The issue of whether viruses are subject to restriction by endogenous microRNAs (miRNAs) and/or by virus-induced small interfering RNAs (siRNAs) in infected human somatic cells has been ...controversial. Here, we address this question in two ways. First, using deep sequencing, we demonstrate that infection of human cells by the RNA virus dengue virus (DENV) or West Nile virus (WNV) does not result in the production of any virus-derived siRNAs or viral miRNAs. Second, to more globally assess the potential of small regulatory RNAs to inhibit virus replication, we used gene editing to derive human cell lines that lack a functional Dicer enzyme and that therefore are unable to produce miRNAs or siRNAs. Infection of these cells with a wide range of viruses, including DENV, WNV, yellow fever virus, Sindbis virus, Venezuelan equine encephalitis virus, measles virus, influenza A virus, reovirus, vesicular stomatitis virus, human immunodeficiency virus type 1, or herpes simplex virus 1 (HSV-1), failed to reveal any enhancement in the replication of any of these viruses, although HSV-1, which encodes at least eight Dicer-dependent viral miRNAs, did replicate somewhat more slowly in the absence of Dicer. We conclude that most, and perhaps all, human viruses have evolved to be resistant to inhibition by endogenous human miRNAs during productive replication and that dependence on a cellular miRNA, as seen with hepatitis C virus, is rare. How viruses have evolved to avoid inhibition by endogenous cellular miRNAs, which are generally highly conserved during metazoan evolution, remains to be determined. Importance: Eukaryotic cells express a wide range of small regulatory RNAs, including miRNAs, that have the potential to inhibit the expression of mRNAs that show sequence complementarity. Indeed, previous work has suggested that endogenous miRNAs have the potential to inhibit viral gene expression and replication. Here, we demonstrate that the replication of a wide range of pathogenic viruses is not enhanced in human cells engineered to be unable to produce miRNAs, indicating that viruses have evolved to be resistant to inhibition by miRNAs. This result is important, as it implies that manipulation of miRNA levels is not likely to prove useful in inhibiting virus replication. It also focuses attention on the question of how viruses have evolved to resist inhibition by miRNAs and whether virus mutants that have lost this resistance might prove useful, for example, in the development of attenuated virus vaccines.
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric ...problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
Contact tracing has been essential to reducing spread of COVID-19. Singapore leveraged technology to assist with contact tracing efforts using a Bluetooth-based app and token platform called ...'TraceTogether'.
We reviewed the impact of this system during the country's Delta and Omicron waves (24 August 2021 to 17 February 2022) to identify differences in number of close contacts and time savings between full automation using TraceTogether alone as compared to manual contact tracing supplemented by TraceTogether. Characteristics of digital contact tracing app or token users were reviewed. Thereafter, the number of close contacts identified by manual and digital contact tracing methods, and the number of confirmed COVID-19 cases among contacts were analysed. The difference in time taken for identification of close contacts was also determined.
Adoption rate for TraceTogether was high, with 93.3% of cases having a registered device. There was a 9.8 h (34.9%) reduction in time savings for close contacts to be informed using TraceTogether alone compared to manual contact tracing supplemented by TraceTogether. The proportion of close contacts automatically identified through TraceTogether alone and turned positive was 3.6%. For those identified through manual contact tracing supplemented by TraceTogether, this proportion was 12.5% and 6.2% for those served quarantine orders and health risk warnings respectively.
The high adoption rate of 'TraceTogether' suggest that digital solutions remain a promising option to improve contact tracing in future epidemics. This may have been through its concurrent use with vaccine differentiated public health measures and policies which engender public trust. There is future potential for utilising such technology in managing communicable diseases to achieve good public health outcomes.
Biomechanical study and the review of literature on lumbar interbody fusion constructs.
To demonstrate the comparative stabilizing effects of lateral interbody fusion with various supplemental ...internal fixation options.
Lumbar interbody fusion procedures are regularly performed using anterior, posterior, and more recently, lateral approaches. The biomechanical profile of each is determined by the extent of resection of local supportive structures, implant size and orientation, and the type of supplemental internal fixation used.
