Association of non-insulin-based insulin resistance indices with disease severity and adverse outcome in idiopathic pulmonary arterial hypertension: a multi-center cohort study.

BACKGROUND: Insulin resistance (IR) plays an important role in the pathophysiology of cardiovascular disease. Recent studies have shown that diabetes mellitus and impaired lipid metabolism are associated with the severity and prognosis of idiopathic pulmonary arterial hypertension (IPAH). However, the relationship between IR and pulmonary hypertension is poorly understood. This study explored the association between four IR indices and IPAH using data from a multicenter cohort. METHODS: A total of 602 consecutive participants with IPAH were included in this study between January 2015 and December 2022. The metabolic score for IR (METS-IR), triglyceride to high-density lipoprotein cholesterol (TG/HDL-C) ratio, triglyceride and glucose (TyG) index, and triglyceride-glucose-body mass index (TyG-BMI) were used to quantify IR levels in patients with IPAH. The correlation between non-insulin-based IR indices and long-term adverse outcomes was determined using multivariate Cox regression models and restricted cubic splines. RESULTS: During a mean of 3.6 years' follow-up, 214 participants experienced all-cause death or worsening condition. Compared with in low to intermediate-low risk patients, the TG/HDL-C ratio (2.9 ± 1.7 vs. 3.3 ± 2.1, P = 0.003) and METS-IR (34.5 ± 6.7 vs. 36.4 ± 7.5, P < 0.001) were significantly increased in high to intermediate-high risk patients. IR indices correlated with well-validated variables that reflected the severity of IPAH, such as the cardiac index and stroke volume index. Multivariate Cox regression analyses indicated that the TyG-BMI index (hazard ratio [HR] 1.179, 95% confidence interval [CI] 1.020, 1.363 per 1.0-standard deviation [SD] increment, P = 0.026) and METS-IR (HR 1.169, 95% CI 1.016, 1.345 per 1.0-SD increment, P = 0.030) independently predicted adverse outcomes. Addition of the TG/HDL-C ratio and METS-IR significantly improved the reclassification and discrimination ability beyond the European Society of Cardiology (ESC) risk score. CONCLUSIONS: IR is associated with the severity and long-term prognosis of IPAH. TyG-BMI and METS-IR can independently predict clinical worsening events, while METS-IR also provide incremental predictive performance beyond the ESC risk stratification.

A Survey of 6DoF Object Pose Estimation Methods for Different Application Scenarios.

Recently, 6DoF object pose estimation has become increasingly important for a broad range of applications in the fields of virtual reality, augmented reality, autonomous driving, and robotic operations. This task involves extracting the target area from the input data and subsequently determining the position and orientation of the objects. In recent years, many new advances have been made in pose estimation. However, existing reviews have the problem of only summarizing category-level or instance-level methods, and not comprehensively summarizing deep learning methods. This paper will provide a comprehensive review of the latest progress in 6D pose estimation to help researchers better understanding this area. In this study, the current methods about 6DoF object pose estimation are mainly categorized into two groups: instance-level and category-level groups, based on whether it is necessary to acquire the CAD model of the object. Recent advancements about learning-based 6DoF pose estimation methods are comprehensively reviewed. The study systematically explores the innovations and applicable scenarios of various methods. It provides an overview of widely used datasets, task metrics, and diverse application scenarios. Furthermore, state-of-the-art methods are compared across publicly accessible datasets, taking into account differences in input data types. Finally, we summarize the challenges of current tasks, methods for different applications, and future development directions.

Enhanced YOLOv5s-Based Algorithm for Industrial Part Detection.

