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Background: High-flow nasal cannula (HFNC) systems employ different methods to provide aerosol to patients. This study compared delivery efficiency, particle size, and regional deposition of aerosolized bronchodilators during HFNC in neonatal, pediatric, and adult upper-airway and lung models between a proximal aerosol adapter and distal aerosol circuit chamber., Methods: A filter was connected to the upper airway to a spontaneously breathing lung model. Albuterol was nebulized using the aerosol adapter and circuit at different clinical flow settings. The aerosol mass deposited in the upper airway and lung was quantified. Particle size was measured with a laser diffractometer. Regional deposition was assessed with a gamma camera at each nebulizer location and patient model with minimum flow settings., Results: Inhaled lung doses ranged from 0.2-0.8% for neonates, 0.2-2.2% for the small child, and 0.5-5.2% for the adult models. Neonatal inhaled lung doses were not different between the aerosol circuit and adapter, but the aerosol circuit showed marginally greater lung doses in the pediatric and adult patient models. Impacted aerosols and condensation in the non-heated HFNC and aerosol delivery components contributed to the dispersion of coarse liquid droplets, high deposition (11-44%), and occlusion of the supine neonatal upper airway. In contrast, the upright pediatric and adult upper-airway models had minimal deposition (0.3-7.0%) and high fugitive losses (∼24%) from liquid droplets leaking out of the nose. The high impactive losses in the aerosol adapter (56%) were better contained than in the aerosol circuit, resulting in less cannula sputter (5% vs 22%), fewer fugitive losses (18% vs 24%), and smaller inhaled aerosols (5 µm vs 13 µm)., Conclusions: The inhaled lung dose was low (1-5%) during HFNC. Approaches that streamline aerosol delivery are needed to provide safe and effective therapy to patients receiving aerosolized medications with this HFNC system., Competing Interests: Mr DiBlasi discloses relationships with Medtronic, ABM Respiratory Care, Vapotherm, Dräger, and Aerogen Pharma. The remaining authors have disclosed no conflicts of interest., (Copyright © 2024 by Daedalus Enterprises.)

Introduction: Many physicians administer steroids after radiofrequency ablation (RFA) to mitigate postprocedural inflammation and decrease postprocedural pain. However, robust evidence supporting the benefits of steroids after RFA is lacking and steroids have risks., Methods: This study was a single-center, prospective, observational study designed to assess whether RFA alone is inferior to RFA with steroids for postprocedure pain. Eligible patients were at least 18 years of age and scheduled to undergo cervical or lumbar RFA. The primary outcome measure was the average pain score on the numeric rating scale (NRS) 7 days after the RFA. The secondary outcome measures included anxiety, depression and physical function, measured via the Patient-Reported Outcomes Measurement Information System short forms. All outcome measures were completed prior to the procedure and at 7 and 60 days postprocedure., Results: Out of the 365 participants who completed baseline assessments, 175 received steroids and 190 did not receive steroids. The pain intensity at 7 days postprocedure was similar between the steroid and non-steroid groups (mean difference (steroid-non-steroid): -0.23). The 95% CI of the estimate (-0.76 to 0.30) was within the prespecified non-inferiority margin of 1.5 NRS points. Similar results were obtained for pain at 60 days (mean difference: 0.09; 95% CI -0.48 to 0.65). No significant differences between groups were observed for anxiety, depression or physical function at either 7 or 60 days., Conclusion: This study suggests that the addition of steroids to the RFA procedure does not provide added benefits and is therefore not worth the additional risks that they pose., Competing Interests: Competing interests: JG has received compensation from Neurometrix for serving on a scientific advisory board (past relationship) and grant funding for an investigator-initiated trial in an unrelated indication. Neurometrix had no influence over the design, analysis, interpretation or writing of this manuscript. In the past 36 months, JG has also received consulting income from Algo Therapeutix, Eikonizo Therapeutics, Eli Lilly, GW Pharma, Hoba Therapeutics and Saluda Medical. She owns vesting shares in Eisana Corp. She has also received personal compensation for serving as Associate Editor for the Clinical Journal of Pain., (© American Society of Regional Anesthesia & Pain Medicine 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

Neurophysiological brain activity underpins cognitive functions and behavioural traits. Here, we sought to establish to what extent individual neurophysiological traits spontaneously expressed in ongoing brain activity are primarily driven by genetic variation. We also investigated whether changes in such neurophysiological features observed across the lifespan are supported by longitudinal changes in cortical gene expression. We studied the heritability of neurophysiological traits from task-free brain activity of monozygotic and dizygotic twins as well as non-related individuals recorded with magnetoencephalography. We found that these traits were more similar between monozygotic twins compared to dizygotic twins, and that these heritable core dynamical properties of brain activity are predominantly influenced by genes involved in neurotransmission processes. These genes are expressed in the cortex along a topographical gradient aligned with the distribution of major cognitive functions and psychological processes. Our data also show that the impact of these genetic determinants on cognitive and psychological traits increases with age. These findings collectively highlight the persistent genetic influence across the lifespan on neurophysiological brain activity that supports individual cognitive and behavioural traits.

