Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches.

Three RpoD-family sigma factors, RpoD, RpoS, and RpoH, play critical roles in transcriptional regulation in Salmonella enterica serovar Typhimurium under heat shock conditions. However, the genome-wide regulatory mechanisms of these sigma factors in response to heat stress have remained elusive. In this study, we comprehensively identified 2,319, 2,226, and 213 genome-wide binding sites for RpoD, RpoS, and RpoH, respectively, under sublethal heat shock conditions (42°C).

Experimental promoter identification of a foodborne pathogen subsp. serovar Typhimurium with near single base-pair resolution.

serovar Typhimurium ( Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for . Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq.

Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure.

Antimicrobial resistance (AMR) in pathogenic bacteria poses a significant threat to public health, yet there is still a need for development in the tools to deeply understand AMR genes based on genetic or structural information. In this study, we present an interactive web database named Blanket Overarching Antimicrobial-Resistance gene Database with Structural information (BOARDS, sbml.unist.

Severe Adverse Events of Periocular Acupuncture: A Review of Cases.

Acupuncture is recognized as a component of alternative medicine and is increasingly used worldwide. Many studies have shown the various effects of acupuncture around the eyes for ophthalmologic or nonophthalmologic conditions. For ophthalmologic conditions, the effect of acupuncture on dry eye syndrome, glaucoma, myopia, amblyopia, ophthalmoplegia, allergic rhinoconjunctivitis, blepharospasm, and blepharoptosis has been reported.

Multifocal skull-compensated transcranial focused ultrasound system for neuromodulation applications based on acoustic holography.

Transcranial focused ultrasound stimulation is a promising therapeutic modality for human brain disorders because of its noninvasiveness, long penetration depth, and versatile spatial control capability through beamforming and beam steering. However, the skull presents a major hurdle for successful applications of ultrasound stimulation. Specifically, skull-induced focal aberration limits the capability for accurate and versatile targeting of brain subregions.

The optimal allocation of Covid-19 vaccines.

We develop a simple model of vaccine prioritization for a potential pandemic. We illustrate how the model applies to the case of Covid-19, using an early 2020 primitive estimate of occupation-based exposure risks and age-based infection fatality rates. Even based on primitive estimates the vaccine distribution strongly emphasizes age-based mortality risk rather than occupation-based exposure risk.

Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.

Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair resolution. However, the peak calling step hinders ChIP-exo application since the published algorithms tend to generate false-positive and false-negative predictions.

Model-driven experimental design workflow expands understanding of regulatory role of Nac in .

The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in .

A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp. in Cattle.

Although Mycobacterium avium subsp. (MAP) has threatened public health and the livestock industry, the current diagnostic tools (e.g.

Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis.

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts.

FPCB as an Acoustic Matching Layer for 1D Linear Ultrasound Transducer Arrays.

An acoustic matching layer is an essential component of an ultrasound transducer to achieve maximum ultrasound transmission efficiency. Here, we develop a flexible printed circuit board (FPCB) with a composite structure consisting of multiple polyimide and copper layers and demonstrate it as a novel acoustic matching layer. With a flexible substrate and robust ACF bonding, the FPCB not only serves as an acoustic matching layer between piezoelectric elements and the surrounding medium but also as a ground for the electrical connection between the transducer array elements and the folded substrate.

Analysis of Korean Retinal Specialists' Opinions on Implanting Diffractive Multifocal Intraocular Lenses in Eyes with Underlying Retinal Diseases.

Multifocal intraocular lenses (MF-IOLs) are increasingly implanted as the need for good near- and intermediate-distance vision increases. Although retinal disease is known to be a relative contraindication for MF-IOL implantation, there are no detailed guidelines for MF-IOL implantation with respect to the type and severity of retinal diseases/statuses. In this study, because retinal diseases can affect the performance of MF-IOLs, we analyzed the opinions of 111 retinal specialists, who were members of the Korean Retina Society, on the implantation of diffractive MF-IOLs in eyes with 15 retinal diseases/statuses using a web-based survey.

Calcium-Modified Silk Patch as a Next-Generation Ultrasound Coupling Medium.

There is an increasing interest in developing next-generation wearable ultrasound patch systems because of their wide range of applications, such as home healthcare systems and continuous monitoring systems for physiological conditions. A wearable ultrasound patch system requires a stable interface to the skin, an ultrasound coupling medium, a flexible transducer array, and miniaturized operating circuitries. In this study, we proposed a patch composed of calcium (Ca)-modified silk, which serves as both a stable interface and a coupling medium for ultrasound transducer arrays.