In complex industrial environments, accurate recognition and localization of industrial targets are crucial. This study aims to improve the precision and accuracy of object detection in industrial scenarios by effectively fusing feature information at different scales and levels, and introducing edge detection head algorithms and attention mechanisms. We propose an improved YOLOv5-based algorithm for industrial object detection. Our improved algorithm incorporates the Crossing Bidirectional Feature Pyramid (CBiFPN), effectively addressing the information loss issue in multi-scale and multi-level feature fusion. Therefore, our method can enhance detection performance for objects of varying sizes. Concurrently, we have integrated the attention mechanism (C3_CA) into YOLOv5s to augment feature expression capabilities. Furthermore, we introduce the Edge Detection Head (EDH) method, which is adept at tackling detection challenges in scenes with occluded objects and cluttered backgrounds by merging edge information and amplifying it within the features. Experiments conducted on the modified ITODD dataset demonstrate that the original YOLOv5s algorithm achieves 82.11% and 60.98% on mAP@0.5 and mAP@0.5:0.95, respectively, with its precision and recall being 86.8% and 74.75%, respectively. The performance of the modified YOLOv5s algorithm on mAP@0.5 and mAP@0.5:0.95 has been improved by 1.23% and 1.44%, respectively, and the precision and recall have been enhanced by 3.68% and 1.06%, respectively. The results show that our method significantly boosts the accuracy and robustness of industrial target recognition and localization.

Adaptive evolution and co-evolution of chloroplast genomes in Pteridaceae species occupying different habitats: overlapping residues are always highly mutated.

BACKGROUND: The evolution of protein residues depends on the mutation rates of their encoding nucleotides, but it may also be affected by co-evolution with other residues. Chloroplasts function as environmental sensors, transforming fluctuating environmental signals into different physiological responses. We reasoned that habitat diversity may affect their rate and mode of evolution, which might be evidenced in the chloroplast genome. The Pteridaceae family of ferns occupy an unusually broad range of ecological niches, which provides an ideal system for analysis. RESULTS: We conducted adaptive evolution and intra-molecular co-evolution analyses of Pteridaceae chloroplast DNAs (cpDNAs). The results indicate that the residues undergoing adaptive evolution and co-evolution were mostly independent, with only a few residues being simultaneously involved in both processes, and these overlapping residues tend to exhibit high mutations. Additionally, our data showed that Pteridaceae chloroplast genes are under purifying selection. Regardless of whether we grouped species by lineage (which corresponded with ecological niches), we determined that positively selected residues mainly target photosynthetic genes. CONCLUSIONS: Our work provides evidence for the adaptive evolution of Pteridaceae cpDNAs, especially photosynthetic genes, to different habitats and sheds light on the adaptive evolution and co-evolution of proteins.

Coptisine modulates the pharmacokinetics of florfenicol by targeting CYP1A2, CYP2C11 and CYP3A1 in the liver and P-gp in the jejunum of rats: a pilot study.

Coptisine (COP) is the main active ingredient of Coptis chinensis. In Chinese veterinary clinics, Coptis chinensis is commonly used alongside florfenicol to treat intestinal infections. The goal of this study was to investigate the impact of COP co-administration on the pharmacokinetics of florfenicol in rats.Male Sprague-Dawley rats were orally administered COP (50 mg/kg BW) or sterile water for 7 consecutive days, followed by a single oral dose of florfenicol (25 mg/kg BW) on the 8th day. Pharmacokinetics of florfenicol were analysed using non-compartmental methods, while expression levels of cytochrome P450 (CYP) isoforms in the liver and P-glycoprotein (P-gp) in the jejunum were measured using real-time RT-PCR, Western blot and immunohistochemical analyses.Co-administration of COP and florfenicol significantly increased AUC(0-∞), MRT(0-∞), and Cmax of florfenicol, while CLz/F was significantly decreased. COP down-regulated the expression of CYP1A2, CYP2C11, and CYP3A1 in the liver, as well as P-gp in the jejunum.These findings suggest that co-administration of COP with florfenicol alters the pharmacokinetics of florfenicol in rats. The down-regulation of CYP and P-gp expression may contribute to this effect. Therefore, the co-administration of COP with florfenicol may enhance the prophylactic or therapeutic efficacy of florfenicol in veterinary practice.

Impact of tectoridin on the pharmacokinetics of florfenicol via targeting cytochrome P450 and P-glycoprotein of rats.