R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H., (© 2023 The Authors.)

Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.

Background: Rib resection in thoracic outlet decompression can result in significant postoperative pain requiring high levels of opioid medications. We evaluated the impact of a bupivacaine infusing pleural catheter on postoperative pain and opioid usage in patients undergoing rib resection for thoracic outlet syndrome. We hypothesized that delivery of local anesthetic via the pleural catheter would improve postoperative pain control compared to standard multimodal analgesia, and that the use of the catheter would decrease opioid use during the index hospitalization and prescriptions for opioid pain medications at discharge., Methods: We conducted a single-center retrospective cohort study of 26 patients who underwent rib resection for thoracic outlet decompression. Primary outcome was opioid consumption during the index hospitalization, measured in morphine milligram equivalents (MME). Secondary outcomes were MME prescribed at discharge and pain scores during the index hospitalization before and after the pleural drain and pleural catheter were removed., Results: Patients in the bupivacaine infusion pleural catheter group (n = 11) had significantly lower MME usage during the index hospitalization (22.5 [1.9, 65.6] vs. 119.8 [76.5, 167.4]), and significantly lower MME prescribed at discharge (0 [0, 37.5] vs. 225 [183, 315]), compared to standard multimodal analgesia in controls (n = 15). Only 3 patients in the bupivacaine pleural catheter group were discharged with any opioid prescriptions (27%), compared to 14 patients in the control group (93%). There was no difference in postoperative pain scores between groups before or after removal of the pleural drain, which was placed in all cases (P = 0.31 and P = 0.76, respectively)., Conclusions: Intraoperative placement of a bupivacaine infusion pleural catheter significantly reduced opioid use during the index hospitalization and opioid prescribing at discharge. Anesthetic infusion pleural catheters should be the treatment modality of choice for postoperative pain management in patients undergoing thoracic outlet decompression., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background: A novel Palladium-103 low-dose rate (LDR) brachytherapy device was developed to provide dose-escalation to the tumor bed after resection while shielding adjacent tissues. This multicenter report describes the initial experience with this device in patients with retroperitoneal sarcoma (RPS)., Materials and Methods: Patients with recurrent RPS, prior radiotherapy, and/or concern for positive margins were considered. An LDR brachytherapy dose of 20-60 Gy was administered, corresponding to biologically effective dose values of 15-53 Gy and equivalent dose values of 12-43 Gy., Results: Six patients underwent implantation at four institutions. Of these, five had recurrent disease in the retroperitoneum or pelvic sidewall, one had untreated locally advanced leiomyosarcoma, two had prior external beam radiation therapy at the time of initial diagnosis, and four received neoadjuvant external beam radiation therapy plus brachytherapy. The device was easily implanted and conformed to the treatment area. Median follow-up was 16 mo; radiation was delivered to the at-risk margin with minimal irradiation of adjacent structures. No local recurrences at the site of implantation, device migration, or radiation-related toxicities were observed., Conclusions: The novel LDR directional brachytherapy device successfully delivered a targeted dose escalation to treat RPS high-risk margins. Lack of radiation-related toxicity demonstrates its safety., (Copyright © 2021. Published by Elsevier Inc.)

Upon replication stress, budding yeast checkpoint kinase Mec1 ATR triggers the downregulation of transcription, thereby reducing the level of RNA polymerase (RNAP) on chromatin to facilitate replication fork progression. Here, we identify a hydroxyurea-induced phosphorylation site on Mec1, Mec1-S1991, that contributes to the eviction of RNAPII and RNAPIII during replication stress. The expression of the non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. This defect can be suppressed by destabilizing chromatin-bound RNAPII through a TAP fusion to its Rpb3 subunit, suggesting that lethality in mec1-S1991A mutants arises from replication-transcription conflicts. Coincident with a failure to repress gene expression on hydroxyurea in mec1-S1991A cells, highly transcribed genes such as GAL1 remain bound at nuclear pores. Consistently, we find that nuclear pore proteins and factors controlling RNAPII and RNAPIII are phosphorylated in a Mec1-dependent manner on hydroxyurea. Moreover, we show that Mec1 kinase also contributes to reduced RNAPII occupancy on chromatin during an unperturbed S phase by promoting degradation of the Rpb1 subunit., (© 2021 The Authors. Published under the terms of the CC BY 4.0 license.)

