The purpose of this paper is 2-fold. First, we present several extensions to the ONIOM(QM:MM) scheme. In its original formulation, the electrostatic interaction between the regions is included at the ...classical level. Here we present the extension to electronic embedding. We show how the behavior of ONIOM with electronic embedding can be more stable than QM/MM with electronic embedding. We also investigate the link atom correction, which is implicit in ONIOM but not in QM/MM. Second, we demonstrate some of the practical aspects of ONIOM(QM:MM) calculations. Specifically, we show that the potential surface can be discontinuous when there is bond breaking and forming closer than three bonds from the MM region.
Abstract
Background
To evaluate inter-fractional variations in bladder and rectum during prostate stereotactic body radiation therapy (SBRT) and determine dosimetric and clinical consequences.
...Methods
Eighty-five patients with 510 computed tomography (CT) images were analyzed. Median prescription dose was 40 Gy in 5 fractions. Patients were instructed to maintain a full bladder and empty rectum prior to simulation and each treatment. A single reviewer delineated organs at risk (OARs) on the simulation (Sim-CT) and Cone Beam CTs (CBCT) for analyses.
Results
Bladder and rectum volume reductions were observed throughout the course of SBRT, with largest mean reductions of 86.9 mL (19.0%) for bladder and 6.4 mL (8.7%) for rectum noted at fraction #5 compared to Sim-CT (
P
< 0.01). Higher initial Sim-CT bladder volumes were predictive for greater reduction in absolute bladder volume during treatment (ρ = − 0.69;
P
< 0.01). Over the course of SBRT, there was a small but significant increase in bladder mean dose (+ 4.5 ± 12.8%;
P
< 0.01) but no significant change in the D2cc (+ 0.8 ± 4.0%;
P
= 0.28). The mean bladder trigone displacement was in the anterior direction (+ 4.02 ± 6.59 mm) with a corresponding decrease in mean trigone dose (− 3.6 ± 9.6%;
P
< 0.01) and D2cc (− 6.2 ± 15.6%;
P
< 0.01). There was a small but significant increase in mean rectal dose (+ 7.0 ± 12.9%,
P
< 0.01) but a decrease in rectal D2cc (− 2.2 ± 10.1%;
P
= 0.04). No significant correlations were found between relative bladder volume changes, bladder trigone displacements, or rectum volume changes with rates of genitourinary or rectal toxicities.
Conclusions
Despite smaller than expected bladder and rectal volumes at the time of treatment compared to the planning scans, dosimetric impact was minimal and not predictive of detrimental clinical outcomes. These results cast doubt on the need for excessively strict bladder filling and rectal emptying protocols in the context of image guided prostate SBRT and prospective studies are needed to determine its necessity.
The nuclear RNA exosome is an essential multi-subunit complex that controls RNA homeostasis. Congenital mutations in RNA exosome genes are associated with neurodegenerative diseases. Little is known ...about the role of the RNA exosome in the cellular response to pathogens. Here, using NGS and human and mouse genetics, we show that influenza A virus (IAV) ribogenesis and growth are suppressed by impaired RNA exosome activity. Mechanistically, the nuclear RNA exosome coordinates the initial steps of viral transcription with RNAPII at host promoters. The viral polymerase complex co-opts the nuclear RNA exosome complex and cellular RNAs en route to 3′ end degradation. Exosome deficiency uncouples chromatin targeting of the viral polymerase complex and the formation of cellular:viral RNA hybrids, which are essential RNA intermediates that license transcription of antisense genomic viral RNAs. Our results suggest that evolutionary arms races have shaped the cellular RNA quality control machinery.
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•The nuclear RNA exosome coordinates viral polymerase and RNAPII transcription•The nuclear RNA exosome enhances host-viral RNA hybrids, chimeras, and viral ribogenesis•RNA exosome loss-of-function in epithelial and immune cells impairs viral growth•Broken symmetry hypothesis: Viruses target genes whose mutations lead to disease
The RNA exosome is critical for influenza virus ribogenesis and infectivity, working as a platform that coordinates the activity of viral and cellular RNA polymerases.
To determine the proportion of children with herpes simplex encephalitis (HSE) displaying TLR3 deficiency, the extent of TLR3 allelic heterogeneity, and the specific clinical features of TLR3 ...deficiency.
We determined the sequence of all exons of TLR3 in 110 of the 120 patients with HSE enrolled in our study who do not carry any of the previously described HSE-predisposing mutations of TLR3 pathway genes (TLR3, UNC93B1, TRIF, TRAF3, and TBK1). All the new mutant TLR3 alleles detected were characterized experimentally in-depth to establish the causal relationship between the genotype and phenotype.
