Tag: pubmed

Genome Biol. 2026 Jul 23;27(1):235. doi: 10.1186/s13059-026-04207-7.

ABSTRACT

BACKGROUND: Large language models (LLMs) are increasingly used to extract knowledge from text, yet their coverage and reliability in biology remain unclear. Microbial phenotypes are especially important to assess, as comprehensive data remain sparse except for well-studied organisms and they underpin our understanding of microbial characteristics, functional roles, and applications.

RESULTS: Here, we systematically assessed the biological knowledge encoded in publicly available LLMs for structured phenotype assignment of microbial species. We evaluated the performance of up to 57 LLMs across different experiments, including state-of-the-art models such as Claude Sonnet 4 and the GPT-5 family of models. Across phenotypes, LLMs reached accurate assignments for many species, but performance varied widely by model and trait, and no single model dominated. Model self-reported confidence is informative, with higher confidence aligning with higher accuracy, and can be used to prioritize phenotype assignment, effectively distinguishing between high- and low-confidence inferences.

CONCLUSIONS: Overall, our study outlines the utility and limitations of text-based LLMs for phenotype characterization in microbiology.

PMID:42493805 | DOI:10.1186/s13059-026-04207-7

Microbiome. 2026 Jul 23;14(1):186. doi: 10.1186/s40168-026-02463-0.

ABSTRACT

The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape ( https://metaproteomics.org/ ). We outline the Initiative’s organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.

PMID:42493801 | DOI:10.1186/s40168-026-02463-0

Microbiome. 2026 Jul 23;14(1):185. doi: 10.1186/s40168-026-02455-0.

ABSTRACT

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.

PMID:42493800 | DOI:10.1186/s40168-026-02455-0

Stem Cell Res Ther. 2026 Jul 24;17(1):259. doi: 10.1186/s13287-026-05053-x.

ABSTRACT

BACKGROUND: Severe burn injury induces a rapid systemic inflammatory response, and early survival depends heavily on timely fluid resuscitation and thermal support. However, optimal supportive care may be difficult to deliver in austere or resource-limited environments. Placenta-derived choriodecidual mesenchymal stem cells (pcMSCs) possess immunomodulatory properties and may improve outcomes when supportive care is suboptimal. This study investigated whether intravenous pcMSC therapy improves early survival after severe burn injury in a preclinical model.

METHODS: Sixty adult male Sprague-Dawley rats underwent standardized 40% total body surface area full-thickness burns and were randomly assigned to six groups (n = 10/group) differing in fluid resuscitation (1× vs. 3× Ringer’s lactate), thermal support (heating lamp vs. incubator warming), and intravenous pcMSC therapy. Survival was monitored for 14 days and analyzed using Kaplan-Meier methods with log-rank testing. Serum TNF-α, IL-1β, and IL-6 levels, body weight, water intake, and core body temperature were assessed longitudinally in selected groups.

RESULTS: Survival differed significantly among groups, with 93% of deaths occurring within the first 3 days post-burn. Under low-volume resuscitation, survival declined to 30% in untreated animals and improved to 50% with pcMSC therapy, indicating a survival benefit under insufficient resuscitation conditions. With adequate fluid resuscitation and thermal support, survival was high without pcMSCs (80%) and numerically higher with pcMSCs (90%), although this difference was not statistically significant after adjustment. Thermal support exerted a marked effect on outcomes, with warmed animals demonstrating substantially higher survival despite similar or lower fluid volumes. PcMSC treatment attenuated post-burn hypothermia, reduced weight loss and dehydration, and significantly decreased circulating TNF-α, IL-1β, and IL-6 levels.

CONCLUSIONS: Placenta-derived choriodecidual mesenchymal stem cells may confer an additive survival benefit after severe burn injury, particularly under inadequate fluid resuscitation and thermal support, likely through stabilization of body temperature, improved hydration, and attenuation of systemic inflammation, supporting their potential role as an adjunctive therapy in austere or resource-limited settings.