Aim: Radiofrequency ablation (RFA) of genicular nerves can treat refractory chronic knee pain. This study evaluated association between patient and procedural characteristics and pain improvement after genicular nerve RFA. Materials & methods: A retrospective chart review. Data were extracted from patients who underwent thermal or cooled RFA of the knee. Results: A total of 124 patients were included. 81% of patients reported ≥75% pain relief after diagnostic nerve blocks. 35% reported ≥50% pain reduction from the RFA. Predictors of improved pain outcomes included higher baseline pain, no depression and thermal (vs cooled) RFA. Conclusion: Identifying patients who may benefit the most from genicular RFA is still not clear. Pain reduction differences between patients with and without depression and RFA type deserves further exploration.

Transcription-replication conflicts (TRCs) represent a potential source of endogenous replication stress (RS) and genomic instability in eukaryotic cells but the mechanisms that underlie this instability remain poorly understood. Part of the problem could come from non-B DNA structures called R-loops, which are formed of a RNA:DNA hybrid and a displaced ssDNA loop. In this review, we discuss different scenarios in which R-loops directly or indirectly interfere with DNA replication. We also present other types of TRCs that may not depend on R-loops to impede fork progression. Finally, we discuss alternative models in which toxic RNA:DNA hybrids form at stalled forks as a consequence - but not a cause - of replication stress and interfere with replication resumption., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Abstract: In honeys, several molecules have been known for their antibacterial or wound healing properties. Corsican honeys just began to be tested for their antimicrobial activity with promising results on Pseudomonas aeruginosa. So, identification of active molecules and their mode of action was determined. Hydrogen peroxide concentrations were evaluated and, in parallel, the minimal inhibitory concentrations (MIC) values were performed with and without catalase. More, the quantity of phenolic compounds and ORAC assay were measured. Observation of antibacterial action was done using scanning electron microscopy (SEM) followed by plasmidic DNA extraction. MIC values of chestnut grove and honeydew maquis honeys vary between 7 and 8%, showing a strong antimicrobial capacity, associated with a plasmidic DNA degradation. When catalase is added, MIC values significatively increase (25%) without damaging DNA, proving the importance of H2O2. This hypothesis is confirmed by SEM micrographies which did not show any morphological damages but a depletion in bacterial population. Although, such low concentrations of H2O2 (between 23 μmol l−1 and 54 μmol l−1) cannot explain antimicrobial activity and might be correlated with phenolic compounds concentration. Thus, Corsican honeys seem to induce DNA damage when H2O2 and phenolic compounds act in synergy by a putative pro‐oxidant effect. Significance and Impact of the Study:: We started to determine the antibacterial efficiency of Corsican chestnut grove and honeydew maquis honeys on Pseudomonas aeruginosa. No morphological alteration of the bacterial surface was observed. Antimicrobial action seems to be related to the synergy between hydrogen peroxide and phenolic compounds. The exerted pro‐oxidant activity leads to a degradation of P. aeruginosa plasmidic DNA. This is the first study that investigate the primary antibacterial mechanism of Corsican honeys. [ABSTRACT FROM AUTHOR]

This protocol describes how to culture, image, and determine the nuclear position of a fluorescently tagged DNA locus in the 3D nucleoplasm of fixed Saccharomyces cerevisiae cells. Here, we propose a manual scoring method based on widefield images and an automated method based on 3D-SIM images. Yeast culture conditions have to be followed meticulously to get the best biological response in a given environment. For complete details on the use and execution of this protocol, please refer to Forey et al. (2020)., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)

Mre11-Rad50-Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. MRX restricts transcription of coding and noncoding DNA by a mechanism that does not require the nuclease activity of Mre11. MRX is required to tether transcriptionally active loci to the nuclear pore complex (NPC), and it also promotes large-scale gene-NPC interactions. Moreover, MRX-mediated chromatin anchoring to the NPC contributes to chromosome folding and helps to control gene expression. Together, these findings indicate that MRX has a role in transcription and chromosome organization that is distinct from its known function in DNA repair., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Honey has a characteristic microbiological profile depending on their physical and chemical composition, results of the concentration sugar, with a high degree of resistance to the proliferation of microorganisms. Thus, the aim of the present study was to compare the morphophysiological and molecular methods for identification of yeast isolated from the honey obtained from the Apis mellifera L. bee. To this end, 97 samples of floral honey acquired at two of Piauí's, Brazil, honey cooperatives were analyzed. Yeast identification was conducted by the morphophysiological method and by the molecular analysis of the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. Six yeast strains were isolated, two of them new isolated species; however comparisons between the morphophysiological and molecular methods showed divergence in the identification all the isolated species. Thus, it is concluded that morphophysiological identification tests alone are unreliable as a single yeast identification means and that molecular methods showed higher effectiveness in the identification of yeast isolates. [ABSTRACT FROM AUTHOR]

