REXO5 promotes genomic integrity through regulating R-loop using its exonuclease activity.

Chronic myeloid leukemia (CML), caused by BCR::ABL1 fusion gene, is known to regulate disease progression by altering the expression of genes. However, the molecular mechanisms underlying these changes are largely unknown. In this study, we identified RNA Exonuclease 5 (REXO5/LOC81691) as a novel gene with elevated mRNA expression levels in chronic myeloid leukemia (CML) patients. Additionally, using the REXO5 knockout (KO) K562 cell lines, we revealed a novel role for REXO5 in the DNA damage response (DDR). Compared to wild-type (WT) cells, REXO5 KO cells showed an accumulation of R-loops and increased DNA damage. We demonstrated that REXO5 translocates to sites of DNA damage through its RNA recognition motif (RRM) and selectively binds to R loops. Interestingly, we identified that REXO5 regulates R-loop levels by degrading mRNA within R-loop using its exonuclease domain. REXO5 KO showed ATR-CHK1 activation. Collectively, we demonstrated that REXO5 plays a key role in the physiological control of R-loops using its exonuclease domain. These findings may provide novel insights into how REXO5 expression changes contribute to CML pathogenesis.

Primary palatal sarcoma exhibiting EWSR1::RORß fusion: a first case report and literature review.

In this report, a tumor exhibited EWSR1::RORß gene fusion, to our knowledge, is the first such reported case. The Ewing sarcoma breakpoint region 1 gene (EWSR1) is known to be associated with several soft tissue tumors although its specific role remains unclear. Its fusion with a member of the ETS family, including FLI1 and ERG, results in Ewing sarcoma, and its fusion with other genes unrelated to the ETS family, including NFATC2 and PATZ1, results in round cell sarcoma with EWSR1-non-ETS fusions, previously referred to as Ewing-like sarcoma. RORß encodes retinoic acid-related orphan receptor ß, a nuclear receptor (NR), and is involved in circadian rhythm modulation and cancer regulation. The specific role of RORß in tumorigenesis remains unclear; however, this case report suggests that it may form part of a new tumorigenic entity.

Unlocking Phytate with Phytase: A Meta-Analytic View of Meat-Type Chicken Muscle Growth and Bone Mineralization Potential.

The inclusion of exogenous phytase in P- and Ca-deficient diets of broilers to address the growing concern about excessive P excretion into the environment over the years has been remarkably documented. However, responses among these studies have been inconsistent because of the several factors affecting P utilization. For this reason, a systematic review with a meta-analysis of results from forty-one studies published from 2000 to February 2024 was evaluated to achieve the following: (1) quantitatively summarize the size of phytase effect on growth performance, bone strength and mineralization in broilers fed diets deficient in P and Ca and (2) estimate and explore the heterogeneity in the effect size of outcomes using subgroup and meta-regression analyses. The quality of the included studies was assessed using the Cochrane Collaboration's SYRCLE risk of bias checklists for animal studies. Applying the random effects models, Hedges' g effect size of supplemented phytase was calculated using the R software (version 4.3.3, Angel Food Cake) to determine the standardized mean difference (SMD) at a 95% confidence interval. Subgroup analysis and meta-regression were used to further explore the effect size heterogeneity (PSMD ≤ 0.05, I2 > 50%, n ≥ 10). The meta-analysis showed that supplemental phytase increases ADFI and BWG and improves FCR at each time point of growth (p < 0.0001). Additionally, phytase supplementation consistently increased tibia ash, P and Ca, and bone strength (p < 0.0001) of broilers fed P- and Ca-deficient diets. The results of the subgroup and meta-regression analyses showed that the age and strain of broiler, dietary P source, and the duration of phytase exposure significantly influence the effect size of phytase on growth and bone parameters. In conclusion, phytase can attenuate the effect of reducing dietary-available phosphorus and calcium and improve ADFI, BWG, and FCR, especially when added to starter diets. It further enhances bone ash, bone mineralization, and the bone-breaking strength of broilers, even though the effects of bone ash and strength can be maximized in the starter phase of growth. However, the effect sizes of phytase were related to the age and strain of the broiler, dietary P source, and the duration of phytase exposure rather than the dosage.

DNA-encoded probe-based assay for profiling plant kinase activities.

Elucidating kinase-substrate relationships is pivotal for deciphering cellular signaling mechanisms, yet it remains challenging due to the complexity of kinase networks. Herein, we report the development of a versatile DNA-based kinase assay platform for high-throughput profiling of plant protein kinase activities and substrate preferences. Our approach employs DNA-linked peptide substrates, facilitating quantitative and specific kinase activity detection through next-generation DNA sequencing. Leveraging DNA barcodes as quantitative readouts, our approach establishes a high-throughput, sensitive, and specific platform for dissecting kinase-substrate networks in plants, representing a powerful tool for elucidating signaling mechanisms in plants.

Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers.

Critical evaluation of computational tools for predicting variant effects is important considering their increased use in disease diagnosis and driving molecular discoveries. In the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, a dataset of 28 STK11 rare variants (27 missense, 1 single amino acid deletion), identified in primary non-small cell lung cancer biopsies, was experimentally assayed to characterize computational methods from four participating teams and five publicly available tools. Predictors demonstrated a high level of performance on key evaluation metrics, measuring correlation with the assay outputs and separating loss-of-function (LoF) variants from wildtype-like (WT-like) variants. The best participant model, 3Cnet, performed competitively with well-known tools. Unique to this challenge was that the functional data was generated with both biological and technical replicates, thus allowing the assessors to realistically establish maximum predictive performance based on experimental variability. Three out of the five publicly available tools and 3Cnet approached the performance of the assay replicates in separating LoF variants from WT-like variants. Surprisingly, REVEL, an often-used model, achieved a comparable correlation with the real-valued assay output as that seen for the experimental replicates. Performing variant interpretation by combining the new functional evidence with computational and population data evidence led to 16 new variants receiving a clinically actionable classification of likely pathogenic (LP) or likely benign (LB). Overall, the STK11 challenge highlights the utility of variant effect predictors in biomedical sciences and provides encouraging results for driving research in the field of computational genome interpretation.

Influence of Intermolecular Structural Effects on Radiative Efficiency in Xanthene-Based Carboranyl Luminophores.

Two o-carboranes with (i) 9,9-dimethyl-9H-xanthene and (ii) spiro[fluorene-9,9'-xanthene] moieties (XTC and sXTC, respectively) were prepared and characterized. Single X-ray crystallography analysis revealed the presence of intermolecular hydrogen bonds in XTC crystals. Although both compounds did not exhibit emission in tetrahydrofuran solutions at 298 K, intense bluish emission was observed in the solid states and frozen tetrahydrofuran solutions at 77 K. According to the results of theoretical calculations, this emission originated from an intramolecular charge transfer (ICT) transition with the o-carborane moiety. The absolute quantum efficiency (Φem) of the ICT-based emission in the film state equaled 49% for XTC and 20% for sXTC but was as high as 90% for the crystals of both compounds. The crystal structures of XTC and sXTC revealed that the o-carboranyl-appended phenyl plane was orthogonal (85-89°) to the carbon-carbon bonding axis in the o-carborane, indicating the existence of a strong exo-π-interaction, which was identified as the structural basis for the ICT-based transition. These results implied that the intermolecular structural effect of XTC in the randomly aggregated solid state (film) helped maintain the above orthogonality and, hence, the high efficiency from the ICT radiative mechanism. Thus, we concluded that the ICT radiative efficiency of o-carboranyl luminophores in the aggregated solid state can be controlled by specific intermolecular interactions and that the molecular geometric design inducing this feature can be important for developing highly efficient carboranyl luminophores.

Visible-Light-Promoted Enantioselective α-Amidation of Aldehydes by Harnessing Organo-Iron Dual Catalysis.

The strategic integration of organocatalysis with transition-metal catalysis to achieve otherwise unattainable stereoselective transformations may serve as a powerful synthetic tool. Herein, we present a synthetically versatile α-amidation of aldehydes by leveraging dual iron and chiral enamine catalysis in an enantioselective manner (up to >99:1 er). Experimental and computational studies have led us to propose a new mechanistic platform, wherein visible-light-promoted LMCT generates [Fe(II)Cl3-], which effectively activates dioxazolones to form an iron-acylnitrenoid radical that inserts into chiral enamine intermediates.

Is immediate dental implant in fibula free flap beneficial for implant survival and osteoradionecrosis in jaw reconstruction?