Corneal Lymphangiogenesis: Current Pathophysiological Understandings and Its Functional Role in Ocular Surface Disease.

The cornea is a transparent and avascular tissue that plays a central role in light refraction and provides a physical barrier to the external environment. Corneal avascularity is a unique histological feature that distinguishes it from the other parts of the body. Functionally, corneal immune privilege critically relies on corneal avascularity.

The Role of Neuropeptides in Pathogenesis of Dry Dye.

Neuropeptides are known as important mediators between the nervous and immune systems. Recently, the role of the corneal nerve in the pathogenesis of various ocular surface diseases, including dry eye disease, has been highlighted. Neuropeptides are thought to be important factors in the pathogenesis of dry eye disease, as suggested by the well-known role between the nervous and immune systems, and several recently published studies have elucidated the previously unknown pathogenic mechanisms involved in the role of the neuropeptides secreted from the corneal nerves in dry eye disease.

Synbiotics Containing Nanoprebiotics: A Novel Therapeutic Strategy to Restore Gut Dysbiosis.

A new formulation, nanoprebiotics [e.g., phthalyl pullulan nanoparticles (PPNs)], was demonstrated to enhance the antimicrobial activity of probiotics [e.

Corneal lymphangiogenesis in dry eye disease is regulated by substance P/neurokinin-1 receptor system through controlling expression of vascular endothelial growth factor receptor 3.

Purpose: To evaluate the role of substance P (SP)/neurokinin-1 receptor (NK1R) system in the regulation of pathologic corneal lymphangiogenesis in dry eye disease (DED).

Methods: Immunocytochemistry, angiogenesis assay, and Western blot analysis of human dermal lymphatic endothelial cells (HDLECs) were conducted to assess the involvement of SP/NK1R system in lymphangiogenesis. DED was induced in wild-type C57BL/6 J mice using controlled-environment chamber without scopolamine.

PM10 and PM2.5 real-time prediction models using an interpolated convolutional neural network.

In this paper, we propose a real-time prediction model that can respond to particulate matters (PM) in the air, which are an indication of poor air quality. The model applies interpolation to air quality and weather data and then uses a Convolutional Neural Network (CNN) to predict PM concentrations. The interpolation transforms the irregular spatial data into an equally spaced grid, which the model requires.

Large diameter scleral lens benefits for Asians with intractable ocular surface diseases: a prospective, single-arm clinical trial.

To report the efficacy and safety of large diameter scleral lenses and determine their suitability in Asian subjects with intractable ocular surface diseases. This prospective study enrolled intractable ocular surface diseases subjects with uncorrected visual acuity > counting finger but ≥ 0.3 logMAR and best-corrected visual acuity (BCVA) ≥ 0.

Acoustic Matching Layer Films Using B-Stage Thermosetting Polymer Resins for Ultrasound Transducer Applications.

Acoustic matching layer films (MLFs) were fabricated using B-stage thermosetting polymer resins with various volume fractions of alumina and tungsten powders. After making certain thickness MLFs, ultrasonic matching layers were fabricated using a simple molding process. The thickness of the matching layers can be precisely adjusted from several micrometer to hundreds of micrometer, without any grinding process.

Mortality and causes of death in a population with blindness in Korea: A longitudinal follow-up study using a national sample cohort.

The influence of visual impairment and blindness on the risk of mortality has been reported in diverse cohort studies. However, the results reported have varied from nonsignificant to significant associations. In the present study, we evaluated the influence of blindness on the risk of mortality from 2002 to 2013 using a longitudinal database with a national sample cohort provided by the Korean National Health Insurance Service.

Variable Responses to Corneal Grafts: Insights from Immunology and Systems Biology.

Corneal grafts interact with their hosts via complex immunobiological processes that sometimes lead to graft failure. Prediction of graft failure is often a tedious task due to the genetic and nongenetic heterogeneity of patients. As in other areas of medicine, a reliable prediction method would impact therapeutic decision-making in corneal transplantation.

Complex System Analysis of Korean Peninsula Earthquake Data.

Earthquakes are natural disasters that cause damage in a wide range of regions and represent a complex system that does not have a clear causal relationship with specific observable factors. This research analyzes the earthquake activities on the Korean Peninsula with respect to spatial and temporal factors. Using logarithmic regression analysis, we showed that the relationship between the location of the earthquake and its frequency in these locations follows a power law distribution.