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Objectives To compare the incidence of persistent air leak (PAL) following cryoablation vs MWA of lung tumors when the ablation zone includes the pleura. Methods This bi-institutional retrospective cohort study evaluated consecutive peripheral lung tumors treated with cryoablation or MWA from 2006 to 2021. PAL was defined as an air leak for more than 24 h after chest tube placement or an enlarging postprocedural pneumothorax requiring chest tube placement. The pleural area included by the ablation zone was quantified on CT using semi-automated segmentation. PAL incidence was compared between ablation modalities and a parsimonious multivariable model was developed to assess the odds of PAL using generalized estimating equations and purposeful selection of predefined covariates. Time-to-local tumor progression (LTP) was compared between ablation modalities using Fine-Gray models, with death as a competing risk. Results In total, 260 tumors (mean diameter, 13.1 mm ± 7.4; mean distance to pleura, 3.6 mm ± 5.2) in 116 patients (mean age, 61.1 years ± 15.3; 60 women) and 173 sessions (112 cryoablations, 61 MWA) were included. PAL occurred after 25/173 (15%) sessions. The incidence was significantly lower following cryoablation compared to MWA (10 [9%] vs 15 [25%]; p  = .006). The odds of PAL adjusted for the number of treated tumors per session were 67% lower following cryoablation (odds ratio = 0.33 [95% CI, 0.14–0.82]; p  = .02) vs MWA. There was no significant difference in time-to-LTP between ablation modalities ( p  = .36). Conclusions Cryoablation of peripheral lung tumors bears a lower risk of PAL compared to MWA when the ablation zone includes the pleura, without adversely affecting time-to-LTP. Key Points • The incidence of persistent air leaks after percutaneous ablation of peripheral lung tumors was lower following cryoablation compared to microwave ablation (9% vs 25%; p  =  .006). • The mean chest tube dwell time was 54% shorter following cryoablation compared to MWA (p  =  .04). • Local tumor progression did not differ between lung tumors treated with percutaneous cryoablation compared to microwave ablation (p  =  .36).

Objective To compare temporal changes of ablation zones and lymph nodes following lung microwave ablation (MWA) and cryoablation. Methods This retrospective cohort study compared lung ablation zones and thoracic lymph nodes following MWA and cryoablation performed 2006–2020. In the ablation zone cohort, ablation zone volumes were measured on serial CT for 12 months. In the lymph node cohort, the sum of bidimensional products of lymph node diameters was measured before (baseline) and up to 6 months following ablation. Cumulative incidence curves estimated the time to 75% ablation zone reduction and linear mixed-effects regression models compared the temporal distribution of ablation zones and lymph node sizes between modalities. Results Ablation zones of 59 tumors treated in 45 sessions (16 MWA, 29 cryoablation) in 36 patients were evaluated. Differences in the time to 75% volume reduction between modalities were not detected. Following MWA, half of the ablation zones required an estimated time of 340 days to achieve a 75% volume reduction compared to 214 days following cryoablation ( p = .30). Thoracic lymph node sizes after 33 sessions (13 MWA, 20 cryoablation) differed between modalities (baseline–32 days, p = .01; 32–123 days, p = .001). Following MWA, lymph nodes increased on average by 38 mm 2 (95%CI, 5.0–70.7; p = .02) from baseline to 32 days, followed by an estimated decrease of 50 mm 2 (32–123 days; p = .001). Following cryoablation, changes in lymph nodes were not detected (baseline–32 days, p = .33). Conclusion The rate of ablation zone volume reduction did not differ between MWA and cryoablation. Thoracic lymph nodes enlarged transiently after MWA but not after cryoablation. Key Points • Contrary to current belief, the rate of lung ablation zone volume reduction did not differ between microwave and cryoablation. • Transient enlargement of thoracic lymph nodes after microwave ablation was not associated with regional tumor spread and decreased within six months following ablation. • No significant thoracic lymph node enlargement was observed following cryoablation.

The viral hemagglutinins of conventional influenza A viruses (IAVs) bind to sialylated glycans on host cell surfaces for attachment and subsequent infection. In contrast, hemagglutinins of bat-derived IAVs target major histocompatibility complex class II (MHC-II) for cell entry. MHC-II proteins from various vertebrate species can facilitate infection with the bat IAV H18N11. Yet, it has been difficult to biochemically determine the H18:MHC-II binding. Here, we followed a different approach and generated MHC-II chimeras from the human leukocyte antigen DR (HLA-DR), which supports H18-mediated entry, and the nonclassical MHC-II molecule HLA-DM, which does not. In this context, viral entry was supported only by a chimera containing the HLA-DR α1, α2, and β1 domains. Subsequent modeling of the H18:HLA-DR interaction identified the α2 domain as central for this interaction. Further mutational analyses revealed highly conserved amino acids within loop 4 (N149) and β-sheet 6 (V190) of the α2 domain as critical for virus entry. This suggests that conserved residues in the α1, α2, and β1 domains of MHC-II mediate H18-binding and virus propagation. The conservation of MHC-II amino acids, which are critical for H18N11 binding, may explain the broad species specificity of this virus.