This letter proposes a novel synthetic aperture radar (SAR) time series analysis method based on the scattering power decomposition algorithm with a reasonable ensemble average in both temporal and spatial domains. We reveal that the ensemble average is effective not only in the spatial domain but also in the temporal–spatial domains in the scattering power decomposition. That is, if we extend the ensemble average window in the temporal domain, the proposed method can accurately achieve volume scattering power with a higher spatial resolution than conventional approaches. The precise volume scattering power serves accurate forest monitoring. As an application, we performed forest disturbance detection in the Amazon rainforest using Sentinel-1 time series data. The proposed method detected the disturbances earlier, in less than 2 months, compared to other methods that take about 3 months. [ABSTRACT FROM AUTHOR]

Objectives: Extraskeletal myxoid chondrosarcoma (EMC) is a rare malignancy for which the role of radiotherapy is not well-defined. We examine the effect of external beam radiotherapy (EBRT) on cancer-specific survival (CSS) for patients with localized EMC, in a propensity score weighted, population-based analysis., Materials and Methods: The Surveillance, Epidemiology, and End Results database (1973 to 2012) was queried for cases of localized EMC arising from soft connective tissues of the trunk and extremities treated with surgery and/or EBRT. Inverse probability treatment weighting was utilized, with survival analysis by weighted Cox regression and Kaplan-Meier analysis with log-rank testing. The primary endpoint was CSS., Results: One hundred seventy-two patients were identified, diagnosed from 2004 to 2012. Ninety-four percent and 32% of 156 assessable patients underwent surgery and EBRT, respectively. By inverse probability treatment weighting, balancing covariates of age group, sex, race, grade, T stage, N stage, receipt of surgery, and anatomic site, we observed CSS of 97% versus 85% and 94% versus 85% in patients receiving EBRT versus no EBRT, at 3 and 5 years, respectively, at median follow-up of 33 months, P=0.01. A trend toward an overall survival benefit associated with EBRT was noted, P=0.06. Further adjusting for type of resection performed, CSS benefit persisted, 97% versus 85% at 3 years and 94% versus 85% at 5 years, P=0.02, with trend toward an overall survival benefit, P=0.08., Conclusions: The receipt of EBRT is associated with a CSS benefit in localized EMC. Aggressive local therapy, including EBRT, should be considered in these patients.

Fatigue modifies the kinematics of various sports-related movements. Basketball induces fatigue, however, the effects of fatigue on the kinematics of shooting have never been studied. This study analysed the effects of fatigue induced by repeated sprints on the kinematics of 3-point shooting (3PS) in young, elite basketball players (U18 level). 3D joint angles were calculated at the maximum and minimum heights of the centre of mass during 3PS, using inertial measurement units (Biomech system, Xsens Technologies BV, Enschede, The Netherlands). Height, velocity and the angle of the ball at the time of release were extrapolated from the wrist joint angles. All players performed four 3PS actions in dynamic conditions before and after a fatigue protocol at 70% of their maximal exercise capacity. The fatigue protocol consisted of a shuttle test with repeated 20-m sprints interspersed with sets of 5 jumps. There was no change in the kinematics of 3PS (p > 0.05), or the ball release variables (p > 0.05) following the fatigue protocol. This suggests that elite basketball players are able to cope with physical fatigue while performing coordinated movements such as 3PS.

