA2, EP400). Several identified RNAs are transcribed from genes with CAG tract mutations described, mainly those implicated in polyQ...	10.1146/annurev-pathmechdis-012418-012857	Polyglutamine Repeats in Neurodegenerative Diseases	PMC13313202	dq0011	cc by
JAK kinases—particularly JAK1, JAK2, JAK3, and TYK2—are firmly established as druggable nodes due to their essential roles in cytokine receptor signalling and transcriptional control [CITATION] .	10.1080/25785826.2023.2183594	JAK inhibitors ∼ overview∼	PMC13019105	dq0012	cc by
Collectively, these observations support the view that PHB functions less as a canonical viral receptor and more as a context-dependent membrane-associated host factor involved in regulating viral attachment or entry-associated processes [CITATION] .	10.1038/s41419-018-0661-3	Significance of prohibitin domain family in tumorigenesis and its implication in cancer diagnosis and treatment	PMC13288833	dq0013	cc by
To verify this, we established an acidic culture (pH 4.5 and 5 mM urea) to enable long-term cultivation of H. pylori dependent on urease activity (Supplementary Figure S2a). [CITATION] We knocked out urease and found that H.	10.1016/j.ejps.2017.02.004	Epiberberine, a natural protoberberine alkaloid, inhibits urease of Helicobacter pylori and jack bean: Susceptibility and mechanism	PMC13051613	dq0014	cc by
NPH manifests in three subtypes based on the age of ESKD onset: infantile, juvenile, and adolescent/adult. The juvenile subtype predominates clinically, typically culminating in ESKD at a median age of 13.5 years [CITATION] .	10.1016/j.ekir.2022.05.035	Refining kidney survival in 383 genetically characterized patients with nephronophthisis	PMC13292302	dq0015	cc by
In recent years, advances in synthetic biology have enabled detailed elucidation and rational engineering of the l-histidine biosynthetic network [CITATION] .	10.1021/acssynbio.0c00163	Highly Efficient Production of <scp>l</scp> ‑Histidine from Glucose by Metabolically Engineered <i>Escherichia coli</i>	PMC13226134	dq0016	cc by
Early selective inhibitors struggled to achieve high isoform selectivity. For instance, compound 1 (IC50 = 29 nM for FGFR2) showed only 13.4-fold selectivity over FGFR1 [CITATION] (Figure 1).	10.1021/acs.jmedchem.1c01163	From Fragment to Lead: De Novo Design and Development toward a Selective FGFR2 Inhibitor	PMC13037149	dq0017	cc by
Although low IAA production has been described for some Bacteroides spp. under certain conditions, [CITATION] none of the 66 Bacteroidota strains in our collection produced quantifiable IAA in the conditions tested here.	10.1002/mnfr.201200594	Major phenylpropanoid‐derived metabolites in the human gut can arise from microbial fermentation of protein	PMC13290082	dq0018	cc by
Among the proteins that compose the ECM, collagen is the most prominent, corresponding to around 30% of the total protein mass contained in the human body. There are almost 30 collagen types identified with different structures, functions and locations [CITATION] .	10.1016/j.tig.2003.11.004	Collagens, modifying enzymes and their mutations in humans, flies and worms	PMC13262103	dq0019	cc by
Written informed consent was acquired from the patients. Organoid establishment and culture procedures were performed as described in a previous publication. [CITATION]	10.1038/nm.4438	Human primary liver cancer–derived organoid cultures for disease modeling and drug screening	PMC13313231	dq0020	cc by
In-depth biological annotations could provide valuable insights into the ecological roles of BGCs in the gut and improve the functional interpretation of predicted clusters. [CITATION] Knowledge of the temporal dynamics of BGCs allows a better understanding of how SM contribute to the microbial composition structure.	10.1007/s00253-019-09708-z	Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi	PMC12940132	dq0021	cc by
The World Health Organization’s 2025 Global Antimicrobial Resistance and Use Surveillance (GLASS) report reveals that approximately one in six bacterial infections worldwide are now resistant to antibiotics, with resistance rates highest in the WHO South-East Asian and Eastern Mediterranean Regions [CITATION] .	10.1016/s0140-6736(24)01867-1	GBD 2021 Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050	PMC13312829	dq0022	cc by
In response to these limitations, regenerative medicine has emerged as a promising avenue for developing patient-specific replacement tissues and organs. The use of autologous cells or patient-derived stem cells offers a potential route to minimize immune rejection and reduce dependence on donor organs [CITATION] .	10.1186/s13578-021-00698-y	Allogeneic vs. autologous mesenchymal stem/stromal cells in their medication practice	PMC13054579	dq0023	cc by