OBJECTIVES: This study aimed to compare the risk of osteoradionecrosis and implant survival in oral cancer patients undergoing immediate dental implants during jaw reconstruction, termed "Jaw in a Day" (JIAD), with those receiving no implants or delayed implants (non-JIAD). PATIENTS & METHODS: Clinicopathologic data were collected from prospectively enrolled JIAD patients (n = 10, 29 implants) and retrospectively from non-JIAD patients (n = 117, 86 implants). Survival analyses were performed to assess implant survival and osteoradionecrosis-free survival. RESULTS: Osteoradionecrosis occurred in 0 % of JIAD cases compared to 19.3 % in non-JIAD cases without implants and 71.4 % in non-JIAD cases with delayed implants (p = 0.008). Osteoradionecrosis-free survival was significantly better in the JIAD group than the non-JIAD group (p = 0.0059). Implants in the JIAD group all survived regardless of radiation therapy (29/29, 100 %) and 95.1 % (58/61) of implants survived in delayed implants in non-irradiated fibula without radiotherapy. Meanwhile, only 11 of 25 implants placed in irradiated fibula flaps survived, even when the implants were placed after a median time interval of 624 days after radiotherapy, and none of them were earlier than 360 days. The survival analysis revealed a significant difference (p < 0.0001). CONCLUSION: JIAD appears to offer superior outcomes in terms of implant survival and osteoradionecrosis prevention compared to delayed implant placement. Placing implants in irradiated fibula, even after years, significantly poses high risk of implant failure and osteoradionecrosis. JIAD represents a promising approach for optimal rehabilitation, particularly in oral cancer patients requiring postoperative radiotherapy. Proper positioning and orientation of implants and flaps are crucial for implant survival.

Prediction of lifespan and assessing risk factors of large-sample implant prostheses: a multicenter study.

PURPOSE: This study aimed to analyze factors influencing the success and failure of implant prostheses and to estimate the lifespan of prostheses using standardized evaluation criteria. An online survey platform was utilized to efficiently gather large samples from multiple institutions. MATERIALS AND METHODS: During the one-year period, patients visiting 16 institutions were assessed using standardized evaluation criteria (KAP criteria). Data from these institutions were collected through an online platform, and various statistical analyses were conducted. Risk factors were assessed using both the Cox proportional hazard model and Cox regression analysis. Survival analysis was conducted using Kaplan-Meier analysis and nomogram, and lifespan prediction was performed using principal component analysis. RESULTS: The number of patients involved in this study was 485, with a total of 841 prostheses evaluated. The median survival was estimated to be 16 years with a 95% confidence interval. Factors found to be significantly associated with implant prosthesis failure, characterized by higher hazard ratios, included the 'type of clinic', 'type of antagonist', and 'plaque index'. The lifespan of implant prostheses that did not fail was estimated to exceed the projected lifespan by approximately 1.34 years. CONCLUSION: To ensure the success of implant prostheses, maintaining good oral hygiene is crucial. The estimated lifespan of implant prostheses is often underestimated by approximately 1.34 years. Furthermore, standardized form, online platform, and visualization tool, such as nomogram, can be effectively utilized in future follow-up studies.

Loop-mediated isothermal amplification polymerase chain reaction in place of a modified Knott test in screening dogs for heartworm (Dirofilaria immitis) infection combined with antigen detection test.

OBJECTIVE: To improve the current recommendations for the diagnosis of canine heartworm (Dirofilaria immitis) disease. ANIMALS: Blood samples collected from 35 shelter dogs in the Republic of Korea. METHODS: Samples were tested for the presence of microfilaria using the modified Knott (MK) test and D immitis DNA using species-specific loop-mediated isothermal amplification (LAMP) PCR. The blood samples were additionally assessed for the presence of heartworm antigens using the Antigen Rapid Canine Heartworm AG Test Kit 2.0 (Bionote Co). The performance of the MK test and LAMP PCR was assessed through statistical analysis, with a paired McNemar test utilized for comparison. RESULTS: The heartworm antigen was detected in 28.5% of the subjects. Of the 10 positive animals, the MK test detected microfilaria in 4 of 35 (11.4%) animals, and LAMP PCR detected D immitis DNA in 6 of 35 (17.1%). The results of this study indicate that the LAMP PCR showed more positive results in samples compared to the conventional MK test. CLINICAL RELEVANCE: The D immitis-specific LAMP PCR assay has the potential to function as an alternative to current detection methods. It could complement the existing antigen detection tests in diagnosing canine heartworm infections.

Early dose reduction of dasatinib does not compromise clinical outcomes in patients with chronic myeloid leukemia: A comparative analysis of two prospective trials.

