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Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding—responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.

Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.

The Al/Au alloy was investigated to improve the ohmic characteristic and light efficiency of reflective infrared light-emitting diodes (IR-LEDs). The Al/Au alloy, which was fabricated by combining 10% aluminum and 90% gold, led to considerably improved conductivity on the top layer of p-AlGaAs of the reflective IR-LEDs. In the wafer bond process required for fabricating the reflective IR-LED, the Al/Au alloy, which has filled the hole patterns in Si3N4 film, was used for improving the reflectivity of the Ag reflector and was bonded directly to the top layer of p-AlGaAs on the epitaxial wafer. Based on current-voltage measurements, it was found that the Al/Au alloyed material has a distinct ohmic characteristic pertaining to the p-AlGaAs layer compared with those of the Au/Be alloy material. Therefore, the Al/Au alloy may constitute one of the favored approaches for overcoming the insulative reflective structures of reflective IR-LEDs. For a current density of 200 mA, a lower forward voltage (1.56 V) was observed from the wafer bond IR-LED chip made with the Al/Au alloy; this voltage was remarkably lower in value than that of the conventional chip made with the Au/Be metal (2.29 V). A higher output power (182 mW) was observed from the reflective IR-LEDs made with the Al/Au alloy, thus displaying an increase of 64% compared with those made with the Au/Be alloy (111 mW).

This study estimated ambient long-term average NO2 concentrations using TROPOspheric Monitoring Instrument (TROPOMI) tropospheric column NO2 data and land use parameters in California, U.S. for the years 2018–2019. Exploiting unprecedentedly high spatial resolution of TROPOMI NO2 (3.5×7 km prior to August 6, 2019 and 3.5×5.5 km thereafter) and the point statistics function implemented in ArcGIS (Environmental Systems Research Institute, ESRI), the NO2 concentration estimates were downscaled to 500 m, which enabled the neighborhood-scale exposure assessment of ambient NO2. Our satellite-land use hybrid regression model demonstrated cross-validation R2= 0.76, mean absolute error (MAE)= 1.95 ppb, and root mean squared error (RMSE)= 2.51 ppb in a comparison between site-specific average measured and estimated NO2 concentrations. These high-resolution NO2 concentration estimates enhanced the capability of human exposure assessment, enabling (1) the evaluation of ground NO2 monitors to represent population exposures and (2) the attribution of micro-level NO2 exposures. When measured NO2 concentrations were compared to population-weighted NO2 concentrations, calculated by using the satellite-based NO2 estimates, in each county, the differences in NO2 concentrations (i.e., population-weighted average NO2 – arithmetic average NO2 measurements) ranged from -38.6% (San Bernardino) to 82.2% (Humboldt). Though both negative and positive differences represented exposure errors without considering the spatial co-variations of NO2 and populations, monitor-based NO2 higher than the population-weighted NO2 demonstrated the overestimation of population NO2 exposures and was at least protective with current NO2 monitoring locations in the counties. However, the opposite was detrimental, while underestimating population NO2 exposures and likely not motivating NO2 mitigation efforts. In addition, the high-resolution NO2 estimates were further overlaid with parcel-level property data in Los Angeles County to attribute the spatial variation of NO2 exposures to that of the property types. The micro-level NO2 hotspots were identified at high-density residential complexes such as (high-rise) apartments. When the traffic impacts on NO2 were adjusted, the NO2 hotspots at the residential complexes still remained. This finding may suggest residential complexes as an emerging source type of NO2 due to emissions from boilers (space heating and hot water) and other indoor-to-outdoor ventilation systems.

BackgroundZebrafish pigment cell differentiation provides an attractive model for studying cell fate progression as a neural crest progenitor engenders diverse cell types, including two morphologically distinct pigment cells: black melanophores and reflective iridophores. Nontrivial classical genetic and transcriptomic approaches have revealed essential molecular mechanisms and gene regulatory circuits that drive neural crest-derived cell fate decisions. However, how the epigenetic landscape contributes to pigment cell differentiation, especially in the context of iridophore cell fate, is poorly understood.ResultsWe chart the global changes in the epigenetic landscape, including DNA methylation and chromatin accessibility, during neural crest differentiation into melanophores and iridophores to identify epigenetic determinants shaping cell type-specific gene expression. Motif enrichment in the epigenetically dynamic regions reveals putative transcription factors that might be responsible for driving pigment cell identity. Through this effort, in the relatively uncharacterized iridophores, we validatealx4aas a necessary and sufficient transcription factor for iridophore differentiation and present evidence onalx4a’s potential regulatory role in guanine synthesis pathway.ConclusionsPigment cell fate is marked by substantial DNA demethylation events coupled with dynamic chromatin accessibility to potentiate gene regulation through cis-regulatory control. Here, we provide a multi-omic resource for neural crest differentiation into melanophores and iridophores. This work led to the discovery and validation of iridophore-specificalx4atranscription factor.