[CITATION] , and recent data have demonstrated anticoronavirus activity against the Omicron strain (71.4% at 10 μM; IC50 = 6.08 μM) (Uminska et al.	10.1007/s11418-018-1239-1	Oenothein B, dimeric hydrolysable tannin inhibiting HCV invasion from Oenothera erythrosepala	PMC13185070	dq0024	cc by
The isocitrate lyase (AceA) catalyzes the first step of the glyoxylate shunt in Escherichia coli, enabling the assimilation of simple carbon sources such as acetate for net synthesis of biomass and target products (Fig. 1A) [CITATION] .	10.1016/j.coph.2006.06.004	Novel targets for tuberculosis drug discovery	PMC13224001	dq0025	cc by
Previous studies have isolated Tulasnella strains from cultivated plants, [CITATION] however, a comprehensive assessment of the functional diversity among these symbiotic fungi—particularly their efficacy in promoting different developmental stages (germination vs.	10.3390/jof9060597	Isolation of Tulasnella spp. From cultivated Paphiopedilum orchids and screening of germination-enhancing fungi	PMC13285646	dq0026	cc by
Structure-based drug design of HF derivatives and ATP mimetics has further led to the development of more potent and specific inhibitors against protozoans relative to human ProRS, which also binds HF and has become a therapeutic target in some cancer and other human diseases [CITATION] .	10.1016/j.str.2017.07.015	Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis	PMC13003883	dq0027	cc by
Bacillus subtilis is a soil bacterium known for its ability to form biofilms in diverse environments, making it a well-established system for studying bacterial biofilm formation. [CITATION] In this study, we have used B.	10.1128/jb.00102-23	Bacillus subtilis, a Swiss army knife in science and biotechnology	PMC13285563	dq0028	cc by
With advances in sequencing technologies, Boros et al. identified a potential novel PSV genotype in Hungary using viral metagenomics [CITATION] .	10.1099/jgv.0.001410	High prevalence, genetic diversity and a potentially novel genotype of Sapelovirus A (Picornaviridae) in enteric and respiratory samples in Hungarian swine farms	PMC13327365	dq0029	cc by
In some organisms (e.g., Vibrio spp.), flagellar motility promotes early adherence and is subsequently downregulated as cells transition to a sessile state, whereas in others (e.g., Escherichia coli), flagella facilitate surface approach and microcolonial attachment, and may become physically entangled within the devel...	10.1111/1574-6976.12018	Regulation of flagellar motility during biofilm formation	PMC13271334	dq0030	cc by
Leveraging the unique properties of pseudouridine, an RNA Codon Expansion (RCE) strategy was developed to utilize biorthogonal Ψ-based codons (ΨGA, ΨAA, ΨAG) for site-specific incorporation of non-canonical amino acids in mammalian systems. This approach enabled precise decoding of engineered mRNA transcripts bearing t...	10.1038/s41586-025-09165-x	RNA codon expansion via programmable pseudouridine editing and decoding	PMC13090712	dq0031	cc by
Therefore, the observed size variation likely reflects methodological differences combined with intrinsic vesicle heterogeneity rather than significant aggregation or large contaminating particles. [CITATION]	10.1038/s41598-018-37120-6	Isolation and characterization of Lactobacillus-derived membrane vesicles	PMC12977271	dq0032	cc by
These proteins play essential roles in shaping gene expression during development and maintaining cellular homoeostasis. Moreover, RBP functions are often dysregulated in diseases, including cancer and neurodegenerative disorders [CITATION] .	10.1038/s41576-020-00302-y	RNA-binding proteins in human genetic disease	PMC12915805	dq0033	cc by
This conceptual shift has been driven in part by advances in high-throughput analytical technologies, enabling the simultaneous detection and quantification of hundreds to thousands of metabolites, [CITATION] and revealing metabolism as a highly interconnected and responsive network rather than a collection of static p...	10.1023/a:1013713905833	Metabolomics – the link between genotypes and phenotypes	PMC13174010	dq0034	cc by
Notably, alterations in the composition, diversity, or functional capacity of the gut microbiota commonly referred to as dysbiosis have been linked to the development of several complex diseases, including inflammatory bowel disease (IBD), obesity, type 2 diabetes mellitus, and colorectal cancer. [CITATION]	10.1038/nrg3182	The human microbiome: at the interface of health and disease	PMC13274142	dq0035	cc by
A major milestone came in 2009, when GlaxoSmithKline (GSK) developed the first large-scale industrial application of DEL [CITATION] .	10.1038/nchembio.211	Design, synthesis and selection of DNA-encoded small-molecule libraries	PMC13019106	dq0036	cc by