Introduction: This study was designed to evaluate short-term physiologic outcomes of transitioning neonates with bronchopulmonary dysplasia (BPD) from intensive care unit (ICU) ventilators to both the Trilogy 202 (Philips Healthcare, Andover, MA) and LTV 1200 (CareFusion, Yorba Linda, CA) subacute ventilators., Methods: Six infants with BPD requiring tracheostomies for support with a neonatal-specific ICU ventilator underwent placement of esophageal balloon catheters, airway pressure transducers, flow sensors, oxygen saturation (SpO 2 ), and end tidal carbon dioxide (P ET CO 2 ) monitors. Noninvasive gas exchange, airflow, and airway and esophageal pressures (P ES ) were recorded following 20 min on the ICU ventilator. The infants were placed on the Trilogy 202 and LTV 1200 ventilators in random order at identical settings as the ICU ventilator. We measured noninvasive gas exchange, pressure-rate product (respiratory rate × ΔP ES ), ventilator response times, and the percentage of spontaneous breaths that triggered the ventilator at 20 min in each subject while being supported with each of the different subacute ventilators., Results: The mean (SD) weight of the six infants was 4.983 (0.56) kg. There were no differences in heart rate ( p = 0.51) or SpO 2 ( p = 0.97) but lower P ET CO 2 , ΔP ES , respiratory rate, pressure rate-product, response times, and greater percentage of subject initiated breaths that triggered the ventilator ( p < 0.05) was observed with the Trilogy 202 than the LTV 1200. All six infants transitioned successfully from the ICU ventilator to the Trilogy 202 ventilator., Conclusion: In this small group of infants with BPD, the Trilogy 202 ventilator performed better than the LTV 1200. The improved subject efforts, per cent subject triggering, and response times observed with the Trilogy are likely related to differences in triggering algorithms, location of triggering mechanisms, and gas delivery system performance within the ventilators. These pilot data may be useful for informing future clinical study design and understanding differences in the level of support provided by different subacute ventilators in infants with BPD.

The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'., (© 2017 The Author(s).)

The Mre11-Rad50-Xrs2 (MRX) complex is related to SMC complexes that form rings capable of holding two distinct DNA strands together. MRX functions at stalled replication forks and double-strand breaks (DSBs). A mutation in the N-terminal OB fold of the 70 kDa subunit of yeast replication protein A, rfa1-t11, abrogates MRX recruitment to both types of DNA damage. The rfa1 mutation is functionally epistatic with loss of any of the MRX subunits for survival of replication fork stress or DSB recovery, although it does not compromise end-resection. High-resolution imaging shows that either the rfa1-t11 or the rad50Δ mutation lets stalled replication forks collapse and allows the separation not only of opposing ends but of sister chromatids at breaks. Given that cohesin loss does not provoke visible sister separation as long as the RPA-MRX contacts are intact, we conclude that MRX also serves as a structural linchpin holding sister chromatids together at breaks., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Little is known about how cells ensure DNA replication in the face of RNA polymerase II (RNAPII)-mediated transcription, especially under conditions of replicative stress. Here we present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1-Ddc2 (ATR-ATRIP), the chromatin remodeling complex INO80C (INO80 complex), and the transcription complex PAF1C (PAF1 complex). We found that a subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea (HU). On HU, Mec1 triggers the efficient removal of PAF1C and RNAPII from transcribed genes near early firing origins. Failure to evict RNAPII correlates inversely with recovery from replication stress: paf1Δ cells, like ino80 and mec1 mutants, fail to restart forks efficiently after stalling. Our data reveal unexpected synergies between INO80C, Mec1, and PAF1C in the maintenance of genome integrity and suggest a mechanism of RNAPII degradation that reduces transcription-replication fork collision., (© 2016 Poli et al.; Published by Cold Spring Harbor Laboratory Press.)

Synthesis and maturation of Okazaki Fragments is an incessant and highly efficient metabolic process completing the synthesis of the lagging strands at replication forks during S phase. Accurate Okazaki fragment maturation (OFM) is crucial to maintain genome integrity and, therefore, cell survival in all living organisms. In eukaryotes, OFM involves the consecutive action of DNA polymerase Pol ∂, 5' Flap endonuclease Fen1 and DNA ligase I, and constitutes the best example of a sequential process coordinated by the sliding clamp PCNA. For OFM to occur efficiently, cooperation of these enzymes with PCNA must be highly regulated. Here, we present evidence of a role for the K164-PCNA-deubiquitylase Ubp10 in the maturation of Okazaki fragments in the budding yeast Saccharomyces cerevisiae. We show that Ubp10 associates with lagging-strand DNA synthesis machineries on replicating chromatin to ensure timely ligation of Okazaki fragments by promoting PCNA dissociation from chromatin requiring lysine 164 deubiquitylation. Synthesis and maturation of Okazaki fragments is crucial for lagging strand DNA replication. Here the authors find that the ubiquitin-specific protease Ubp10 works with the DNA synthesis machinery to promote Okazaki fragments joining by removal of PCNA through deubiquitylation of PCNA-K164. [ABSTRACT FROM AUTHOR]

Pd-catalyzed regioselective amination of unactivated alkene remains a challenge and is of great interest. Herein, a palladium-catalyzed and ligand-controlled strategy for the Markovnikov selective oxidative amination of 4-pentenoic acid has been described. The protocol effectively reverses the carboxylic acid-directed anti-Markovnikov selectivity in oxidative amination of 4-pentenoic acid, successfully constructing γ-ketoamide derivatives. [ABSTRACT FROM AUTHOR]