Belamcanda chinensis (L.) DC, commonly used with florfenicol in Chinese veterinary clinics for respiratory tract infections, contains the major effective isoflavone, tectoridin (TEC). This study aimed to investigate the impact of TEC co-administration on the pharmacokinetics of florfenicol in vivo.Male rats received oral TEC (50 mg/kg BW) or sterile water for seven days, followed by a single oral dose of florfenicol (25 mg/kg BW) on the 8th day. Non-compartmental methods analysed the pharmacokinetics of florfenicol, while real-time reverse transcription polymerase chain reaction (RT-PCR), Western blot, and immunohistochemical analyses measured expression levels of cytochrome P450 (CYP) isoforms in the liver and P-glycoprotein (P-gp) in the jejunum.TEC significantly decreased florfenicol's AUC(0-∞), MRT(0-∞), t1/2z, Vz/F, and Cmax by 24.75%, 18.43%, 55.47%, 43.05%, and 19.48%, while increasing CLz/F by 33.33%. TEC also up-regulated hepatic CYP1A2 and CYP3A1 mRNA expression, as well as intestinal MDR1, by 1.39-fold, 1.85-fold, and 1.65-fold. This coincided with a respective increase in protein expression by 1.37-fold, 1.39-fold, and 1.43-fold.These findings suggest that TEC-induced alterations in the pharmacokinetics of florfenicol may be attributed to increased CYP and P-gp expression. Further investigations are warranted to understand the implications of these findings on the clinical effectiveness of florfenicol in veterinary practice.

Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States.

SARS-CoV-2 is a newly discovered beta coronavirus at the end of 2019, which is highly pathogenic and poses a serious threat to human health. In this paper, 1875 SARS-CoV-2 whole genome sequences and the sequence coding spike protein (S gene) sampled from the United States were used for bioinformatics analysis to study the molecular evolutionary characteristics of its genome and spike protein. The MCMC method was used to calculate the evolution rate of the whole genome sequence and the nucleotide mutation rate of the S gene. The results showed that the nucleotide mutation rate of the whole genome was 6.677 × 10-4 substitution per site per year, and the nucleotide mutation rate of the S gene was 8.066 × 10-4 substitution per site per year, which was at a medium level compared with other RNA viruses. Our findings confirmed the scientific hypothesis that the rate of evolution of the virus gradually decreases over time. We also found 13 statistically significant positive selection sites in the SARS-CoV-2 genome. In addition, the results showed that there were 101 nonsynonymous mutation sites in the amino acid sequence of S protein, including seven putative harmful mutation sites. This paper has preliminarily clarified the evolutionary characteristics of SARS-CoV-2 in the United States, providing a scientific basis for future surveillance and prevention of virus variants.

Evaluation of regions suitable for vicarious calibration of ocean color satellite sensors in the South China Sea.

Accurate retrieval of biogeochemical components of the ocean at a global scale from space requires accurately calibrated top-of-atmosphere (TOA) radiance, which is usually achieved by deriving a vicarious gain coefficient (g-factor) through a process called system vicarious calibration (SVC). Currently, only two SVC sites, Marine Optical Buoy (MOBY) and BOUée pour l'acquiSition d'une Série Optique à Long termE (BOUSSOLE), are routinely operated to support the SVC process for all on-orbit ocean color satellite payloads. However, high-quality matchups between satellite observations and in situ measurements are rare because of the strict requirements of the SVC process. Meanwhile, a stable g-factor is usually computed by averaging sufficient gain measurements. Therefore, more SVC sites are required to derive a stable g-factor in a short duration, particularly for the initial calibration of newly launched satellite sensors. In this study, nearly twenty years of well-calibrated ocean color satellite data were used to calculate the mean and standard deviation of physical and optical properties of waters and the atmosphere in the South China Sea (SCS) to evaluate the feasibility of establishing a SVC site. A region was identified that meets all requirements that were used to evaluate the MOBY and BOUSSOLE sites. Two in situ measurements within this region were used to derive a g-factor for MODIS-Terra and MODIS-Aqua and were compared with the g-factor derived using MOBY data. The consistence of the two g-factors indicates that the identified region in the SCS could be a potential area for establishing a long-term moored SVC site.