Our previous one-year, two-location study demonstrated that PfFAD3-1 soybeans, which overexpress the Physaria fendleri ω-3 fatty acid desaturase gene (PfFAD3-1), are substantially equivalent to reference varieties in terms of proximates, minerals, and anti-nutrients. [CITATION] In this context, the present study provid...	10.1002/jsfa.11028	Comparison of the seed nutritional composition between conventional varieties and transgenic soybean overexpressing Physaria FAD3 -1	PMC12867456	dq0037	cc by
[CITATION] reported that, this recognition triggers a robust inflammatory response, which is followed by the release of cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β) and interleukin-6 (IL-6).	10.1097/shk.0000000000000473	The endothelium in sepsis	PMC13274129	dq0038	cc by
Our previous work has contributed to this understanding by demonstrating that the 3D-structure of single-species S. maltophilia biofilms is highly strain-specific [CITATION] Extending these investigations to multispecies biofilms, we previously showed that S.	10.1128/aem.02038-20	Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle	PMC13311295	dq0039	cc by
BAs are usually found in fermented foods, such as cheese, wine, and fermented vegetables. However, excessive intake of BAs can cause nausea, gastrointestinal problems, hypertension, and cancer [CITATION] .	10.4315/jfp-21-047	Presence of biogenic amines in food and their public health implications: a review	PMC13318553	dq0040	cc by
Due to its essential role, bacterial IMPDH is an attractive target for the development of novel inhibitors to combat infections caused by multidrug-resistant strains [CITATION] .	10.1002/med.20104	Inosine monophosphate dehydrogenase (IMPDH) as a target in drug discovery	PMC12781933	dq0041	cc by
In fact, a smattering of evidence accumulated over the years indicates that there are important differences in the SA signaling pathway amongst these two clades. [CITATION] Taking it one step further, there appear to be major differences in the SA and ET response within the monocot clade, as reported by Kakei et al.	10.1104/pp.119.4.1251	Hypersensitive Cell Death and Papilla Formation in Barley Attacked by the Powdery Mildew Fungus Are Associated with Hydrogen Peroxide but Not with Salicylic Acid Accumulation1	PMC13313262	dq0042	cc by
A meta-analysis of 82 individual studies and 18 unique health outcomes reported that plasma TMAO is associated with hypertension, CVD, kidney function, diabetes mellitus and all-cause mortality. [CITATION] TMAO is a product of the combined metabolic activities of the gut microbiome and the host.	10.1093/ajcn/nqac074	Gut microbiota–derived metabolite trimethylamine-N-oxide and multiple health outcomes: an umbrella review and updated meta-analysis	PMC13274163	dq0043	cc by
Its classic ‘multi-hit’ pathogenesis is based on aberrant Gd-IgA1-mediated immune dysregulation [CITATION] : Gd-IgA1 elevation (Hit 1) forms immune complexes with autoantibodies in genetically susceptible individuals (Hit 2), and the deposition of these complexes in the mesangium (Hit 3) activates mesangial cells and t...	10.1038/s41581-024-00885-3	The pathogenesis of IgA nephropathy and implications for treatment	PMC13202647	dq0044	cc by
Perinatal exposure to diets differing in fatty acid composition shapes offspring developmental trajectories and metabolism. [CITATION] We observed higher weight gain, though largely from increased muscle mass, and longer intestines and their villi in the n3 group, suggesting enriched nutrient absorption (Figures 2 and ...	10.1113/jphysiol.2008.163477	Maternal nutritional history predicts obesity in adult offspring independent of postnatal diet	PMC13251521	dq0045	cc by
schindleri SR-5-1 encourages morphological and biochemical changes in pea and linseed plants, which enhances their resistance to Cd wastewater stress and improves their general health. [CITATION] Its potential as a bioinoculant for sustainable agriculture in polluted soils is shown by its use in pea growing under cadmi...	10.1007/s11356-022-23920-x	Acinetobacter schindleri SR-5–1 decipher morpho-physio-biochemical and nutritional improvements to Pisum sativum L. And Linum usitatissimum L. maintained under wastewater/cadmium stress	PMC13313229	dq0046	cc by
Furthermore, oseltamivir exerts limited effects on the growth and biofilm formation of bacteria such as Streptococcus pneumoniae [CITATION] , highlighting the need for developing BNA-specific inhibitors.	10.1038/srep27156	Discovery of prenylated flavonoids with dual activity against influenza virus and Streptococcus pneumoniae	PMC13202655	dq0047	cc by
Cyclic peptides represent an essential class of bioactive molecules distinguished by their conformational rigidity, improved stability, and enhanced target affinity relative to linear peptides [CITATION] .	10.1002/anie.202308251	Cyclic peptides for drug development	PMC13320435	dq0048	cc by