Dasatinib is a potent second-generation tyrosine kinase inhibitor (TKI) used as a first-line treatment option for patients with chronic myeloid leukemia (CML). Currently, dose modification due to adverse events (AEs) is common in patients treated with dasatinib. This study compared the outcomes of two sequential prospective trials that enrolled patients with newly diagnosed chronic phase of CML (CP-CML) and initiated dasatinib at a starting dose of 100 mg daily. In the PCR-DEPTH study, CP-CML patients who started dasatinib 100 mg daily were enrolled and followed up, while in the DAS-CHANGE study, when patients achieved early molecular response with any grade of AEs were enrolled and treated with dasatinib 80 mg once daily. A total of 102 patients (PCR-DEPTH) and 90 patients (DAS-CHANGE) were compared. Although the median value of the relative dose intensity (RDI) of dasatinib was significantly higher in PCR-DEPTH than in DAS-CHANGE (99.6 % vs. 80.1 %, p <0.001), the MMR rate at 12months showed a trend toward superiority in DAS-CHANGE compared to PCR-DEPTH (77.1 % vs 65.2 %, p = 0.084). The frequencies of MR4.0 at 24 and 36 months were higher in DAS-CHANGE than in PCR-DEPTH (44.4 % vs 28.8 %, p = 0.052 and 63.6 % vs 40.3 %, p= 0.013, respectively). RDIs were not different according to the MMR, MR4.0 or MR4.5 in analyses using a pooled population. Our results suggest that early dose reduction of dasatinib does not compromise efficacy in patients achieving EMR at 3 months and could be an interventional strategy for improving long term outcomes.

Photoinduced Group Transposition via Iridium-Nitrenoid Leading to Amidative Inner-Sphere Aryl Migration.

We herein report a fundamental mechanistic investigation into photochemical metal-nitrenoid generation and inner-sphere transposition reactivity using organometallic photoprecursors. By designing Cp*Ir(hydroxamate)(Ar) complexes, we induced photo-initiated ligand activation, allowing us to explore the amidative σ(Ir-aryl) migration reactivity. A combination of experimental mechanistic studies, femtosecond transient absorption spectroscopy, and density functional theory (DFT) calculations revealed that the metal-to-ligand charge transfer enables the σ(N-O) cleavage, followed by Ir-acylnitrenoid generation. The final inner-sphere σ(Ir-aryl) group migration results in a net amidative group transposition.

Geometry-Driven Fabrication of Mini-Tablets via 3D Printing: Correlating Release Kinetics with Polyhedral Shapes.

The aim of this study was to fabricate mini-tablets of polyhedrons containing theophylline using a fused deposition modeling (FDM) 3D printer, and to evaluate the correlation between release kinetics models and their geometric shapes. The filaments containing theophylline, hydroxypropyl cellulose (HPC), and EUDRAGIT RS PO (EU) could be obtained with a consistent thickness through pre-drying before hot melt extrusion (HME). Mini-tablets of polyhedrons ranging from tetrahedron to icosahedron were 3D-printed using the same formulation of the filament, ensuring equal volumes. The release kinetics models derived from dissolution tests of the polyhedrons, along with calculations for various physical parameters (edge, SA: surface area, SA/W: surface area/weight, SA/V: surface area/volume), revealed that the correlation between the Higuchi model and the SA/V was the highest (R2 = 0.995). It was confirmed that using 3D- printing for the development of personalized or pediatric drug products allows for the adjustment of drug dosage by modifying the size or shape of the drug while maintaining or controlling the same release profile.

Preparation and Evaluation of Inhalable Microparticles with Improved Aerodynamic Performance and Dispersibility Using L-Leucine and Hot-Melt Extrusion.

Dry-powder inhalers (DPIs) are valued for their stability but formulating them is challenging due to powder aggregation and limited flowability, which affects drug delivery and uniformity. In this study, the incorporation of L-leucine (LEU) into hot-melt extrusion (HME) was proposed to enhance dispersibility while simultaneously maintaining the high aerodynamic performance of inhalable microparticles. This study explored using LEU in HME to improve dispersibility and maintain the high aerodynamic performance of inhalable microparticles. Formulations with crystalline itraconazole (ITZ) and LEU were made via co-jet milling and HME followed by jet milling. The LEU ratio varied, comparing solubility, homogenization, and aerodynamic performance enhancements. In HME, ITZ solubility increased, and crystallinity decreased. Higher LEU ratios in HME formulations reduced the contact angle, enhancing mass median aerodynamic diameter (MMAD) size and aerodynamic performance synergistically. Achieving a maximum extra fine particle fraction of 33.68 ± 1.31% enabled stable deep lung delivery. This study shows that HME combined with LEU effectively produces inhalable particles, which is promising for improved drug dispersion and delivery.

The single-cell opioid responses in the context of HIV (SCORCH) consortium.