In recent years, metaphors have been used to understand how abstract concepts are processed, and developing metaphorical database can aid this research agenda. Accordingly, the present study aimed to produce a broad Chinese olfactory and gustatory database of metaphors. Expressions for two sensory types (olfaction/gustation) were compiled and classified according to two conditions (metaphorical/literal) and three parts of speech (adjective/noun/verb). To test the validity of this database, we enrolled 199 participants, of whom 97 completed the olfactory test (319 items) and 102 completed the gustatory test (352 items). Each item was rated on seven dimensions: familiarity, meaningfulness, figurativeness, valence, difficulty, imageability, and naturalness. Descriptive statistics and reliability and correlation analyses were conducted for the items under the two sensory types, two conditions, three parts of speech, and seven dimensions mentioned above. The results showed high internal consistency and split-half reliability for the participants' scores; the correlations between the seven dimensions resembled those of previous studies. We concluded by suggesting several ways the database might be applied to aid future research efforts. [ABSTRACT FROM AUTHOR]

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins. [ABSTRACT FROM AUTHOR]

Objective: Common Variable Immunodeficiency (CVID) is the most prevalent symptomatic primary immunodeficiency in adults. This study evaluates the clinical, immune, and immunohistological characteristics of hepatic involvement in CVID. Materials and Methods: Medical records of 72 CVID patients, including 7 with liver biopsies, were retrospectively reviewed. Immunohistochemical staining was performed to identify immune cell infiltration. Results: We enrolled 72 patients with a median age of 38 (22--77) years, and 47% (n = 34) were female. Elevated alkaline phosphatase (ALP) levels were found in 58.3% (n=42) of the patients. Hepatic involvement was more prevalent among females, and those with hepatic involvement displayed a higher incidence of autoimmune disease. Splenomegaly was identified in 85% of the patients with hepatic involvement. Notably, switched memory B cells (IgD- CD19+ CD27+) and the CD4+/CD8+ ratio were statistically lower in patients with hepatic involvement (p=0.031, p=0.047). Liver biopsies were performed on 7 patients, revealing minimal to severe chronic hepatitis. Immunohistologic analysis of these liver biopsies revealed varying degrees of positivity of CD8+, CD4+, and CD16+. However, staining for CD21, CD56, and CD138 yielded negative results. Conclusion: Our findings suggest that immune cells, particularly CD8+, CD4+, and CD16+ cells, may play a role in developing hepatic involvement. Understanding the underlying causes and mechanisms of hepatic involvement in CVID patients can lead to early diagnosis and targeted treatments, ultimately improving the prognosis. [ABSTRACT FROM AUTHOR]

DNA replication and transcription occur in all living cells across all domains of life. Both essential processes occur simultaneously on the same template, leading to conflicts between the macromolecular machines that perform these functions. Numerous studies over the past few decades demonstrate that this is an inevitable problem in both prokaryotic and eukaryotic cells. We have learned that conflicts lead to replication fork reversal, breaks in the DNA, R-loop formation, topological stress, and mutagenesis and can ultimately impact evolution. Recent studies have also provided insight into the various mechanisms that mitigate, resolve, and allow tolerance of conflicts and how conflicts result in pathological consequences across divergent species. In this review, we summarize our current knowledge regarding the outcomes of the encounters between replication and transcription machineries and explore how these clashes are dealt with across species. [ABSTRACT FROM AUTHOR]

In recent years, an increasing number of studies have shown that prokaryotes and eukaryotes are armed with sophisticated mechanisms to restart stalled or collapsed replication forks. Although these processes are better understood in bacteria, major breakthroughs have also been made to explain how fork restart mechanisms operate in eukaryotic cells. In particular, repriming on the leading strand and fork regression are now established as critical for the maintenance and recovery of stalled forks in both systems. Despite the lack of conservation between the factors involved, these mechanisms are strikingly similar in eukaryotes and prokaryotes. However, they differ in that fork restart occurs in the context of chromatin in eukaryotes and is controlled by multiple regulatory pathways.