Nanozymes refer to nanomaterials with intrinsic enzyme-like catalytic activities. Since the concept was first introduced in 2007, the field has experienced explosive growth [CITATION] .	10.1002/adma.202211041	Nanozymes: Definition, Activity, and Mechanisms	PMC13292316	dq0049	cc by
Thus, in addition to targeting cancer cells, hormonal chemotherapeutics and combination drug regimens also injure healthy cells and contribute to the development of drug resistance [CITATION] .	10.1016/j.biopha.2020.110409	Probiotics for cancer alternative prevention and treatment	PMC13284426	dq0050	cc by
Additionally, a biosensor-based screening method was developed, leading to the identification of an efficient tyramine oxidase mutant (TYOYM9-2) that addressed the toxicity issue caused by the accumulation of the intermediate dopamine, ultimately increasing HT production to 4.69 g/L [CITATION] .	10.1038/s41467-019-08781-2	Promiscuous enzymatic activity-aided multiple-pathway network design for metabolic flux rearrangement in hydroxytyrosol biosynthesis	PMC13251646	dq0051	cc by
The reported morphology of Abraxane is a 130 nm spherical nanoparticle formed by the stacking of numerous HSA molecules, each bound with PTX (Desai [CITATION] .	10.1007/978-981-10-2116-9_6	Nanoparticle Albumin-Bound Paclitaxel (Abraxane®)	PMC12821350	dq0052	cc by
Biofilm development proceeds through sequential stages of initial attachment, intercellular aggregation and maturation, and eventual dispersal [CITATION] .	10.1128/mmbr.00026-19	Staphylococcal biofilm development: structure, regulation, and treatment strategies	PMC13316651	dq0053	cc by
Given the intricate and dynamic nature of physiological environments, the development of biomaterials usually needs extensive experimental studies. Beyond meeting mechanical requirements, biomaterials have to exhibit excellent biocompatibility to minimize adverse biological reactions [CITATION] .	10.1002/jbm.a.36930	Biomaterials and biocompatibility: An historical overview	PMC13196466	dq0054	cc by
Together, these observations support a conceptual and testable link between gut virome sensing and lung mucosal immunity: “gut virome–RIG-I/MDA5–IFN-I–lung mucosal immunity”. [CITATION]	10.1016/j.autrev.2022.103161	Friend or foe: RIG- I like receptors and diseases	PMC13285657	dq0055	cc by
Another recent study [CITATION] reported that the AT domain in PfaB from gammaproteobacterial PUFA synthases exhibits acyltransferase activity, with substrate specificity distinct from that of PfaA-KS-MAT.	10.1002/pro.70497	Prokaryotic <scp>PfaB</scp> is a terminal acyltransferase that determines the final <scp>PUFA</scp> product	PMC13311796	dq0056	cc by
From birth through infancy and into early childhood, the gut microbiome undergoes profound changes, shaping both physiological and immunological development. [CITATION] As the gut microbiome matures, it helps in the establishment of a balanced immune system, protection against harmful pathogens, and proper regulation o...	10.1073/pnas.1002601107	Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns	PMC13232880	dq0057	cc by
PGBs are globular plant proteins that contain a heme group, enabling them to take part in both oxygen and NO metabolism. [CITATION] When plants experience hypoxia, oxy-phytoglobin helps to convert NO into nitrate, a process that is vital for keeping the cell’s redox balance and energy levels stable.	10.1038/ncomms6401	S-nitrosothiols regulate nitric oxide production and storage in plants through the nitrogen assimilation pathway	PMC12818808	dq0058	cc by
As per World Health Organization, 830,000 global deaths were reported due to hepatobiliary cancer or hepatocellular carcinoma (HCC) in 2020 [CITATION] .	10.1016/j.jhep.2023.03.017	Global burden of liver disease: 2023 update	PMC13235279	dq0059	cc by
Ovarian cancer (OC) is a leading gynecological malignancy typically diagnosed in postmenopausal women. Recent epidemiological data, however, indicate a concerning trend toward earlier onset, with increasing cases identified in younger women [CITATION] .	10.3322/caac.21660	Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries	PMC13215434	dq0060	cc by
In contrast, we previously observed that deletion of the capsule biosynthesis gene wcaJ markedly reduced serum resistance in NTUH-K2044 [CITATION] , suggesting that serum survival is more sensitive to major disruptions in capsule biosynthesis than to the regulatory modulation achieved by rmpA2 deletion.	10.3389/fcimb.2023.1108818	Different regulatory mechanisms of the capsule in hypervirulent Klebsiella pneumonia: “direct” wcaJ variation vs. “indirect” rmpA regulation	PMC13313197	dq0061	cc by