The authors have established a method for the analysis of gene expression in tissue specimens preserved in formaldehyde. The expression profile of tissue adjacent to primary hepatocellular carcinoma, rather than the cancer itself, is associated with late recurrence. This finding, together with other data, suggests that the late recurrences are actually second primary tumors. The gene expression profile of tissue adjacent to primary hepatocellular carcinoma, rather than the cancer itself, is associated with late recurrence. This finding, together with other data, suggests that the late recurrences are actually second primary tumors. In developing countries, hepatocellular carcinoma often comes to medical attention when the tumors are at an advanced stage and curative therapies are of limited benefit. In developed countries, however, at-risk populations of patients (e.g., those who are infected with hepatitis virus and have cirrhosis) are often under close surveillance; as a result, hepatocellular carcinoma is usually detected when the tumors are small and treatment is more likely to be successful. 1 , 2 Nevertheless, recurrences eventually occur in most patients. 1 , 2 Studies suggest that chemopreventive strategies may suppress recurrence and prolong survival, 1 , 3 – 6 although these findings are still uncertain. It would . . .

Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C2C1im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C2C1im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C2C1im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

The influence of NH4NO3 and NH4ClO4 on the porous texture and structure development of activated carbons produced from a non-porous polymeric precursor synthesized from furfuryl alcohol has been studied. The non-doped counterparts were prepared and studied for comparison purposes. NH4NO3 and NH4ClO4-doped polymers were carbonized under N2 atmosphere at 600 °C, followed by CO2 activation at 1000 °C and the obtained carbon materials and activated carbons were thoroughly characterized. The porosity characterization data have shown that NH4NO3-derived ACs present the highest specific surface area (up to 1523 m2/g in the experimental conditions studied), and the resulting porosity distributions are strongly dependent on the activation conditions. Thus, 1 h activation is optimum for the microporosity development, whereas larger activation times lead to micropores enlargement and conversion into mesopores. The type of doping salts used also has a substantial impact on the surface chemical composition, i.e., C=O groups. Moreover, NH4NO3 and NH4ClO4 constitute good sources of nitrogen. The type and contribution of nitrogen species are dependent on the preparation conditions. Quaternary nitrogen only appears in doped samples prepared by carbonization and pyrrolic, pyrydinic, and nitrogen oxide groups appear in the NH4NO3 -series. NH4NO3 incorporation has led to optimized materials towards CO2 and C2H4 sorption with just 1 h activation time.

Crohn's disease (CD) is a heterogeneous disorder characterized by diverse clinical phenotypes. Childhood-onset CD has been described as a more aggressive phenotype. Genetic and immune factors may influence disease phenotype and clinical course. We examined the association of immune responses to microbial antigens with disease behavior and prospectively determined the influence of immune reactivity on disease progression in pediatric CD patients. Sera were collected from 196 pediatric CD cases and tested for immune responses: anti-I2, anti-outer membrane protein C (anti-OmpC), anti-CBir1 flagellin (anti-CBir1), and anti-Saccharomyces-cerevisiae (ASCA) using ELISA. Associations between immune responses and clinical phenotype were evaluated. Fifty-eight patients (28%) developed internal penetrating and/or stricturing (IP/S) disease after a median follow-up of 18 months. Both anti-OmpC (p < 0.0006) and anti-I2 (p < 0.003) were associated with IP/S disease. The frequency of IP/S disease increased with increasing number of immune responses (p trend = 0.002). The odds of developing IP/S disease were highest in patients positive for all four immune responses (OR (95% CI): 11 (1.5-80.4); p = 0.03). Pediatric CD patients positive for > or =1 immune response progressed to IP/S disease sooner after diagnosis as compared to those negative for all immune responses (p < 0.03). The presence and magnitude of immune responses to microbial antigens are significantly associated with more aggressive disease phenotypes among children with CD. This is the first study to prospectively demonstrate that the time to develop a disease complication in children is significantly faster in the presence of immune reactivity, thereby predicting disease progression to more aggressive disease phenotypes among pediatric CD patients.

There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney’s active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3 , KLF6 , and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1 . Further, combined perturbation of ELF3 , KLF6 , and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks. Comprehensive integration of gene expression with epigenetic features is needed to understand the transition of kidney cells from health to injury. Here, the authors integrate dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and histone modifications to decipher the chromatin landscape of the kidney in reference and adaptive injury cell states, identifying a transcription factor network of ELF3, KLF6, and KLF10 which regulates adaptive repair and maladaptive failed repair.

IntroductionRecent discoveries have identified shortened telomeres and related mutations in people with pulmonary fibrosis (PF). There is evidence to suggest that androgens, including danazol, may be effective in lengthening telomeres in peripheral blood cells. This study aims to assess the safety and efficacy of danazol in adults and children with PF associated with telomere shortening.Methods and analysisA multi-centre, double-blind, placebo-controlled, randomised trial of danazol will be conducted in subjects aged >5 years with PF associated with age-adjusted telomere length ≤10th centile measured by flow fluorescence in situ hybridisation; or in children, a diagnosis of dyskeratosis congenita. Adult participants will receive danazol 800 mg daily in two divided doses or identical placebo capsules orally for 12 months, in addition to standard of care (including pirfenidone or nintedanib). Paediatric participants will receive danazol 2 mg/kg/day orally in two divided doses or identical placebo for 6 months. If no side effects are encountered, the dose will be escalated to 4 mg/kg/day (maximum 800 mg daily) orally in two divided doses for a further 6 months. The primary outcome is change in absolute telomere length in base pairs, measured using the telomere shortest length assay (TeSLA), at 12 months in the intention to treat population.Ethics and disseminationEthics approval has been granted in Australia by the Metro South Human Research Ethics Committee (HREC/2020/QMS/66385). The study will be conducted and reported according to Standard Protocol Items: Recommendations for Interventional Trials guidelines. Results will be published in peer-reviewed journals and presented at international and national conferences.Trial registration numbersNCT04638517; Australian New Zealand Clinical Trials Registry (ACTRN12620001363976p).