PMID:42493791 | DOI:10.1186/s13287-026-05053-x

BMC Oral Health. 2026 Jul 24;26(1):1335. doi: 10.1186/s12903-026-09358-4.

ABSTRACT

BACKGROUND: This in vitro study aimed to compare and analysis degree of Manufacture accuracy and geometric discrepancy measurements of Cobalt-Chromium (C0-Cr) bar joint attachment supporting a mandibular complete overdenture fabricated directly by Direct Laser Sintering (DMLS) and indirectly fabricated by conventional casting of 3D printed resin pattern using Co-Cr alloys with the same reference design.

METHODS: A total of twelve bar joint attachment for two implant-retained mandibular overdentures were fabricated through additive manufacturing process indirectly by using 3D printed resin pattern and directly by using DMLS (n = six for each group). All the sample specimens of metal bars were scanned and superimposed with the reference STL reference design by using the Geomagic Control X software program.

RESULTS: There was no significant statistical difference in manufacture accuracy and geometric discrepancy in the bars fabricated by DMLS compared to indirectly 3D-printed conventional Co-Cr bars in mandibular implant retained overdenture. The Casted group has a mean of 0.1128 ± 0.006, while the DMLS group has a mean of 0.1206 ± 0.01. There was no significant difference between the groups, Regarding Internal Discrepancy, the Casted group shows a mean of 0.1659 ± 0.118, and the DMLS group has a mean of 0.1678 ± 0.035. The research indicates no significant difference between the groups for this variable.

CONCLUSION: No significant difference in Manufacture accuracy and geometric discrepancy of direct laser sintering versus cast 3D printed resin pattern of Co-Cr bars in mandibular implant retained complete overdenture.

PMID:42493783 | DOI:10.1186/s12903-026-09358-4

Photobiomodul Photomed Laser Surg. 2026 Jul 23:25785478261472294. doi: 10.1177/25785478261472294. Online ahead of print.

ABSTRACT

BACKGROUND: Cervicogenic headache (CGH) is a secondary disorder caused by cervical musculoskeletal dysfunction in the cervical vertebrae, with involvement of the upper three cervical segments. The pain initiates in the neck and is often intensified by head or neck movements. This condition imposes a considerable socioeconomic burden, affecting both community well-being and public health systems.

OBJECTIVE: To explore how high-power laser therapy influences pain intensity, suboccipital muscle activity, functional disability, and quality of life (QoL) in patients with CGH.

METHODS: A randomized controlled trial was conducted on 40 participants (both males and females) diagnosed with CGH for a duration of at least 6 months, experiencing unilateral neck pain radiating to the suboccipital region. Participants were randomly allocated into two equal groups. The study group (A) received high-power Laser therapy in addition to a conventional physical therapy program, while the control group (B) received a placebo laser alongside the same conventional physical therapy program. Both groups received 3 times per week for 6 weeks, with each session lasting approximately 45-60 min. Outcome measures included the visual analog scale for pain intensity measurement, electromyography (EMG) to assess suboccipital muscle myoelectric activity, the Headache Impact Test-6 questionnaire to assess participants’ functional health and well-being, the Neck Disability Index to assess functional impairment, and the 36-Item Short Form Health Survey to evaluate QoL. Assessments were performed before and after the intervention (6 weeks).

RESULTS: Group A showed statistically significant improvements in pain intensity, EMG parameters, functional disability, headache impact, and QoL compared with Group B.

CONCLUSIONS: High-power laser therapy, when used alongside conventional physiotherapy, may be an effective approach for reducing symptoms and improving functional outcomes in patients with CGH.

PMID:42493768 | DOI:10.1177/25785478261472294

J Thromb Thrombolysis. 2026 Jul 23. doi: 10.1007/s11239-026-03359-4. Online ahead of print.