Binding can be quantified using immobilized ligand-based or on-cell binding assays, but is most frequently reported as a 1:1 monovalent binding interaction using ligand-binding assays such as surface plasmon resonance (SPR). [CITATION]	10.1080/19420862.2025.2459795	Quantifying antibody binding: techniques and therapeutic implications	PMC13240941	dq0062	cc by
Liquorice has a long history of use in traditional medicine systems worldwide for its diverse pharmacological properties, including anti-inflammatory, anti-viral, and hepatoprotective effects. 18β-GA itself has significant anti-inflammatory effects and great potential in the development of anti-inflammatory drugs [CITA...	10.3389/fphar.2021.681525	Anti-inflammatory and Pro-apoptotic Effects of 18beta-Glycyrrhetinic Acid In Vitro and In Vivo Models of Rheumatoid Arthritis	PMC12973793	dq0063	cc by
To date, there are no established pharmacological or surgical treatments that can effectively improve the prognosis of ICH [CITATION] .	10.1016/s0140-6736(13)60986-1	STICH Ⅱ Investigators. Early surgery versus initial conservative treatment in patients with spontaneous supratentorial lobar intracerebral haematomas (STICH Ⅱ): a randomised trial	PMC13316761	dq0064	cc by
We recently proposed a psychophysiological framework to explain how hypoxia can influence the perception of effort, and how this perceptual response to exercise could be used as a training tool [CITATION] .	10.1080/02640414.2025.2474352	Could the perception of effort help us unravel the potential of “ <i>living low–training high</i> ”? A perspective article	PMC13295106	dq0065	cc by
In addition, one fungal gene encoding the ergothioneine biosynthetic protein NcEgt1 and the ergothioneine biosynthetic C–S lyase NcEgt2 were first identified in Neurospora crassa [CITATION] .	10.1016/j.fgb.2011.12.007	The Neurospora crassa mutant NcΔEgt-1 identifies an ergothioneine biosynthetic gene and demonstrates that ergothioneine enhances conidial survival and protects against peroxide toxicity during conidial germination	PMC13276445	dq0066	cc by
Brachypetalum, further demonstrated that even among physically similar native habitats, root-associated fungal community structure differed significantly across host species, which may reflect the association between habitat filtering and host-specific root microbiomes. [CITATION] Notably, despite their geographical se...	10.1080/15592324.2023.2227365	Habitat ecological characteristics and soil fungal community structure of <i>Paphiopedilum</i> subgenus <i>Brachypetalum</i> Hallier (Orchidaceae) plants in Southwest China	PMC13285552	dq0067	cc by
In these pathways, carbon condensation of formaldehyde to dihydroxyacetone (DHA) and sequential conversion of DHA to fructose-6-phosphate (F6P), the key precursor for synthesis of starch and hexoses, were achieved with the aid of formolase [CITATION] and aldolases.	10.1073/pnas.1500545112	Computational protein design enables a novel one-carbon assimilation pathway	PMC13259622	dq0068	cc by
These supplements are broadly classified as ergogenic (direct) supplements, which acutely enhance performance, and medical (indirect) supplements that enable consistent training and improved physical resilience. Ergogenic supplements can increase power output, endurance and fatigue resistance across both high intensity...	10.1123/ijsnem.2017-0343	Evidence-Based Supplements for the Enhancement of Athletic Performance	PMC12912213	dq0069	cc by
Moreover, increased levels of metal ions that cause redox catastrophe in cells, including iron, have been described in HAND patients and in gp120-treated neurons [CITATION] .	10.1016/j.ajpath.2019.03.004	Nitrosative Stress Is Associated with Dopaminergic Dysfunction in the HIV-1 Transgenic Rat	PMC13312838	dq0070	cc by
Key achievements include the identification of plant-derived compounds, probiotics, and novel acetylcholinesterase (AChE) reactivators as potential therapeutic agents [CITATION] .	10.1155/2020/3960170	Croton campestris A. St.-Hill methanolic fraction in a chlorpyrifos-induced toxicity model in Drosophila melanogaster : protective role of gallic acid	PMC13313226	dq0071	cc by
Studies have demonstrated that disruption of key ESCRT components does not completely abolish exosome secretion, indicating the presence of ESCRT-independent mechanisms [CITATION] .	10.1146/annurev-biochem-013118-111902	Exosomes	PMC13182160	dq0072	cc by
towards the development of a cell-permeable small molecule PROTAC capable of degrading androgen receptor (AR) through recruiting the E3 ligase MDM2. [CITATION] In later years, Buckley et al.	10.1016/j.bmcl.2008.07.114	Targeted intracellular protein degradation induced by a small molecule: En route to chemical proteomics	PMC13084866	dq0073	cc by