We studied broad-spectrum light emitting diodes appropriate for special lighting applications in terms of their optical behaviors and device performances according to the chirped multi-quantum well structures. As the well thickness from 1 st to 3rd well was changed from 6 nm to 15 nm and repeated three times, the electroluminescent spectrum was broadened by 65% and the light output power was increased by 8% in comparison to light emitting diodes having conventional multi-quantum well structures. In the case of the chirped multi-quantum well structures having sequentially decreasing the well thickness from 15 nm to 6 nm and repeating three times, the optical output power was decreased by 5% due to the carrier leakage out of the active region.

This study estimated long-term average ambient NO

In this paper, we report the synthesis and transmittance of a titanium–indium–tin oxide (TITO) film, fabricated through a low-temperature process. The TITO film was fabricated by incorporating a 2-nm-thick titanium barrier at the bottom of an ITO film. The transmittance characteristics of the TITO film were examined for light-emitting diodes (LEDs) of various wavelengths at different post-annealing temperatures. A saturated high transmittance was observed at a temperature of 550 °C, which is relatively low when compared to that in the case of a conventional ITO film. Photoluminescence studies demonstrated that a 450-nm-thick TITO film, fabricated at 550 °C, was highly effective in improving the performance of the LED, when compared to conventional ITO films. The X-ray diffraction peaks, scanning electron microscopy images, and transmittance electron microscopy images confirmed that titanium atoms could improve the crystallization of ITO. It was found that non-crystallization in ITO was effectively activated by the titanium barrier. Furthermore, the optical bandgap (3.77 eV for the conventional ITO film) was improved to 3.92 eV in the TITO film. An infrared LED fabricated with a TITO film displayed 70% higher light output power than that with a conventional ITO film. These results suggest that using a titanium barrier is essential to effectively improve inactive nucleation sites in ITO films grown at low temperatures.

The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tubingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.

[1]. Relations of trust were a major weakness in social capital between communities, where 66% of the Pulo had a low level of trust in the Bajo. This negative relationship was reinforced by the conduct of the Bajo in Pulo territories, poverty, and lack of communication and political representation of the Bajo people. Educating the two communities about equality and conservation using the established marine-resource groups and organisations such as the Forkani can facilitate the generation of social capital and improve social conditions for implementing a successful conservation management strategy.[1]Kruskal-Wallis is a statistical test which analyses the variance between 3 or more groups of data, where h = the rank sum statistic, d.f. = degrees of freedom or number of variables (-1) and P = the significance value, whereby the probability of this result occurring by coincidence is 0.01 or 1%, Essex Student Journal Volume 2 Issue 1 2009

California experienced extreme and prolonged drought conditions during the early 2010s. To date, little is known regarding the influence of drought on air quality. Our study quantified site-specific associations between drought (defined by the Standardized Precipitation-Evapotranspiration Index; SPEI) and daily maximum 8-h ozone (O

As small obsolete buildings are exposed to high fire risks, governments are trying to evaluate their fire risks and preferentially improve fire protection performance for high risk buildings, however, the evaluation manpower and time are insufficient compared to the rapidly increasing number of obsolete buildings. Therefore, this study aimed to derive major fire risk index (FRI) evaluation items as part of developing a platform to quickly and efficiently evaluate fire risks in dense areas of small obsolete buildings utilizing spatial information convergence technology. To this end, 20 preliminary evaluation items specifically tailored to dense areas of small obsolete buildings were derived through a field survey, investigation of FRI evaluation items from existing works, and expert pre-reviews. Based on the derived 20 preliminary items, an importance survey was conducted with a total of 181 fire safety experts including fire officers, university professors, researchers, industry experts, and fire insurers. As a result, a total of 12 major evaluation items (e.g., outdoor fire extinguisher, distance to 119 Safety Center, building structure, building cladding, illegal alterations, illegal parking, and liquefied natural gas cylinder) were derived. Results can help to evaluate the fast and efficient fire risks in dense areas of small obsolete buildings.

