Abstract
Rotational-translational decoupling, in which translational motion is apparently enhanced over rotational motion in violation of Stokes-Einstein (SE) and Debye-Stokes-Einstein (DSE) ...predictions, has been observed in materials near their glass transition temperatures (T
g
). This has been posited to result from ensemble averaging in the context of dynamic heterogeneity. In this work, ensemble and single molecule experiments are performed in parallel on a fluorescent probe in high molecular weight polystyrene near its T
g
. Ensemble results show decoupling onset at approximately 1.15T
g
, increasing to over three orders of magnitude at T
g
. Single molecule measurements also show a high degree of decoupling, with typical molecules at T
g
showing translational diffusion coefficients nearly 400 times higher than expected from SE/DSE predictions. At the single molecule level, higher degree of breakdown is associated with particularly mobile molecules and anisotropic trajectories, providing support for anomalous diffusion as a critical driver of rotational-translational decoupling and SE/DSE breakdown.
The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequencing. However, structural variations ...often yield features that can be mistaken for chromosomal interactions. Here, we describe a computational method HiNT (Hi-C for copy Number variation and Translocation detection), which detects copy number variations and interchromosomal translocations within Hi-C data with breakpoints at single base-pair resolution. We demonstrate that HiNT outperforms existing methods on both simulated and real data. We also show that Hi-C can supplement whole-genome sequencing in structure variant detection by locating breakpoints in repetitive regions.
Fear of crime is one of the most significant factors affecting citizen’s quality of life. It isparticularly necessary to control the environmental factors that cause fear of crime in the ...neighborhood, as that is more worrisome. This study aimed to investigate women’s fear of crime in public streets in their neighborhoods and to identify the environmental factors that affect their fear of crime using a questionnaire and an eye-tracking experiment, respectively. Thirty participants watched four low-rise residential streets in Seoul and responded to a survey about their fear of crime. Through a multiple regression analysis, Factors such as “maintenance”, “pilotis”, “building entrance”, and “emergency bell” were found to largely influence fear of crime. This study contributes to the literature by identifying specific physical environment factors in parallel with eye tracking experiments, and our results have implications for future street design aimed at reducing the fear of crime.
Pareidolias, or the misperception of ambiguous stimuli as meaningful objects, are complex visual illusions thought to be phenomenologically similar to Visual Hallucination (VH). VH are a major ...predictor of dementia in Parkinson's Disease (PD) and are included as a core clinical feature in Dementia with Lewy Bodies (DLB). A newly developed Noise Pareidolia Test (NPT) was proposed as a possible surrogate marker for VH in DLB patients as increased pareidolic responses correlated with informant-corroborated accounts of VH. This association could, however, be mediated by visuoperceptual impairment. To understand the drivers of performance on the NPT, we contrasted performances in patient groups that varied both in terms of visuoperceptual ability and rates of VH. N = 43 patients were studied of whom n = 13 had DLB or PD with Dementia (PDD); n = 13 had PD; n = 12 had typical, memory-onset Alzheimer's Disease (tAD); and n = 5 had Posterior Cortical Atrophy (PCA) due to Alzheimer's disease. All patient groups reported pareidolias. Within the Lewy body disorders (PD, DLB, PDD), there was no significant difference in pareidolic response rates between hallucinating and non-hallucinating patients. Visuoperceptual deficits and pareidolic responses were most frequent in the PCA group-none of whom reported VH. Regression analyses in the entire patient cohort indicated that pareidolias were strongly predicted by visuoperceptual impairment but not by the presence of VH. These findings suggest that pareidolias reflect the underlying visuoperceptual impairment of Lewy body disorders, rather than being a direct marker for VH.
From an economic model in which education and growth reinforced each other, South Korea has developed a pathological equilibrium holding back economic and social progress. Low labour productivity and ...skills mismatch undermine the economic prospects of the country, and sharp rises in inequality in an ever more dualised labour market erode social cohesion. Governments of different political persuasion have recognised these challenges, and they have thought to reinvigorate vocational education and training (VET). However, this article shows that large employers - which were at the heart of a segmentalist coalition between business and government when collective skills formation of the Developmental State was dismantled - continue to undermine any efforts of meaningful vocational skills formation. It is argued that the country's hierarchical production regime and, related to this, labour market dualisation provide the micro-foundations for successive failure in VET reform; and without challenging large employers' dominant position in the Korean political economy and without addressing labour market dualism, the reform of VET policy can be expected to remain a futile endeavour.
The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data ...Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.