Hanstruepera crassostreae He et al. 2018 is a later heterotypic synonym of Pseudobizionia ponticola Park et al. 2018.

Hanstruepera crassostreae L53T was compared with Pseudobizionia ponticola MM-14T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of H. crassostreae L53T had complete similarity (100.0%) to that of P. ponticola MM-14T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Pseudobizionia. Draft genomic comparison between the two strains revealed an average nucleotide identity of 96.9 % and a digital DNA-DNA hybridization estimate of 75.3±2.8 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking difference in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Hanstruepera crassostreae is a later heterotypic synonym of Pseudobizionia ponticola.

Nonomuraea nitratireducens Qu et al. 2020 is a later heterotypic synonym of Nonomuraea phyllanthi Klykleung et al. 2020.

Nonomuraea nitratireducens WYY166T was compared with Nonomuraea phyllanthi PA1-10T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of N. nitratireducens WYY166T had high similarity (99.9 %) to that of N. phyllanthi PA1-10T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Nonomuraea. Draft genomic comparison between the two strains revealed an average nucleotide identity of 99.3 % and a digital DNA-DNA hybridization estimate of 94.4±1.8 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking difference in metabolic, physiological or chemotaxonomic features. Therefore, we propose Nonomuraea nitratireducens as a later heterotypic synonym of Nonomuraea phyllanthi.

Effects of paeoniflorin on the activities and mRNA expression of rat CYP1A2, CYP2C11 and CYP3A1 enzymes in vivo.

Paeoniflorin is the major constituent in extracts of the paeony root, the purpose of the present study was to assess the effects of paeoniflorin on the activities and mRNA expression of the rat hepatic drug-metabolizing enzymes cytochrome P450 (CYP1A2), CYP2C11 and CYP3A1 in vivo.Sprague-Dawley (SD) male rats were treated with paeoniflorin at the dosage of 25, 50 and 100 mg/kg or 0.9% sodium chloride solution by intragastric administration for 7 days, then were given probe drugs phenacetin (CYP1A2), tolbutamide (CYP2C11), or midazolam (CYP3A1) orally on the eighth day. Blood samples were collected at various times, and the plasma concentrations of the probe drugs were estimated with ultra-high-performance liquid chromatography. The mRNA expression levels of rat hepatic CYP1A2, CYP2C11 and CYP3A1 were analysed with real-time PCR.The pharmacokinetic results indicated that paeoniflorin inhibits the activities of CYP1A2, CYP2C11 and CYP3A1 in vivo. The effect was most pronounced on CYP3A1, according to the United States Food and Drug Administration classification of inhibitors of CYP3A, it reached the category of moderate inhibition. The mRNA expression levels of 3 CYP enzymes were also tended to be inhibited.We conclude that paeoniflorin can inhibit the activities of CYP1A2, CYP2C11 and CYP3A1 in vivo, which may affect the metabolism of drugs that are primarily dependent on these pathways.

Methyltransferases of gentamicin biosynthesis.

Gentamicin C complex from Micromonospora echinospora remains a globally important antibiotic, and there is revived interest in the semisynthesis of analogs that might show improved therapeutic properties. The complex consists of five components differing in their methylation pattern at one or more sites in the molecule. We show here, using specific gene deletion and chemical complementation, that the gentamicin pathway up to the branch point is defined by the selectivity of the methyltransferases GenN, GenD1, and GenK. Unexpectedly, they comprise a methylation network in which early intermediates are ectopically modified. Using whole-genome sequence, we have also discovered the terminal 6'-N-methyltransfer required to produce gentamicin C2b from C1a or gentamicin C1 from C2, an example of an essential biosynthetic enzyme being located not in the biosynthetic gene cluster but far removed on the chromosome. These findings fully account for the methylation pattern in gentamicins and open the way to production of individual gentamicins by fermentation, as starting materials for semisynthesis.