Pure moment flexibility testing was performed using a custom-built 6 degree-of-freedom system to apply a moment of ±7.5 Nm in each motion plane, while motion segment kinematics were evaluated using an optoelectronic motion system. Constructs tested included the intact spine, stand-alone extreme lateral interbody implant, interbody implant with lateral plate, unilateral and bilateral pedicle screw fixation. These results were evaluated against those from literature-reported biomechanical studies of other lumbar interbody constructs.
All conditions demonstrated a statistically significant reduction in range of motion (ROM) as a percentage of intact. In flexion-extension, ROM was 31.6% stand-alone, 32.5% lateral fixation, and 20.4% and 13.0% unilateral and bilateral pedicle screw fixation, respectively. In lateral bending, the trend was similar with greater reduction with lateral fixation than in flexion-extension; ROM was 32.5% stand-alone, 15.9% lateral fixation, and 21.6% and 14.4% unilateral and bilateral pedicle screw fixation. ROM was greatest in axial rotation; 69.4% stand-alone, 53.4% lateral fixation, and 51.3% and 41.7% unilateral and bilateral pedicle screw fixation, respectively.
The extreme lateral interbody construct provided the largest stand-alone reduction in ROM compared with literature-reported ALIF and TLIF constructs. Supplemental bilateral pedicle screw-based fixation provided the overall greatest reduction in ROM, similar among all interbody approach techniques. Lateral fixation and unilateral pedicle screw fixation provided intermediate reductions in ROM. Clinically, surgeons may evaluate these comparative results to choose fixation options commensurate with the stability requirements of individual patients.
Primary open angle glaucoma (POAG) is a complex disease and a leading cause of irreversible blindness, and its underlying pathophysiology remains poorly understood. Proteomic characterization of the ...protein composition of aqueous humor (AH) may identify prognostic candidate proteins involved in pathogenesis and progression of the disease. To delineate the possible mechanisms that lead to POAG, this study adopted state-of-art mass spectrometric technique and analyzed AH of POAG and their respective controls. In total, more than 1000 proteins were identified with false discovery rate of less than 1%. Numerous proteins of complement cascade, immunoglobulin, neuronal and amyloidogenic proteins, which were part of processes like acute-phase and inflammatory response, humoral immune and acute inflammatory response, regulation of complement activation and protein processing were identified. Proteins of complement system underwent significant changes, which correlate to pathogenic events characterizing POAG, including altered complement cascade, astrocyte activation, neural degeneration, and apoptosis. Further, protein modification such as deamidation of complement subcomponent was noted, particularly in POAG. Proteomic analysis of AH allows a better understanding of the mechanism involved in the pathogenesis of POAG.
Transit through the carbon liquid phase has significant consequences for the subsequent formation of solid nanocarbon detonation products. We report dynamic measurements of liquid carbon condensation ...and solidification into nano-onions over ∽200 ns by analysis of time-resolved, small-angle X-ray scattering data acquired during detonation of a hydrogen-free explosive, DNTF (3,4-bis(3-nitrofurazan-4-yl)furoxan). Further, thermochemical modeling predicts a direct liquid to solid graphite phase transition for DNTF products ~200 ns post-detonation. Solid detonation products were collected and characterized by high-resolution electron microscopy to confirm the abundance of carbon nano-onions with an average diameter of ∽10 nm, matching the dynamic measurements. We analyze other carbon-rich explosives by similar methods to systematically explore different regions of the carbon phase diagram traversed during detonation. Our results suggest a potential pathway to the efficient production of carbon nano-onions, while offering insight into the phase transformation kinetics of liquid carbon under extreme pressures and temperatures.
To conduct a preliminary evaluation of the feasibility of visual field fast (VFF), a free iPad-based noise-field perimeter, in detecting glaucomatous scotomas versus the clinical-standard Humphrey ...visual field (HVF) test. VFF confronts subjects with a screen of flickering stimulus, allowing the immediate perception of scotomas.