ABSTRACT

Anticoagulation in patients with atrial fibrillation (AF) and liver cirrhosis is challenging due to competing risks of thrombosis and bleeding. While direct oral anticoagulants (DOACs) have emerged as alternatives to warfarin, their comparative safety and effectiveness in cirrhosis remain incompletely defined. We conducted a retrospective cohort study using the TriNetX Global Collaborative Network. Adult patients (≥ 18 years) with AF and cirrhosis receiving DOACs or warfarin were identified. Propensity score matching (1:1) was performed to balance baseline characteristics. The primary outcomes were hepatic decompensation and ischemic stroke within 1 year. Secondary outcomes included all-cause mortality, major bleeding, intracranial hemorrhage, gastrointestinal bleeding, and all-cause hospitalization. Survival (Kaplan-Meier) analysis and hazard ratios were estimated. After propensity score matching, 2,522 matched pairs (5,044 patients) were included. Over 1-year follow-up, hepatic decompensation occurred in 8.8% of DOAC patients and 11.1% of warfarin patients, with a significantly lower risk observed in the DOAC group (HR 0.79, 95% CI 0.67-0.95; p = 0.010). Ischemic stroke occurred in 2.9% of DOAC patients and 2.4% of warfarin patients, with no statistically significant difference between groups (HR 1.22, 95% CI 0.85-1.75; p = 0.289). All-cause mortality was lower in the DOAC group (17.7% vs. 20.3%; HR 0.87, 95% CI 0.77-0.99; p = 0.035). No significant differences were observed in major bleeding (HR 0.84, 95% CI 0.70-1.02), intracranial hemorrhage (HR 0.98, 95% CI 0.59-1.62), gastrointestinal bleeding (HR 0.97, 95% CI 0.77-1.23), or all-cause hospitalization (HR 1.04, 95% CI 0.97-1.12). In patients with atrial fibrillation and cirrhosis, DOAC use was associated with lower risks of hepatic decompensation and all-cause mortality compared with warfarin, while no significant difference was observed in ischemic stroke or other safety outcomes. Given the observational design and modest absolute differences, these findings should be interpreted as associative and hypothesis-generating rather than causal or definitive.

PMID:42493734 | DOI:10.1007/s11239-026-03359-4

J Thromb Thrombolysis. 2026 Jul 23. doi: 10.1007/s11239-026-03349-6. Online ahead of print.

ABSTRACT

Sodium bicarbonate has recently emerged as an alternative additive to purge flow in microaxial blood pumps, offering local antithrombotic effects. However, the systemic effects of additive bicarbonate on coagulation remain incompletely defined. Here, we examined the effect of sodium bicarbonate at varying concentrations (10^{– 2}-10^{– 5}M) on select coagulation parameters to define systemic versus local effects. Fresh human whole blood from healthy adults (N ≥ 4 per assay) was incubated with sodium bicarbonate over a range of concentrations (10^{– 5}-10^{– 2}M). Coagulation and thrombus formation was assessed via whole blood clotting time (WBCT), activated partial thromboplastin time (aPTT), prothrombin time (PT), rotational thromboelastometry (ROTEM) and total thrombus analysis (T-TAS). Sodium bicarbonate at concentrations 10^{– 3}M or less, did not induce significant changes in WBCT, aPTT, PT, ROTEM clot stiffness, or thrombus formation. Notably, at higher bicarbonate concentrations (10^{– 2}M) WBCT was delayed (2.5 ± 0.5 min; p = 0.02), aPTT showed a moderate delay (3.9 ± 2.2 s; p > 0.05), ROTEM revealed increased clot stiffness at 10 min (1.7 ± 0.3 mm; p = 0.004) with high concentrations (10^{– 2} M) and a moderate decrease in thrombus formation (33.5 ± 21.9Kpa∙min; p > 0.05). Sodium bicarbonate, at concentrations encountered during intravenous (IV) use or expected systemic dilution during Impella purge use, was not associated with statistically significant alterations in global coagulation or platelet thrombosis in this in vitro study. Supraphysiologic levels, consistent with via intra-device purge flow in the device microenvironment, produced measurable but mild changes to clotting time and stiffness. These findings underscore the safety and lack of confounding effect of low dose systemic bicarbonate on systemic coagulation, while supporting mechanisms of local device-based antithrombotic efficacy.