In addition to the 3 previously reported TLR3-deficient patients from the same cohort, 6 other children or young adults with HSE carry 1 of 5 unique or extremely rare (minor allele frequency <0.001) missense TLR3 alleles. Two alleles (M374T, D592N) heterozygous in 3 patients are not deleterious in vitro. The other 3 are deleterious via different mechanisms: G743D+R811I and L360P heterozygous in 2 patients are loss-of-function due to low levels of expression and lack of cleavage, respectively, and R867Q homozygous in 1 patient is hypomorphic. The 3 patients' fibroblasts display impaired TLR3 responses and enhanced herpes simplex virus 1 susceptibility. Overall, TLR3 deficiency is therefore found in 6 (5%) of the 120 patients studied. There is high allelic heterogeneity, with 3 forms of autosomal dominant partial defect by negative dominance or haploinsufficiency, and 2 forms of autosomal recessive defect with complete or partial deficiency. Finally, 4 (66%) of the 6 TLR3-deficient patients had at least 1 late relapse of HSE, whereas relapse occurred in only 12 (10%) of the total cohort of 120 patients.
Childhood-onset HSE is due to TLR3 deficiency in a traceable fraction of patients, in particular the ones with HSE recurrence. Mutations in TLR3 and TLR3 pathway genes should be searched and experimentally studied in children with HSE, and patients with proven TLR3 deficiency should be followed carefully.
Profiling the dynamic interaction of p300 with proximal promoters of human T cells identified a class of genes that rapidly coassemble p300 and RNA polymerase II (pol II) following mitogen ...stimulation. Several of these p300 targets are immediate early genes, including FOS, implicating a prominent role for p300 in the control of primary genetic responses. The recruitment of p300 and pol II rapidly transitions to the assembly of several elongation factors, including the positive transcriptional elongation factor (P-TEFb), the bromodomain-containing protein (BRD4), and the elongin-like eleven nineteen lysine-rich leukemia protein (ELL). However, transcription at many of these rapidly induced genes is transient, wherein swift departure of P-TEFb, BRD4, and ELL coincides with termination of transcriptional elongation. Unexpectedly, both p300 and pol II remain accumulated or "bookmarked" at the proximal promoter long after transcription has terminated, demarking a clear mechanistic separation between the recruitment and elongation phases of transcription in vivo. The bookmarked pol II is depleted of both serine-2 and serine-5 phosphorylation of its C-terminal domain and remains proximally positioned at the promoter for hours. Surprisingly, these p300/pol II bookmarked genes can be readily reactivated, and elongation factors can be reassembled by subsequent addition of nonmitogenic agents that, alone, have minimal effects on transcription in the absence of prior preconditioning by mitogen stimulation. These findings suggest that p300 is likely to play an important role in biological processes in which transcriptional bookmarking or preconditioning influences cellular growth and development through the dynamic priming of genes for response to rechallenge by secondary stimuli.
We report the mixed cation compounds Na1-xKxAsSe2 (x = 0.8, 0.65, 0.5) and Na0.1K0.9AsS2 crystallize in the polar noncentrosymmetric space group Cc. The AAsQ(2) (A = alkali metals, Q = S, Se) family ...features one-dimensional (1D) 1/∞AQ2- chains comprising corner-sharing pyramidal AQ3 units in which the packing of these chains is dependent on the alkali metals. The parallel 1/∞AQ(2)- chains interact via short As ∙∙∙Se contacts, which increase in length when the fraction of K atoms is increased. The increase in the As ∙∙∙Se interchain distance increases the band gap from 1.75 eV in γ-NaAsSe2 to 2.01 eV in Na0.35K0.65AsSe2, 2.07 eV in Na0.2K0.8AsSe2, and 2.18 eV in Na0.1K0.9AsS2. The Na1-xKxAsSe2 (x = 0.8, 0.65) compounds melt congruently at approximately 316 °C. Wavelength-dependent second harmonic generation (SHG) measurements on powder samples of Na1-xKxAsSe2 (x = 0.8, 0.65, 0.5) and Na0.1K0.9AsS2 suggest that Na0.2K0.8AsSe2 and Na0.1K0.9AsS2 have the highest SHG response and exhibit significantly higher laser-induced damage thresholds (LIDTs). Theoretical SHG calculations on Na0.5K0.5AsSe2 confirm its SHG response with the highest value of d33 = 22.5 pm/V χ333(2) = 45.0 pm/V). The effective nonlinearity for a randomly oriented powder is calculated to be deff = 18.9 pm/V χeff(2) = 37.8 pm/V), which is consistent with the experimentally obtained value of deff = 16.5 pm/V χeff(2) = 33.0 pm/V). Three-photon absorption is the dominant mechanism for the optical breakdown of the compounds under intense excitation at 1580 nm, with Na0.2K0.8AsSe2 exhibiting the highest stability.