Based on the current knowledge, olive leaves contain secoiridoids, particularly oleuropein and its derivatives, as well as simple phenols, such as hydroxytyrosol and tyrosol [CITATION] .	10.3390/pr8091177	Olive Tree Leaves—A Source of Valuable Active Compounds	PMC13318240	dq0074	cc by
SBPs belong to a highly diverse protein superfamily found in both prokaryotes and eukaryotes, with over 266,000 entries in the InterPro database [CITATION] .	10.1093/nar/gkae1082	InterPro: the protein sequence classification resource in 2025	PMC13311272	dq0075	cc by
In addition, NK cells can eradicate tumor cells beyond their CAR construct due to their innate properties, which is a major benefit in the heterogeneous TME of solid tumors and the risk of antigen escape. The first-in-human clinical trial with CAR NK cells has shown promising results in CD19+ hematological malignancy [...	10.1038/s41591-023-02785-8	Safety, efficacy and determinants of response of allogeneic CD19-specific CAR-NK cells in CD19+ B cell tumors: a phase 1/2 trial	PMC12918307	dq0076	cc by
In addition to this canonical PKS architecture, Pks13 has been shown to harbour acyltransferase activity, suggesting it plays a broader enzymatic role in mycolic acid biosynthesis [CITATION] .	10.1016/j.chembiol.2014.10.011	The Polyketide Synthase Pks13 Catalyzes a Novel Mechanism of Lipid Transfer in Mycobacteria	PMC13324839	dq0077	cc by
found that inhibiting ferroptosis also exacerbates the vicious cycle of bone metastasis in breast tumors. [CITATION] These findings show the crucial involvement of ferroptosis in BRCA progression and therapeutic response.	10.1158/0008-5472.can-24-4391	PRODH2-Mediated metabolism in the bone microenvironment promotes breast cancer metastasis	PMC13327353	dq0078	cc by
Despite progress in understanding the physiological and genetic basis of thermotolerance [CITATION] , the development of robust heat-tolerant cultivars has been constrained by the lack of reliable field-based phenotyping methods.	10.1071/fp11065	Heat-stress-induced reproductive failures in chickpea (Cicer arietinum L.) are associated with impaired sucrose metabolism in leaves and anthers	PMC13311209	dq0079	cc by
In the USA, quantitative analysis of food commodities has shown that 72% of fruits and 45% of vegetables contain detectable neonicotinoids, including acetamiprid, dinotefuran (DINO), flonicamid, imidacloprid, thiacloprid, and thiamethoxam [CITATION] .	10.1021/jf501397m	Quantitative Analysis of Neonicotinoid Insecticide Residues in Foods: Implication for Dietary Exposures	PMC13284504	dq0080	cc by
[CITATION] reported in vivo rat data showing that portal blood was enriched in conjugated forms compared to systemic blood, reinforcing the role of intestinal and hepatic first-pass metabolism in curcumin disposition.	10.1248/bpb.b17-00339	Curcumin β-D-glucuronide plays an important role in maintaining high levels of free curcumin in the blood	PMC13312837	dq0081	cc by
[CITATION] In order to enhance specificity and to reduce off-target editing, engineered variants of Cas9 nucleases have been developed by mutagenesis (Kleinstiver et al.	10.1126/science.1231143	Multiplex Genome Engineering Using CRISPR/Cas Systems	PMC12818331	dq0082	cc by
PET46, a feruloyl esterase isolated from a non-cultivated Candidatus Bathyarchaeota genome recovered from Guaymas Basin deep-sea sediments, hydrolyses semi-crystalline polyethylene terephthalate powder at rates equivalent to wild-type bacterial IsPETase and leaf-branch compost cutinase (LCC) while exhibiting enhanced a...	10.1038/s42004-023-00998-z	An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate	PMC13316681	dq0083	cc by
A metagenomic analysis revealed a significant reduction in the abundance of uric acid-degrading bacteria (e.g., Lachnospiraceae), leading to the accumulation of uric acid precursors. [CITATION] Furthermore, in the pathogenesis of metabolic diseases (such as obesity, T2D, and MAFLD), gut microbiota metabolic reprogrammi...	10.1016/j.chom.2023.05.011	Gut bacterial metabolism contributes to host global purine homeostasis	PMC12990950	dq0084	cc by
muciniphila encodes a large repertoire of glycosidases and accessory enzymes that degrade mucin O-glycans, enabling it to utilize GlcNAc and/or GalNAc as sole carbon and nitrogen sources. [CITATION] Elevated A.	10.1371/journal.pone.0016876	The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes	PMC13313206	dq0085	cc by
muciniphila MucT was found to improve weight loss maintenance and insulin sensitivity in humans with overweight and obesity—here the most prominent effects were observed in subjects with low baseline gut Akkermansia levels. [CITATION]	10.1038/s41591-026-04394-7	Pasteurized Akkermansia muciniphila MucT for weight loss maintenance in people with overweight and obesity: a controlled randomized trial	PMC13313273	dq0086	cc by