This was a cross-sectional observational study of 66 glaucoma patients (66 eyes) and 30 healthy controls (30 eyes). All patients had no other visual field disorders. VFF was compared against HVF in terms of whole field and quadrants for the following: (1) correspondence in scotoma detection. (2) Agreement and correlation of the scotoma size (percentage of abnormal visual field area). (3) Test duration. Other domains tested included: (1) correlation of VFF scotoma area with the severity of visual field loss on HVF (mean deviation, MD; visual field index, VFI). (2) Repeatability of VFF. (3) Patient descriptors of scotomas.
Using HVF pattern deviation plot as a reference, VFF detected 52/57 (91.2%) of glaucoma subjects with 1 false-positive (control) (kappa = 0.86). 146/184 (79.3%) of abnormal quadrants (visual field defect present) were localized and 23/157 (14.6%) healthy quadrants were falsely identified as abnormal (kappa = 0.61). VFF underestimated scotoma area as compared to HVF (21.0% versus 44.0%, p < 0.01) but correlated positively (r = 0.268, p = 0.044) with HVF area and negatively with VFI (r = -0.340, p = 0.01) and MD (r = -0.398, p < 0.01). Using HVF total deviation plot as reference, VFF's glaucoma detection rate remained unchanged (kappa = 0.86) with similar quadrant detection (kappa = 0.68). However, a greater underestimation of scotoma area was observed (21.0% versus 85.4%, p < 0.01). VFF's quantitative repeatability was excellent for whole field (intraclass correlation coefficient, ICC: 0.96; p < 0.0001) and quadrants (ICC: 0.82-0.96; all p < 0.001). Qualitatively, 35/37 (94.6%) of subjects reported reduced luminance and flicker in scotomas, with similar morphologies on retests. VFF is faster than HVF SITA-Standard in glaucoma (3.60 ± 1.85 min versus 6.92 ± 1.12 min, p < 0.01) and control (1.12 ± 0.486 min versus 5.16 ± 0.727 min, p < 0.01).
This early model of VFF accurately detected scotomas with high repeatability. However, its accuracy in localizing and quantifying the scotoma can be improved. Considering its portability and cost-effectiveness, VFF demonstrated potential as a general screening tool for moderate-to-severe glaucoma.
Purpose
To evaluate efficacy and safety of the iStent inject combined with phacoemulsification in Asian eyes with normal-tension glaucoma (NTG) up to 12 months after surgery.
Study design
...Retrospective case series.
Methods
Retrospective case series of eyes undergoing surgery from April 2017 to August 2019. Outcome measures included intraocular pressure (IOP), number of topical glaucoma medications and adverse outcomes. Data were retrieved from the post-operative day 1 (POD1), week 1 (POW1), month 1 (POM1), month 3 (POM3), month 6 (POM6) and month 12 (POM12) timepoints. Data were analysed at each timepoint for eyes with available clinical data at that visit. Subgroup analysis was performed for a consistent cohort which included only eyes with data at all six follow-up timepoints.
Results
Data from 91 eyes in the collective subject group was analysed. Majority of subjects were male (53, 58.2%) and Chinese (79, 86.8%). Mean age was 73.2 ± 7.2 years. Pre-operatively, mean IOP was 14.3 ± 3.0 mmHg and mean number of medications was 1.5 ± 0.8. Significant IOP reduction was observed at all timepoints except POW1 and POM12. The number of medications was reduced at all timepoints (
p
< 0.001). By POM12, there was reduction of 1.2 ± 1.0 medications (
p
< 0.001). Both the collective and consistent cohorts demonstrated a trend towards decreasing surgical efficacy with time, in IOP reduction and decrease in medications. None of the eyes experienced sight-threatening complications.
Conclusions
Asian eyes with NTG undergoing combined phacoemulsification and iStent inject surgery demonstrated significant and sustained reduction in number of glaucoma medications up to 12 months post-operatively.
Microbial genes that are "novel" (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in ...yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examined contained significantly higher proportions of novel genes in their predicted genomic islands compared with the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of novel genes in predicted genomic islands is not due to less accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regions for both bacteria and archaea. This represents the first comprehensive analysis of novel genes in prokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequently associated with a particular microbial adaptation, such as antibiotic resistance, pathogen virulence, or metal resistance, this suggests that microbes may have access to a larger "arsenal" of novel genes for adaptation than previously thought.
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