Prostate cancer is the second most common cancer in men worldwide1. Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients2,3. However, most tumours profiled in these studies were obtained from patients from Western populations. Here we produced and analysed whole-genome, whole-transcriptome and DNA methylation data for 208 pairs of tumour tissue samples and matched healthy control tissue from Chinese patients with primary prostate cancer. Systematic comparison with published data from 2,554 prostate tumours revealed that the genomic alteration signatures in Chinese patients were markedly distinct from those of Western cohorts: specifically, 41% of tumours contained mutations in FOXA1 and 18% each had deletions in ZNF292 and CHD1. Alterations of the genome and epigenome were correlated and were predictive of disease phenotype and progression. Coding and noncoding mutations, as well as epimutations, converged on pathways that are important for prostate cancer, providing insights into this devastating disease. These discoveries underscore the importance of including population context in constructing comprehensive genomic maps for disease.

This study estimated annual average ambient fine particulate matter (PM2.5) concentrations at 1 km resolution using satellite Multi-Angle Implementation of Atmospheric Correction (MAIAC) aerosol op...

The effects of using a rough GaP layer to improve the light efficiency of 860-nm GaAs vertical-cavity surface-emitting laser were investigated. The light efficiency was significant increased by enlargement of current flow path caused from use of GaP layer grown on the top distributed Bragg reflector (DBR) of VCSEL. Furthermore, it was found that improved light efficiency significantly could be further increased by optimizing the surface morphology of the p-GaP layer fabricated in limited surface lighting area of VCSEL. Various surface morphologies could be obtained easily by controlling the RF power of an ICP dry etching. The highest output power of 34 mW was obtained from the VCSEL with a rough GaP layer fabricated at a RF power of 40 W introduced with BCl3 gas, showing a noticeable increase of ∼113% than a conventional one (16 mW). This result clearly insists that light efficiency of 860-nm GaAs based VCSEL could be increased effectively by using the rough GaP layer.

The use of an AlxGa1−xAs bound GazIn1−zP strain compensation structure for optimum strain in latticed mismatched In0.07GaAs/GaAsP0.06 multiple quantum wells (MQWs) and its effect on the output power of an infrared light-emitting diode at 940-nm were investigated. A Ga0.53InP tensile strain structure, which effectively compensate excessive compressive strain in the In0.07GaAs/GaAsP0.06 MQWs, was inserted between a quantum well and a quantum barrier. The Al0.2GaAs material was used as both a growth buffer and a balancing barrier for In0.07GaAs/AlxGa1–x As-bound Ga0.53InP/GaAsP0.06 MQWs. From photoluminescence (PL) measurements and X-ray diffraction (XRD) rocking curves, we verified that the Ga0.53InP tensile strain barrier could effectively compensate the compressive strain of the In0.07GaAs/GaAsP0.06 MQWs. In addition, a further increase in the PL intensity from the In0.07GaAs/AlyGa1−yAs-bound Ga0.53InP/GaAsP0.06 MQWs was found after having adjusted the Al0.2GaAs strain tuning barrier. This result was significantly supported by the stable balance of the energy bandgap structure in the developed MQWs. From fabricated IR-LEDs chips, the LED with an In0.07GaAs/GaAsP0.06 MQW employing the Al0.2GaAs-bound Ga0.53InP strain compensation structure displayed a 48% higher light output power as compared with a conventional LED. These results suggest that the use of an Al0.2GaAs-bound Ga0.53InP strain compensation structure effectively improved both the unbalanced strain and the unbalanced energy bandgap of lattice-mismatched In0.07GaAs/GaAsP0.06 MQWs for 940-nm IR-LEDs.

A highly doped emitting window for a vertical-cavity surface-emitting laser (VCSEL) was fabricated and its effect on the output power at a wavelength of 860-nm was investigated. The highly doped emitting window, which limited in required specific area, could be obtained by using various thermal conditions for patterned zinc oxide (ZnO). Experimental measurements showed that the highest doping concentration of 1.02 × 1019/cm3 was observed from patterned ZnO treated at 600 °C. The highly doped emitting window obtained by Zn diffusion effectively improved the real emission region confined by the current window owing to increase in the central concentration of the current injected from the top electrode. Among the developed VCSEL chips, the highest output power of 110 mW was observed with the use of a Zn-doped emitting widow at 600 °C, indicating an increase 47% compared with the output power of conventional chips (75 mW). For temperatures other than 600 °C, a relatively lower output power was obtained. The results show that the use of an emitting window highly doped with Zn can improve the output power of the VCSEL at a wavelength of 860-nm. It was verified that there exists an optimal thermal condition for the zinc diffusion process for patterned ZnO film required.