A previous study reported that knockout of GS adenylyltransferase and overexpression of GS from Saccharomyces cerevisiae improved glutamine production in C. glutamicum, achieving a titer of 73.5 g L−1 [CITATION] .	10.1016/j.biortech.2021.125799	Enhancing l-glutamine production in Corynebacterium glutamicum by rational metabolic engineering combined with a two-stage pH control strategy	PMC13312541	dq0087	cc by
Similar alterations in exploratory behavior have been reported in previous studies of chronic intestinal inflammation and microbiome perturbation, [CITATION] suggesting that changes in risk-taking behavior may represent an adaptive or compensatory response to chronic physiological stress.	10.1038/s41598-022-19219-z	Colitis-associated intestinal microbiota regulates brain glycine and host behavior in mice	PMC13313184	dq0088	cc by
For instance, the dCas12a-based “MultiduBE” system enables multiplexed base editing to drive complex metabolic reprogramming in bacteria. [CITATION] Concurrently, optimizing transgene expression is critical.	10.1093/nar/gkae228	Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor	PMC13240942	dq0089	cc by
However, since chickpea productivity is adversely affected by both abiotic and biotic stresses, fungi, as one of the obstructive organisms, pose a major threat because 67 out of 172 fungi are reported to affect chickpea, [CITATION] causing severe diseases, including wilt caused by Fusarium oxysporum f.	10.1007/s10681-015-1462-8	Breeding for biotic stress resistance in chickpea: progress and prospects	PMC12928610	dq0090	cc by
nucleatum in atherosclerotic plaques suggests their contribution to vascular endothelial dysfunction and plaque destabilization is induced by the upregulation of pro-inflammatory cytokines and the activation of the immunological response, in terms of increasing cardiovascular diseases. [CITATION] In vitro analyses have...	10.3389/fmicb.2022.798685	Fusobacterium nucleatum Accelerates Atherosclerosis via Macrophage-Driven Aberrant Proinflammatory Response and Lipid Metabolism	PMC13327354	dq0091	cc by
We have previously shown that hypotonic stress activates nucleolar DNA damage response through stabilization of R-loops within rDNA [CITATION] .	10.1093/nar/gkz436	Hypoosmotic stress induces R loop formation in nucleoli and ATR/ATM-dependent silencing of nucleolar transcription	PMC13185464	dq0092	cc by
At later stages, these combined effects are accompanied by reduced excessive ECM deposition and mitigation of fibrotic remodeling, thereby contributing to improved tissue repair outcomes [CITATION] .	10.1038/s41467-025-61795-x	Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models	PMC13316700	dq0093	cc by
The advancement of precision medicine has underscored the critical importance of personalized approaches in cancer treatment. [CITATION] Precision medicine crafts personalized therapeutic interventions based on comprehensive patient profiling.	10.1016/j.ccell.2021.12.004	Functional precision oncology: Testing tumors with drugs to identify vulnerabilities and novel combinations	PMC13224768	dq0094	cc by
Previous efforts to improve PHB under non-limiting nitrogen have focused mainly on blocking intracellular depolymerization for example via deletions on PHB depolymerases encoded by phaZs [CITATION] or strengthening de novo synthesis.	10.1016/j.biortech.2008.11.020	Enhanced production of medium-chain-length polyhydroxyalkanoates (PHA) by PHA depolymerase knockout mutant of Pseudomonas putida KT2442	PMC13101641	dq0095	cc by
To achieve this, L. pneumophila injects up to 330 effector proteins into the cytosol of the host cell through a Dot/Icm type IV secretion system (T4SS) [CITATION] .	10.1099/mic.0.001187	The Legionella pneumophila Dot/Icm type IV secretion system and its effectors	PMC13007446	dq0096	cc by
Mfn2, mainly found at the ERMCS, combines with mitochondrial Mfn1 to form hetero-oligomeric complexes. Disruption of these links, the cell signaling could be disrupted [CITATION] .	10.1016/j.phrs.2018.09.006	Regulation of ER-mitochondria contacts by Parkin via Mfn2	PMC13321281	dq0097	cc by
This balance is especially relevant to situations related to agriculture, where choices based on AI models might have long-run implications on breeding practices, animal welfare, and sustainability [CITATION] .	10.3390/bdcc9080193	Survey on the Role of Mechanistic Interpretability in Generative AI	PMC13214316	dq0098	cc by
For example, a H2 partial pressure of 46 Pa was reported by Laura and Jo in Ref. [CITATION] as the minimum required by A.	10.1111/1462-2920.16429	No acetogen is equal: strongly different H2 thresholds reflect diverse bioenergetics in acetogenic bacteria	PMC13279740	dq0099	cc by