Vicarious calibration of COCTS-HY1C at visible and near-infrared bands for ocean color application.

Remote sensing reflectance obtained from space-borne ocean color sensors is of great importance to carbon cycle and ocean-atmospheric interactions by providing biogeochemical parameters on the global scale using specific algorithms. Vicarious calibration is necessary for obtaining accurate remote sensing reflectance that meets the application demands of atmospheric correction algorithms. For ocean color sensors, vicarious calibration must be done prior to atmospheric correction. The third Chinese Ocean Color and Temperature Scanner (COCTS) aboard the HY1C satellite was launched on September 7, 2018, and it will provide essential ocean color data that will complement those of existing missions. We used field measurements from the Marine Optical Buoy (MOBY) and aerosol information provided by the MODerate Imaging Spectroradiometer (MODIS) aboard the Terra satellite to calculate vicarious calibration coefficients, and we further evaluated the applicability of the established vicarious calibration approach by cross-calibration using MODIS data on the global scale. Finally, the established vicarious calibration coefficients were used to retrieve the aerosol optical depth and remote sensing reflectance, which were compared to Aerosol Robotic Network-Ocean Color (AERONET-OC) data and MODIS-Terra and Ocean and Land Color Instrument (OLCI)-Sentinel-3A operational products. The results show that the vicarious calibration coefficients are relatively stable and reliable for all bands ranging from visible to near-infrared and can be used to obtain accurate high-quality data.

Lymphocyte-sparing effect of stereotactic body radiation therapy compared to conventional fractionated radiation therapy in patients with locally advanced pancreatic cancer.

BACKGROUND: Conventionally fractionated (CF) radiation therapy (RT) has been associated with lymphopenia, leading to compromised overall survival (OS) in cancer patients. It currently remains unknown if stereotactic body (SB) RT induces lymphopenia to the same degree. The aim of this study is to determine if SBRT with either chemotherapy (CMT) (Fluorouracil (5FU) or capecitabine) or Nelfinavir (NFV) to pancreatic adenocarcinoma induces lymphopenia to the same degree as CFRT with 5FU or capecitabine and how any associated difference affects patient survival outcomes. METHODS: Medical records of pancreatic adenocarcinoma patients treated with induction CMT followed by RT with concurrent CMT or NFV were reviewed. Patients with total lymphocyte counts (TLCs) available both prior to and following initiation of RT were included. Three groups were identified: CFRT/CMT, SBRT/CMT, and SBRT/NFV. Median delivered RT doses for CFRT and SBRT were 50.4 Gy in 1.8 Gy fractions and 35 Gy in 7 Gy fractions, respectively. TLCs from day 0 (the first day of RT) to 40 were recorded and analyzed using the Kruskal-Wallis test with p-values adjusted with Bonferroni's method. Linear regressions were utilized to estimate the slope of TLCs as it changes with time and survival analysis was performed via Kaplan-Meier plots. RESULTS: One hundred patients were identified (28 CFRT/CMT, 27 SBRT/CMT, 45 SBRT/NFV). Median pre-RT TLCs were not different among groups. Median lowest TLCs were significantly lower (p <  0.0001) and median TLCs reduction over time were significantly greater (p <  0.0001) in the CFRT group than SBRT groups. There was no difference in lowest TLCs or TLCs reduction over time between SBRT groups. Across all groups, the median time to lowest TLCs was similar. Survival analysis revealed no significant difference in median OS between SBRT and CFRT groups. However, in patients with surgery, Median OS for patients with SBRT/CMT was significantly higher than in those with SBRT/NFV (p = 0.03). CONCLUSIONS: Compared to CFRT, SBRT is associated with less lymphopenia. Further study of the effect of radiation technique on immune status is warranted.

One-step synthesis of methylene-bridged bis-carbazole and evaluation of its antitumor activity and G-quadruplex DNA binding property.