Abstract
Background
The clinical relevance of arachidonic acid (AA) metabolites in chronic kidney disease (CKD) progression is poorly understood. We aimed to compare the concentrations of 85 ...enzymatic pathway products of AA metabolism in patients with CKD who progressed to end-stage kidney disease (ESKD) versus patients who did not in a subcohort of Chronic Renal Insufficiency Cohort (CRIC) and to estimate the risk of CKD progression and major cardiovascular events by levels of AA metabolites and their link to enzymatic metabolic pathways.
Methods
A total 123 patients in the CRIC study who progressed to ESKD were frequency matched with 177 nonprogressors and serum eicosanoids were quantified by mass spectrometry. We applied serum collected at patients’ Year 1 visit and outcome of progression to ESKD was ascertained over the next 10 years. We used logistic regression models for risk estimation.
Results
Baseline 15-hydroxyeicosatetraenoate (HETE) and 20-HETE levels were significantly elevated in progressors (false discovery rate Q ≤ 0.026). The median 20-HETE level was 7.6 pmol/mL interquartile range (IQR) 4.2–14.5 in progressors and 5.4 pmol/mL (IQR 2.8–9.4) in nonprogressors (P < 0.001). In an adjusted model, only 20-HETE independently predicted CKD progression. Each 1 standard deviation increase in 20-HETE was independently associated with 1.45-fold higher odds of progression (95% confidence interval 1.07–1.95; P = 0.017). Principal components of lipoxygenase (LOX) and cytochrome P450 (CYP450) pathways were independently associated with CKD progression.
Conclusions
We found higher odds of CKD progression associated with higher 20-HETE, LOX and CYP450 metabolic pathways. These alterations precede CKD progression and may serve as targets for interventions aimed at halting progression.
Caspases are a conserved family of proteases that play a critical role in the execution of apoptosis by cleaving key cellular proteins at Asp residues and modifying their function. Using an ...expression cloning strategy we recently developed, we isolated human RAD21/SCC1/MCD1 as a novel caspase substrate. RAD21 is a component of the cohesin complex that holds sister chromatids together during mitosis and repairs double-strand DNA breaks. Interestingly, RAD21 is cleaved by a caspase-like Esp1/separase at the onset of anaphase to trigger sister chromatid separation. Here, we demonstrate that human RAD21 is preferentially cleaved at Asp279 by caspases-3 and -7 in vitro to generate two major proteolytic products of ∼65 and 48 kDa. Moreover, we show that RAD21 is specifically proteolyzed by caspases into a similarly sized 65-kDa carboxyl-terminal product in cells undergoing apoptosis in response to diverse stimuli. We also demonstrate that caspase proteolysis of RAD21 precedes apoptotic chromatin condensation and has important functional consequences, viz. the partial removal of RAD21 from chromatin and the production of a proapoptotic carboxyl-terminal cleavage product that amplifies the cell death signal. Taken together, these findings point to an entirely novel function of RAD21 in the execution of apoptosis.
Objective: To systematically review how comorbidities are employed in the empirical literature for adults coping with multiple chronic conditions during common episodes of acute illness that resulted ...in transition across health care setting.
Methods: Evolutionary concept analysis inductively identifies current consensus regarding the usage of a concept and results in exploring attributes and clarification of the concept. Sixty studies from 1965 to 2009 identified from MEDLINE, CINAHL, PsychINFO, and ISI Web of Science databases were analysed.
Results: Comorbidities were used heterogeneously among reviewed studies with most controlling for their presence (n=33) and lacking robust measurement (n=37). The designation of index or principal condition was equally heterogeneous with approximately half (n=26) representing the main disease or diagnosis of interest to the researcher. In this study comorbidities were associated with personal, disease or system level antecedents and consequences. A conceptual framework is proposed.
Discussion: The impact of comorbidities on the care and outcomes of adults coping with multiple chronic conditions is limited by heterogeneous and ambiguous usage. While analytic techniques have become more sophisticated, continued lack of meaningful conceptualization and instrument use has limited maturation of this important concept for research, practice and policy purposes.
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