Substance use disorders (SUD) and drug addiction are major threats to public health, impacting not only the millions of individuals struggling with SUD, but also surrounding families and communities. One of the seminal challenges in treating and studying addiction in human populations is the high prevalence of co-morbid conditions, including an increased risk of contracting a human immunodeficiency virus (HIV) infection. Of the ~15 million people who inject drugs globally, 17% are persons with HIV. Conversely, HIV is a risk factor for SUD because chronic pain syndromes, often encountered in persons with HIV, can lead to an increased use of opioid pain medications that in turn can increase the risk for opioid addiction. We hypothesize that SUD and HIV exert shared effects on brain cell types, including adaptations related to neuroplasticity, neurodegeneration, and neuroinflammation. Basic research is needed to refine our understanding of these affected cell types and adaptations. Studying the effects of SUD in the context of HIV at the single-cell level represents a compelling strategy to understand the reciprocal interactions among both conditions, made feasible by the availability of large, extensively-phenotyped human brain tissue collections that have been amassed by the Neuro-HIV research community. In addition, sophisticated animal models that have been developed for both conditions provide a means to precisely evaluate specific exposures and stages of disease. We propose that single-cell genomics is a uniquely powerful technology to characterize the effects of SUD and HIV in the brain, integrating data from human cohorts and animal models. We have formed the Single-Cell Opioid Responses in the Context of HIV (SCORCH) consortium to carry out this strategy.

Assessment of traumatic mandibular nerve using MR neurography sequence: a preliminary study.

BACKGROUND: Iatrogenic mandibular nerve damage resulting from oral surgeries and dental procedures is painful and a formidable challenge for patients and oral surgeons alike, mainly because the absence of objective and quantitative methods for diagnosing nerve damage renders treatment and compensation ambiguous while often leading to medico-legal disputes. The aim of this study was to examine discriminating factors of traumatic mandibular nerve within a specific magnetic resonance imaging (MRI) protocol and to suggest tangible diagnostic criteria for peripheral trigeminal nerve injury. METHODS: Twenty-six patients with ipsilateral mandibular nerve trauma underwent T2 Flex water, 3D short tau inversion recovery (STIR), and diffusion-weighted imaging (DWI) acquired by periodically rotating overlapping parallel lines with enhanced reconstruction (PROPELLER) pulse sequences; 26 injured nerves were thus compared with contra-lateral healthy nerves at anatomically corresponding sites. T2 Flex apparent signal to noise ratio (FSNR), T2 Flex apparent nerve-muscle contrast to noise ratio (FNMCNR) 3D STIR apparent signal to noise ratio (SSNR), 3D STIR apparent nerve-muscle contrast to noise ratio (SNMCNR), apparent diffusion coefficient (ADC) and area of cross-sectional nerve (Area) were evaluated. RESULTS: Mixed model analysis revealed FSNR and FNMCNR to be the dual discriminators for traumatized mandibular nerve (p < 0.05). Diagnostic performance of both parameters was also determined with area under the receiver operating characteristic curve (AUC for FSNR = 0.712; 95% confidence interval [CI]: 0.5660, 0.8571 / AUC for FNMCNR = 0.7056; 95% confidence interval [CI]: 1.011, 1.112). CONCLUSIONS: An increase in FSNR and FNMCNR within our MRI sequence seems to be accurate indicators of the presence of traumatic nerve. This prospective study may serve as a foundation for sophisticated model diagnosing trigeminal nerve trauma within large patient cohorts.

Critical assessment of missense variant effect predictors on disease-relevant variant data.

Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity of missense variants is necessary to evaluate their clinical and research utility and suggest directions for future improvement. Here, as part of the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, we assess missense variant effect predictors (or variant impact predictors) on an evaluation dataset of rare missense variants from disease-relevant databases. Our assessment evaluates predictors submitted to the CAGI6 Annotate-All-Missense challenge, predictors commonly used by the clinical genetics community, and recently developed deep learning methods for variant effect prediction. To explore a variety of settings that are relevant for different clinical and research applications, we assess performance within different subsets of the evaluation data and within high-specificity and high-sensitivity regimes. We find strong performance of many predictors across multiple settings. Meta-predictors tend to outperform their constituent individual predictors; however, several individual predictors have performance similar to that of commonly used meta-predictors. The relative performance of predictors differs in high-specificity and high-sensitivity regimes, suggesting that different methods may be best suited to different use cases. We also characterize two potential sources of bias. Predictors that incorporate allele frequency as a predictive feature tend to have reduced performance when distinguishing pathogenic variants from very rare benign variants, and predictors supervised on pathogenicity labels from curated variant databases often learn label imbalances within genes. Overall, we find notable advances over the oldest and most cited missense variant effect predictors and continued improvements among the most recently developed tools, and the CAGI Annotate-All-Missense challenge (also termed the Missense Marathon) will continue to assess state-of-the-art methods as the field progresses. Together, our results help illuminate the current clinical and research utility of missense variant effect predictors and identify potential areas for future development.