Most reported carbazolyl G-quadruplex DNA (G4-DNA) ligands possess a rigid structure rather than a flexible one. The conformationally flexible ligands are paid much less attention. In this study, we report a novel class of non-rigid methylene-bridged biscarbazolyl ligand and their G4-DNA binding properties. Moreover, the antitumor activities of all these oligomers have been evaluated. The results show that this family of oligomers could be facilely synthesized via solely one step. Among them, compound 2, the bis-carbazole derivative, displays the best antitumor activity and IC50 values against HT-29, HepG2, A375 and MCF-7 cells are 0.69, 5.09, 3.15 and 3.8 µ mol/L, respectively. Although conformationally flexible, 2 is still capable of binding to as well as stabilizing G4-DNA via π-π stacking interaction. Moreover, 2 selectively binds to G4-DNA over duplex DNA. The current study enriches the category of carbazolyl G4-DNA ligands and paves the way for the search of more efficient G4-DNA ligands and antitumor leads.

A study of the MR imaging manifestations with injection of sedative at the buttocks in pediatric patients.

BACKGROUND: During the MRI examination, pediatric patients sleep under the sedation so that the image artifacts caused by the patient motion could be minimized. However, the sedative injection at the buttocks might cause a difficulty in the diagnosis of the buttock diseases using the MRI manifestations. OBJECTIVE: This study aims to explore the imaging characteristics of MR for the pediatric patients with the sedative injected at the buttocks in order to correctly diagnose the diseases. METHODS: MR imaging data of 64 pediatric patients injected with the sedative at the buttocks were retrospectively collected, including 8 cases of buttock disease. The imaging manifestations were analyzed and compared. RESULTS: Out of 64 patients, 8 were diagnosed as the buttock diseases. MR imaging manifestations of the sedatives injected at the buttocks were the locally patchy and streaky long T1 and long T2 signals and were different from what were shown for the normal tissues and diseases. CONCLUSION: The sedative injected at the buttocks has the MRI manifestations different from the normal tissues and diseases. Correctly understanding the MRI manifestations for the pediatric patients with the injection of sedative at the buttocks would reduce the chances of the misdiagnosis on the diseases.

Evaluation of dose calculations with inhomogeneity correction in intensity-modulated radiation therapy for esophagus cancer.

BACKGROUND: Differences often exist in the dose calculation accuracy caused by using different dose calculation algorithms in non-uniform tissues. OBJECTIVE: To evaluate the accuracy of dose calculation with inhomogeneity correction in intensity-modulated radiation therapy (IMRT) by comparing dose calculated in Monaco with measurements in lung-chest phantom for esophagus cancer treatments. METHODS: Finite size pencil beam (FSPB) and X-ray voxel Monte Carlo (XVMC) were used respectively for IMRT dose recalculations. Ten IMRT plans were recalculated and measured in the chest-lung phantom. The dose measurements using the Gafchromic ® (EBT3) dosimetry films were validated with open fields in the interfaces of materials with various physical densities. The accuracy of dose calculations was then evaluated by both point dose comparison and Gamma analysis against the film measurements. RESULTS: For regular open fields, the discrepancies of the point doses were less than 3.0% and 2.0% between measurement and calculations by FSPB and XVMC, respectively. For 6 MV IMRT plans, the average passing rates based on 3% /3 mm Gamma criteria were 82.8±1.0% and 96.4±0.7% for FSPB and XVMC, respectively. CONCLUSIONS: The XVMC algorithms more accurate in IMRT dose calculations with inhomogeneity correction for esophagus cancer.

Using weighted power mean for equivalent square estimation.