Optimum strain compensation structures for In0.07GaAs-based MQWs were investigated to obtain a higher output power for infrared lighting-emitting diodes (IR-LEDs) requiring a 940 nm wave-length. A GaAsP0.06 tensile strain material for compensating the compressive strain of In0.07GaAs quantum wells was used as a quantum barrier. To improve upon the excessive unbalance strain condition caused due to the In0.07GaAs quantum well and GaAsP0.06 quantum barrier, a conditioned Al0.2GaAs strain balancing barrier was also investigated. Through subsequent photoluminescence (PL) measurements, it was found that the GaAsP0.06 tensile strain barrier could effectively compensate for the compressive strain of In0.07GaAs quantum wells. Furthermore, the PL intensity of In0.07GaAs/GaAsP0.06 MQWs was observed to be markedly improved by using an Al0.2GaAs strain balancing barrier. A fabricated IR-LED chip, having In0.07GaAs/GaAsP0.06 MQWs with an Al0.2GaAs strain balancing barrier, showed a 60% higher light output power than conventional MQWs. These results subsequently suggest that using GaAsP0.06 and Al0.2GaAs barriers effectively improved unbalanced strain conditions of lattice-mismatched In0.07GaAs based MQWs requiring a 940 nm emitting wavelength.

A new technique was used to directly measure O3 response to changes in precursor NOx and volatile organic compound (VOC) concentrations in the atmosphere using three identical Teflon smog chambers equipped with UV lights. One chamber served as the baseline measurement for O3 formation, one chamber added NOx, and one chamber added surrogate VOCs (ethylene, m-xylene, n-hexane). Comparing the O3 formation between chambers over a 3-hour UV cycle provides a direct measurement of O3 sensitivity to precursor concentrations. Measurements made with this system at Sacramento, California, between April–December 2020 revealed that the atmospheric chemical regime followed a seasonal cycle. O3 formation was VOC-limited (NOx-rich) during the early spring, transitioned to NOx-limited during the summer due to increased concentrations of ambient VOCs with high O3 formation potential, and then returned to VOC-limited (NOx-rich) during the fall season as the concentrations of ambient VOCs decreased and NOx increased. This seasonal pattern of O3 sensitivity is consistent with the cycle of biogenic emissions in California. The direct chamber O3 sensitivity measurements matched semi-direct measurements of HCHO/NO2 ratios from the TROPOspheric Monitoring Instrument (TROPOMI) aboard the Sentinel-5 Precursor (Sentinel-5P) satellite. Furthermore, the satellite observations showed that the same seasonal cycle in O3 sensitivity occurred over most of the entire state of California, with only the urban cores of the very large cities remaining VOC-limited across all seasons. The O3-nonattainment days (MDA8 O3>70 ppb) have O3 sensitivity in the NOx-limited regime, suggesting that a NOx emissions control strategy would be most effective at reducing these peak O3 concentrations. In contrast, a large portion of the days with MDA8 O3 concentrations below 55 ppb were in the VOC-limited regime, suggesting that an emissions control strategy focusing on NOx reduction would increase O3 concentrations. This challenging situation suggests that emissions control programs that focus on NOx reductions will immediately lower peak O3 concentrations but slightly increase intermediate O3 concentrations until NOx levels fall far enough to re-enter the NOx-limited regime. The spatial pattern of increasing and decreasing O3 concentrations in response to a NOx emissions control strategy should be carefully mapped in order to fully understand the public health implications.

Recurrent bacterial infections are a major health burden worldwide, yet the mechanisms dictating host susceptibility to recurrence are poorly understood. Here we demonstrate that an initial bacterial infection of the urinary bladder with uropathogenic E. coli (UPEC) can induce sustained epigenetic changes in the bladder epithelial (urothelial) stem cells that reprogram the differentiated urothelium. We established urothelial stem cell (USC) lines from isogenic mice with different urinary tract infection histories (naïve, chronic or self-resolving). Differentiation of the USC lines in Transwell culture resulted in polarized urothelial cultures that recapitulated distinct remodeling morphologies seen in vivo. In addition, we discovered differences in chromatin accessibility that segregated by disease history, resulting in differences in gene expression upon differentiation of the USC lines in vitro, based on ATAC-seq analysis of the USC lines. Differential basal expression of Caspase-1 led to divergent susceptibilities to inflammatory cell death upon UPEC infection. In mice with a history of chronic infection, enhanced caspase 1-mediated inflammatory cell death was found to be a protective response that enhanced bacterial clearance upon challenge infection. Thus, UPEC infection reshapes the epigenome leading to epithelial-intrinsic remodeling that trains the mucosal immune response to subsequent infection. These findings may have broad implications for the prevention of chronic/recurrent bacterial infections.