Purpose: To provide a retrospective analysis of the efficacy of hyperbaric oxygen therapy (HBOT) for treating hemorrhagic cystitis (HC) and proctitis secondary to pelvic- and prostate-only radiotherapy., Methods and Materials: Nineteen patients were treated with HBOT for radiation-induced HC and proctitis. The median age at treatment was 66 years (range, 15-84 years). The range of external-beam radiation delivered was 50.0-75.6 Gy. Bleeding must have been refractory to other therapies. Patients received 100% oxygen at 2.0 atmospheres absolute pressure for 90-120 min per treatment in a monoplace chamber. Symptoms were retrospectively scored according to the Late Effects of Normal Tissues-Subjective, Objective, Management, Analytic (LENT-SOMA) scale to evaluate short-term efficacy. Recurrence of hematuria/hematochezia was used to assess long-term efficacy., Results: Four of the 19 patients were lost to follow-up. Fifteen patients were evaluated and received a mean of 29.8 dives: 11 developed HC and 4 proctitis. All patients experienced a reduction in their LENT-SOMA score. After completion of HBOT, the mean LENT-SOMA score was reduced from 0.78 to 0.20 in patients with HC and from 0.66 to 0.26 in patients with proctitis. Median follow-up was 39 months (range, 7-70 months). No cases of hematuria were refractory to HBOT. Complete resolution of hematuria was seen in 81% (n = 9) and partial response in 18% (n = 2). Recurrence of hematuria occurred in 36% (n = 4) after a median of 10 months. Complete resolution of hematochezia was seen in 50% (n = 2), partial response in 25% (n = 1), and refractory bleeding in 25% (n = 1)., Conclusions: Hyperbaric oxygen therapy is appropriate for radiation-induced HC once less time-consuming therapies have failed to resolve the bleeding. In these conditions, HBOT is efficacious in the short and long term, with minimal side effects., (Copyright © 2012. Published by Elsevier Inc.)

DNA combing is a powerful method developed by Bensimon and colleagues to stretch DNA molecules on silanized glass coverslips. This technique provides a unique way to monitor the activation of replication origins and the progression of replication forks at the level of single DNA molecules, after incorporation of thymidine analogs, such as 5-bromo-2'-deoxyuridine (BrdU), 5-iodo-2'-deoxyuridine (IdU) and 5-chloro-2'-deoxyuridine (CldU) in newly-synthesized DNA. Unlike microarray-based approaches, this assay gives access to the variability of replication profiles in individual cells. It can also be used to monitor the effect of DNA lesions on fork progression, arrest and restart. In this review, we propose standard DNA combing methods to analyze DNA replication in budding yeast and in human cells. We also show that 5-ethynyl-2'-deoxyuridine (EdU) can be used as a good alternative to BrdU for DNA combing analysis, as unlike halogenated nucleotides, it can be detected without prior denaturation of DNA., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Intracellular deoxyribonucleoside triphosphate (dNTP) pools must be tightly regulated to preserve genome integrity. Indeed, alterations in dNTP pools are associated with increased mutagenesis, genomic instability and tumourigenesis. However, the mechanisms by which altered or imbalanced dNTP pools affect DNA synthesis remain poorly understood. Here, we show that changes in intracellular dNTP levels affect replication dynamics in budding yeast in different ways. Upregulation of the activity of ribonucleotide reductase (RNR) increases elongation, indicating that dNTP pools are limiting for normal DNA replication. In contrast, inhibition of RNR activity with hydroxyurea (HU) induces a sharp transition to a slow-replication mode within minutes after S-phase entry. Upregulation of RNR activity delays this transition and modulates both fork speed and origin usage under replication stress. Interestingly, we also observed that chromosomal instability (CIN) mutants have increased dNTP pools and show enhanced DNA synthesis in the presence of HU. Since upregulation of RNR promotes fork progression in the presence of DNA lesions, we propose that CIN mutants adapt to chronic replication stress by upregulating dNTP pools.

Postacute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PASC) represent an urgent public health challenge and are estimated to affect more than 60 million individuals globally. Although a growing body of evidence suggests that dysregulated immune reactions may be linked with PASC symptoms, most investigations have primarily centered around blood-based studies, with few focusing on samples derived from affected tissues. Furthermore, clinical studies alone often provide correlative insights rather than causal mechanisms. Thus, it is essential to compare clinical samples with relevant animal models and conduct functional experiments to understand the etiology of PASC. In this study, we comprehensively compared bronchoalveolar lavage fluid single-cell RNA sequencing data derived from clinical PASC samples and a mouse model of PASC. This revealed a pro-fibrotic monocyte-derived macrophage response in respiratory PASC, as well as abnormal interactions between pulmonary macrophages and respiratory resident T cells, in both humans and mice. Interferon-γ (IFN-γ) emerged as a key node mediating the immune anomalies in respiratory PASC. Neutralizing IFN-γ after the resolution of acute SARS-CoV-2 infection reduced lung inflammation and tissue fibrosis in mice. Together, our study underscores the importance of performing comparative analysis to understand the cause of PASC and suggests that the IFN-γ signaling axis might represent a therapeutic target. Editor's summary: The term "Long Covid" covers a myriad of symptoms that a person may experience after an acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is also referred to as postacute sequelae of SARS-CoV-2 (PASC). The specific drivers of these symptoms are unclear, complicating the development of therapeutics for those suffering from this condition. Here, Li et al. used comparative analysis to interrogate a potential driver of respiratory PASC, one of the most debilitating types of PASC. The authors found that humans with respiratory PASC had evidence of an enhanced monocyte-derived macrophage response in their bronchoalveolar lavage fluid. A similar phenotype was observed in aged C57BL/6 mice infected with mouse-adapted SARS-CoV-2. This phenotype in mice could be reduced by anti–interferon-γ (anti–IFN-γ) treatment initiated after the resolution of acute disease, suggesting that the IFN-γ signaling pathway may represent a potential therapeutic target for humans. —Courtney Malo [ABSTRACT FROM AUTHOR]