PURPOSE: Equivalent Square (ES) enables the calculation of many radiation quantities for rectangular treatment fields, based only on measurements from square fields. While it is widely applied in radiotherapy, its accuracy, especially for extremely elongated fields, still leaves room for improvement. In this study, we introduce a novel explicit ES formula based on Weighted Power Mean (WPM) function and compare its performance with the Sterling formula and Vadash/Bjärngard's formula. METHODS: The proposed WPM formula is ESWPMa,b=waα+1-wbα1/α for a rectangular photon field with sides a and b. The formula performance was evaluated by three methods: standard deviation of model fitting residual error, maximum relative model prediction error, and model's Akaike Information Criterion (AIC). Testing datasets included the ES table from British Journal of Radiology (BJR), photon output factors (Scp ) from the Varian TrueBeam Representative Beam Data (Med Phys. 2012;39:6981-7018), and published Scp data for Varian TrueBeam Edge (J Appl Clin Med Phys. 2015;16:125-148). RESULTS: For the BJR dataset, the best-fit parameter value α = -1.25 achieved a 20% reduction in standard deviation in ES estimation residual error compared with the two established formulae. For the two Varian datasets, employing WPM reduced the maximum relative error from 3.5% (Sterling) or 2% (Vadash/Bjärngard) to 0.7% for open field sizes ranging from 3 cm to 40 cm, and the reduction was even more prominent for 1 cm field sizes on Edge (J Appl Clin Med Phys. 2015;16:125-148). The AIC value of the WPM formula was consistently lower than its counterparts from the traditional formulae on photon output factors, most prominent on very elongated small fields. CONCLUSION: The WPM formula outperformed the traditional formulae on three testing datasets. With increasing utilization of very elongated, small rectangular fields in modern radiotherapy, improved photon output factor estimation is expected by adopting the WPM formula in treatment planning and secondary MU check.

Evidence that the DNA endonuclease ARTEMIS also has intrinsic 5'-exonuclease activity.

ARTEMIS is a member of the metallo-ß-lactamase protein family. ARTEMIS has endonuclease activity at DNA hairpins and at 5'- and 3'-DNA overhangs of duplex DNA, and this endonucleolytic activity is dependent upon DNA-PKcs. There has been uncertainty about whether ARTEMIS also has 5'-exonuclease activity on single-stranded DNA and 5'-overhangs, because this 5'-exonuclease is not dependent upon DNA-PKcs. Here, we show that the 5'-exonuclease and the endonuclease activities co-purify. Second, we show that a point mutant of ARTEMIS at a putative active site residue (H115A) markedly reduces both the endonuclease activity and the 5'-exonuclease activity. Third, divalent cation effects on the 5'-exonuclease and the endonuclease parallel one another. Fourth, both the endonuclease activity and 5'-exonuclease activity of ARTEMIS can be blocked in parallel by small molecule inhibitors, which do not block unrelated nucleases. We conclude that the 5'-exonuclease is intrinsic to ARTEMIS, making it relevant to the role of ARTEMIS in nonhomologous DNA end joining.

A general approach for controlling transcription and probing epigenetic mechanisms: application to the CD4 locus.

Synthetic regulatory proteins such as tetracycline (tet)-controlled transcription factors are potentially useful for repression as well as ectopic activation of endogenous genes and also for probing their regulatory mechanisms, which would offer a versatile genetic tool advantageous over conventional gene targeting methods. In this study, we provide evidence supporting this concept using Cd4 as a model. CD4 is expressed in double-positive and CD4 cells but irreversibly silenced in CD8 cells. The silencing is mediated by heterochromatin established during CD8 lineage development via transient action of the Cd4 silencer; once established, the heterochromatin becomes self-perpetuating independently of the Cd4 silencer. Using a tet-sensitive Cd4 allele harboring a removable Cd4 silencer, we found that a tet-controlled repressor recapitulated the phenotype of Cd4-deficient mice, inhibited Cd4 expression in a reversible and dose-dependent manner, and could surprisingly replace the Cd4 silencer to induce irreversible Cd4 silencing in CD8 cells, thus suggesting the Cd4 silencer is not the (only) determinant of heterochromatin formation. In contrast, a tet-controlled activator reversibly disrupted Cd4 silencing in CD8 cells. The Cd4 silencer impeded this disruption but was not essential for its reversal, which revealed a continuous role of the silencer in mature CD8 cells while exposing a remarkable intrinsic self-regenerative ability of heterochromatin after forced disruption. These data demonstrate an effective approach for gene manipulation and provide insights into the epigenetic Cd4 regulatory mechanisms that are otherwise difficult to obtain.