End of preview. Expand in Data Studio

BioChemCite

120 citation-prediction questions in biochemistry, chemistry and biotechnology. Given a sentence from a paper with its citation blanked out, name the paper being cited.

Built in the shape of CiteME, for the same reason and in a different literature.

Why this exists

CiteME measures finding rather than reading, which is the harder and less measured half of a research agent. But its excerpts are machine-learning papers, the densest region of any frontier model's training. A model can recognise the citation and search only to confirm it, which measures recall dressed as retrieval.

These questions sit in wet-lab and process literature, where that advantage is much weaker and where the answer has to be found rather than remembered.

Where the answers come from

Nowhere expensive. JATS articles link every in-text citation to its reference, and the reference carries a DOI:

<xref rid="B30" ref-type="bibr">30</xref>   →   <ref id="B30"> … 10.1016/j.…

So the ground truth ships with the question. No annotation, no LLM judge, no human labelling — and therefore nothing to disagree with.

Fields


`id`	`dq0000` …
`excerpt`	the sentence, with the citation replaced by `[CITATION]`
`target_doi`	DOI of the cited paper — the answer
`target_title`	title of the cited paper
`source_pmcid`	the article the excerpt came from
`source_license`	always `cc by`

How each question was filtered

Roughly one sentence in twenty survives:

Exactly one citation. "as shown previously [4,7,12]" has three right answers and no way to say which was meant.
No author named. "Li et al. [CITATION]" hands over the answer. CiteME obfuscates these; here they are dropped.
Makes a claim. Methods sections cite reagent suppliers in passing. An early build produced "polymerase was obtained from Vazyme [CITATION]" pointing at a Gibson assembly paper — unfindable, and worthless as a question. Methods, Materials and Protocol sections are excluded outright.
120–600 characters. Long enough to carry a specific claim, short enough to stay a citation task rather than a reading one.
Resolves to a DOI, so scoring is exact rather than a title-matching argument.

Capped at four questions per source article, so no single paper dominates.

Licensing

Every source article is CC BY, verified individually against Europe PMC rather than assumed. This matters: about half the open-access literature in these fields is CC BY-NC-ND, and lifting a sentence out of an article and blanking its citation makes a derivative, which ND forbids. Filtering happens at source selection, not afterwards.

source_pmcid is on every row so each excerpt traces back to the article it came from.

Known limitations

Recency. Source articles are recent Europe PMC deposits, so the cited papers skew toward work published before them. Nothing here tests finding very new work.
Europe PMC only, which means life-sciences-indexed venues. Chemistry published outside PMC is under-represented, and conference proceedings are absent entirely.
Difficulty is not calibrated. Some excerpts describe the cited work precisely; others gesture at it. There is no per-question difficulty label and no human baseline — unlike CiteME, which has one at 69.7%.
One citation per question by construction, so nothing here tests disentangling a multi-citation claim.

Building it yourself

The generator is at benchmarks/build_domainqa.py in the Vela repository. Re-running it produces a different draw from current Europe PMC content rather than this exact set.

Built for Vela, a research agent at Idener.

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