PMID:42493731 | DOI:10.1007/s11239-026-03349-6

Clin Oral Investig. 2026 Jul 24;30(8):358. doi: 10.1007/s00784-026-07022-3.

ABSTRACT

OBJECTIVES: To investigate whether dentin pre-treatment with bioactive glass F18 suspensions modifies dentin surface characteristics and influences the bond strength of bioceramic and epoxy resin-based endodontic sealers.

MATERIAL AND METHODS: Extracted human root canals were treated with distilled water, PBS or Bioglass F18 suspensions (2.5%, 5%, or 10%). Dentin surface morphology and elemental composition were analyzed by scanning electron microscopy and energy-dispersive X-ray spectroscopy. Bovine dentin specimens were treated with distilled water or 5% F18 and filled with a bioceramic (Bio-C Sealer) or epoxy resin-based sealer (AH Plus) for interfacial and mechanical analyses. The material-dentin interface was evaluated by micro-Fourier transform infrared spectroscopy after PBS immersion. Push-out and tensile bond strength tests were performed. Statistical analysis was performed using appropriate parametric or non-parametric tests according to data distribution. The level of significance was set at α = 0.05.

RESULTS: Bioglass F18 promoted the deposition of bioactive material on the dentin surface, with comparable effects observed at 5% and 10% concentrations. All F18 concentrations significantly increased the bond strength of both sealers compared with controls (p < 0.05). In tensile testing, dentin pre-treatment with 5% F18 resulted in significantly higher bond strength (p < 0.05). AH Plus exhibited higher bond strength than Bio-C Sealer in both mechanical tests (p < 0.05).

CONCLUSIONS: Dentin pre-treatment with Bioglass F18 enhanced dentin bioactivity and improved the sealer-dentin adhesion for both Bio-C Sealer and AH Plus. The effects were concentration-dependent across different outcomes, with 5% F18 showing favorable performance in tensile bond strength and comparable behavior to 10% F18 in push-out testing.

CLINICAL RELEVANCE: Dentin pre-treatment with Bioglass F18 may improve sealer-dentin interfacial performance under in vitro conditions and could represent a potential adjunctive approach in root canal sealing strategies, pending further long-term and in vivo investigations.

PMID:42493722 | DOI:10.1007/s00784-026-07022-3

Braz J Microbiol. 2026 Jul 24;57(1):215. doi: 10.1007/s42770-026-02015-6.

ABSTRACT

Endotoxin contamination remains a critical challenge in recombinant protein production using Gram-negative bacteria, particularly for intracellularly expressed, positively charged proteins prone to lipopolysaccharide (LPS) binding. This study introduces an efficient upstream strategy for LPS removal before the cell disruption, aimed at reducing the endotoxin contamination load in the downstream purification process. A recombinant cationic protein (named as 4mer-S3-DP) was expressed in Escherichia coli (E. coli) BL21 (DE3), and biomass was treated with varying concentrations and incubation times of Tris-HCl and EDTA, as defined by a central composite design (CCD) of response surface methodology (RSM). Endotoxin levels in inclusion bodies (IBs) were quantified using a chromogenic Limulus Amebocyte Lysate (LAL) assay, and statistical modelling was performed to optimize treatment conditions. The final quadratic model demonstrated high predictive accuracy, and response surface analysis revealed that both insufficient and excessive treatment conditions could increase endotoxin contamination. Optimal conditions, consisting of 70 mM Tris-HCl for 30 min and 60 mM EDTA for 5 min, achieved a 2.7-log reduction in endotoxin levels (99.8%) without compromising protein integrity, as confirmed by SDS-PAGE analysis. Experimental validation of the optimum criteria predicted by this model showed no significant difference between predicted and observed endotoxin levels of IBs. This upstream intervention as a simple and effective endotoxin removal approach before the cell lysis could be adaptable to other recombinant proteins expressed in Gram-negative bacterial.

PMID:42493718 | DOI:10.1007/s42770-026-02015-6