Acinetobacter baumannii is a highly potent nosocomial pathogen that is associated with increased in-hospital mortality. Here, we investigated the changes in molecular characteristics of ...carbapenem-resistant A. baumannii (CRAB) isolated from the blood samples of patients admitted to a tertiary hospital in South Korea from January 2009 to July 2015. Whole genome sequencing using the Illumina MiSeq platform and multi-locus sequence typing (MLST) were performed for 98 CRAB clinical isolates. In silico analyses for the prediction of antimicrobial resistance and virulence factor genes were performed. Plasmid sequences, including complete forms, were reconstructed from the sequence reads. Epidemiologic data were collected from the hospital database. MLST using the Oxford scheme revealed 10 sequence types of CRAB, of which ST191 was the dominant type (n = 59). Although blaOXA-23 was shared by most analysed strains, the compositions of antimicrobial resistance determinants differed among sequence types. ST447 and ST451/ST1809 with a few resistance genes were isolated during the later years of the study period. The number of virulence genes increased, while that of ST191 did not change significantly over the investigation period. Intriguingly MLST types, compositions of antimicrobial resistance genes, and virulence genes had no association with clinical outcomes of CRAB bacteraemia. In conclusion, active changes in or accumulations of antimicrobial resistance determinants and virulence genes in CRAB were not observed during the research period. Molecular characteristics of CRAB had no association with clinical outcomes of CRAB bacteraemia.
Hi-C Data Formats Lee, Soohyun
Methods in molecular biology (Clifton, N.J.),
2022, Volume:
2301
Journal Article
Processing, storing, and visualizing high-resolution Hi-C data required development of efficient data formats. A sparse matrix format saving only nonzero values has become the norm. A "zoomable" ...matrix style also became popular, storing multiple resolutions in a single file for interactive visualization. This chapter discusses the latest matrix file formats such as .hic and .mcool, and other intermediate formats including SAM/BAM and random-accessible contact lists.
The dyads 3, 4, and 6, combining the Bodipy chromophore with a Pt(bpy)(bdt) (bpy = 2,2′-bipyridine, bdt = 1,2-benzenedithiolate, 3 and 6) or a Pt(bpy)(mnt) (mnt = maleonitriledithiolate, 4) moiety, ...have been synthesized and studied by UV−vis steady-state absorption, transient absorption, and emission spectroscopies and cyclic voltammetry. Comparison of the absorption spectra and cyclic voltammograms of dyads 3, 4, and 6 and those of their model compounds 1a, 2, 5, and 7 shows that the spectroscopic and electrochemical properties of the dyads are essentially the sum of their constituent chromophores, indicating negligible interaction of the constituent chromophores in the ground state. However, emission studies on 3 and 6 show a complete absence of both Bodipy-based fluorescence and the characteristic luminescence of the Pt(bpy)(bdt) unit. Dyad 4 shows a weak Pt(mnt)-based emission. Transient absorption studies show that excitation of the dyads into the Bodipy-based 1ππ* excited state is followed by singlet energy transfer (SEnT) to the Pt(dithiolate)-based 1MMLL′CT (mixed metal-ligand to ligand charge transfer) excited state ( τ S E n T 3 = 0.6 ps, τ S E n T 4 = 0.5 ps, and τ S E n T 6 = 1.6 ps), which undergoes rapid intersystem crossing to the 3MMLL′CT state due to the heavy Pt(II) ion. The 3MMLL′CT state is then depopulated by triplet energy transfer (TEnT) to the low-lying Bodipy-based 3ππ* excited state ( τ T E n T 3 = 8.2 ps, τ T E n T 4 = 5 ps, and τ T E n T 6 = 160 ps). The transition assignments are supported by TD-DFT calculations. Both energy-transfer processes are shown to proceed via a Dexter electron exchange mechanism. The much longer time constants for dyad 6 relative to 3 are attributed to the significantly poorer coupling and resonance of charge-separated species that are intermediates in the electron exchange process.
Piwi-interacting RNAs (piRNAs) silence transposons and maintain genome integrity during germline development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both ...genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed to drive a ping-pong amplification cycle catalyzed by proteins that localize to the perinuclear nuage. We show that the HP1 homolog Rhino is required for nuage organization, transposon silencing, and ping-pong amplification of piRNAs. rhi mutations virtually eliminate piRNAs from the dual-strand clusters and block production of putative precursor RNAs from both strands of the major 42AB dual-strand cluster, but not of transcripts or piRNAs from the uni-strand clusters. Furthermore, Rhino protein associates with the 42AB dual-strand cluster,but does not bind to uni-strand cluster 2 or flamenco. Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle.
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