Background: One of the most widely used medicinal plants in Iranian traditional medicine, Rosa × damascena Herrm. (mohammadi flower) that the people of Kashan use as a sedative and to treat nervous diseases and constipation. In this research, the yield, chemical composition and antimicrobial activity of the essential oil of this plant were evaluated for the first time from Azaran region, Kashan. Methods: The essential oil was extracted by means of hydrodistillation (Clevenger), and its chemical compounds were identified and determined by GC/MS. The antimicrobial activity of the essential oil was determined by the diffusion method in agar, the minimum growth inhibitory concentration (MIC) and the minimum concentration capable of killing bacterial/fungal microorganisms (MBC/MFC). Results: The results showed that the yield of essential oil was 0.1586 ± 0.0331% (w/w). Based on the results of the chemical composition analysis of R. x damascena essential oil, 19 different compounds (98.96%) were identified. The dominant and main components of the essential oil were oleic acid (48.08%), palmitic acid (15.44%), stearic acid (10.17%), citronellol (7.37%) and nonadecane (3.70%). Based on the results of diffusion in agar, the highest zone of inhibition against Candida albicans (ATCC 10231) was ~ 9.5 mm. The strongest inhibitory activity of R. x damascena essential oil against Gram-negative Proteus mirabilis (ATCC 43071) was with the diameter of the inhibition zone (~ 9 mm), which was equal to the strength of rifampin (~ 9 mm). Conclusion: Therefore, this essential oil is a promising natural option rich in fatty acids, which can be a potential for the production of natural antimicrobials against infectious diseases, especially urinary tract infections. [ABSTRACT FROM AUTHOR]

This article provides a model-based design method for heading control based autonomous trajectory tracking of a KVLCC2 ship. Kinematics, dynamics, and hydrodynamic force subsystems are used to represent the ship's motion equations. By contrasting the outcomes with experimental data received from the maneuvering modelling group, the accuracy of the model is confirmed. Heading angle of the ship is controlled by a linear cascade controller, and the settings of the controller are modified by using two separate heuristic optimization techniques: particle swarm optimization and genetic algorithm. The comparison of the findings demonstrates that the particle swarm optimization approach is computationally more effective than the genetic algorithm. Performance in the presence of disturbance has been investigated using the controller parameters discovered using particle swarm optimization. A suitable guidance algorithm is incorporated into the architecture of a trajectory tracking system to establish the necessary heading angle for travel between waypoints. We use a real-time simulator to visualize the ship motion on a graphical environment. [ABSTRACT FROM AUTHOR]

Grey wolf optimizer (GWO) is a highly valued heuristic algorithm in many fields. However, for some complex problems, especially high‐dimensional and multimodal problems, the basic algorithm has limited computational power and cannot get a satisfactory answer. In order to find a better solution, an improved algorithm based on GWO is proposed herein. Gaussian barebone, random selection and chaotic game mechanisms are introduced into the GWO algorithm to enhance the global search ability. The GWO enhanced by three mechanisms is called CBRGWO. To verify the performance of CBRGWO, using IEEE CEC 2017 as a test function, CBRGWO is compared to five GWO variants, five basic algorithms, six advanced algorithms, and four champion algorithms. CBRGWO is evaluated using the Friedman test and Wilcoxon signed‐rank test. Then, the stability of CBRGWO is analyzed. To verify that CBRGWO is still effective in practical application, CBRGWO is applied to five engineering problems and a water quality prediction problem. The experimental findings indicate that CBRGWO maintains excellent optimization ability in practical engineering problems. [ABSTRACT FROM AUTHOR]

DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.How strand-asymmetric processes such as replication and transcription interact with DNA damage to drive mechanisms of repair and mutagenesis is explored. [ABSTRACT FROM AUTHOR]