CRISPR-dCas9-mediated knockdown of prtR, an essential gene in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a widely distributed non-fermentative Gram-negative opportunistic pathogen that is often responsible for nosocomial infections. Gene interference is a potentially valuable tool for investigating essential genes in P. aeruginosa. To establish a gene interference platform in P. aeruginosa, CRISPR system was used with an inactive Cas9 protein. The CRISPR-dCas9 system was cloned into pHERD20T, a shuttle vector with arabinose inducible promoter, and was further modified to target a regulatory gene prtR that is essential for the viability of P. aeruginosa. Cells expressing the prtR-targeting CRISPR interference (CRISPRi) showed growth defect in an arabinose dose-dependent manner. A high-throughput RNA sequencing analysis of bacterial cells with or without the CRISPRi-mediated prtR inhibition indicated that prtRis a global regulator affecting multiple biological processes. In conclusion, the CRISPR-dCas9-based gene knockdown system has been successfully implemented in P. aeruginosa and demonstrated to be an effective tool in the investigation of essential or difficult-to-inactivate genes in this species.

0714 Effect of One-Week Velopharyngeal-Task Training on Genioglossus Corticomotor Excitability and Sleep Apnea Severity

Introduction

The effectiveness of the contraction of the UA dilator muscles plays a crucial role in the maintenance of UA patency. This study aimed to assess the effects of one-week velopharyngeal-task training (VTT) on sleep apnea severity and its genioglossus (GG) corticomotor excitability.

Methods

Ten patients with sleep apnea underwent 1 h VTT on seven consecutive days. During the VTT protocol, subjects were asked to develop repetitive intra-oral positive pressure using cheek-bulging maneuvers while wearing a mouth piece to keep the jaw opened and maintaining an exclusive nasal breathing. They were encouraged to generate approximately 4% of Max pressure by maintaining the pressure inside the corresponding pre-set pressure target window for 2 sec every 10 sec. PSG recording and GG transcranial magnetic stimulation (TMS) response was obtained before and after the one-week VTT.

Results

One-week VTT was associated with a global AHI decrease by 33.8% (pre-VTT: 34.5±31.9 n/h; post-VTT: 25.5±26.7 n/h; p< 0.05) and progressed from moderate/severe to mild/moderate in 40% of patients. Although the bulging pressure remained unchanged (pre-VTT: 17.1±5.6 kPa, post-VTT: 19.4±5.4 kPa, p> 0.05), the amplitude of GG motor evoked potential in response to TMS significantly increased after the one-week VTT (pre-VTT: 639.4±380.9mV; post-VTT: 1128.5±623.9mV; p< 0.05).

Conclusion

One-week VTT is sufficient to confer clinical benefits on patients with sleep apnea. VTT protocol is not oriented toward strength gain, but rather toward an enhancement in the upper airway muscle cortical excitability and improvement in the coordination of their contraction. The authors consider these results to be potentially clinically relevant and worthy of further investigation in a large randomized trial.

Support

National Natural Science Foundation of China, Grant/Award Number: 81670085.

Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma

RNA-sequencing enables accurate and low-cost transcriptome-wide detection. However, expression estimates vary as reference genomes and gene annotations are updated, confounding existing expression-based prognostic signatures. Herein, prognostic 9-gene pair signature (GPS) was applied to 197 patients with stage I lung adenocarcinoma derived from previous and latest data from The Cancer Genome Atlas (TCGA) processed with different reference genomes and annotations. For 9-GPS, 6.6% of patients exhibited discordant risk classifications between the two TCGA versions. Similar results were observed for other prognostic signatures, including IRGPI, 15-gene and ORACLE. We found that conflicting annotations for gene length and overlap were the major cause of their discordant risk classification. Therefore, we constructed a prognostic 40-GPS based on stable genes across GENCODE v20-v30 and validated it using public data of 471 stage I samples (log-rank P < 0.0010). Risk classification was still stable in RNA-sequencing data processed with the newest GENCODE v32 versus GENCODE v20-v30. Specifically, 40-GPS could predict survival for 30 stage I samples with formalin-fixed paraffin-embedded tissues (log-rank P = 0.0177). In conclusion, this method overcomes the vulnerability of existing prognostic signatures due to reference genome and annotation updates. 40-GPS may offer individualized clinical applications due to its prognostic accuracy and classification stability.

Focused characteristics and effects of light reflected from spherical lipid membrane of giant unilamellar vesicles

Lipid vesicle is spherical membranous structure with a concave surface on the inside. When a beam of light illuminates a lipid vesicle, the light reflected from the vesicular concave membrane can be focused to have higher intensity and generate enhanced effects. By observing and simulating light reflected from giant unilamellar vesicles (GUVs), the intensity distribution of the light reflected from a spherical concave lipid membrane was investigated. The reflected light had focused characteristics. Its intensity was concentrated 10,000 times and even exceeded the intensity of incident light in a confined region, creating another effective light source in the lipid vesicle. The fluorescence quenching of sulfo-Cy5 encapsulated in spherical GUVs was stronger than that of the outside solution when irradiated by a 632.8 nm laser. When irradiated with ultraviolet light C (UVC), the damage to plasmid DNA encapsulated with spherical GUVs was greater than that of pure plasmid DNA solution and plasmid DNA mixed with lipid membrane fragments. Therefore, in addition to the effects of incident light, the focused light reflected from GUVs could generate incremental effects on encapsulated photoreactive materials if the spherical structure of the lipid membrane was maintained. These results proved that concave lipid membranes of spherical vesicles can focus light and utilize it to generate enhanced effects. The capability of light focusing and its influence on DNA may provide new insights for understanding the function of lipid membranes in cellular life.

A qualitative transcriptional signature for the histological reclassification of lung squamous cell carcinomas and adenocarcinomas

Background

Targeted therapy for non-small cell lung cancer is histology dependent. However, histological classification by routine pathological assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging. Additionally, the effectiveness of immunomarkers is limited by technical inconsistencies of immunostaining and lack of standardization for staining interpretation.

Results

Using gene expression profiles of pathologically-determined lung adenocarcinomas and squamous cell carcinomas, denoted as pADC and pSCC respectively, we developed a qualitative transcriptional signature, based on the within-sample relative gene expression orderings (REOs) of gene pairs, to distinguish ADC from SCC. The signature consists of two genes, KRT5 and AGR2, which has the stable REO pattern of KRT5 > AGR2 in pSCC and KRT5 < AGR2 in pADC. In the two test datasets with relative unambiguous NSCLC types, the apparent accuracy of the signature were 94.44 and 98.41%, respectively. In the other integrated dataset for frozen tissues, the signature reclassified 4.22% of the 805 pADC patients as SCC and 12% of the 125 pSCC patients as ADC. Similar results were observed in the clinical challenging cases, including FFPE specimens, mixed tumors, small biopsy specimens and poorly differentiated specimens. The survival analyses showed that the pADC patients reclassified as SCC had significantly shorter overall survival than the signature-confirmed pADC patients (log-rank p = 0.0123, HR = 1.89), consisting with the knowledge that SCC patients suffer poor prognoses than ADC patients. The proliferative activity, subtype-specific marker genes and consensus clustering analyses also supported the correctness of our signature.

Conclusions

The non-subjective qualitative REOs signature could effectively distinguish ADC from SCC, which would be an auxiliary test for the pathological assessment of the ambiguous cases.

Microcatheter shaping using three-dimensional printed models for intracranial aneurysm coiling

Background and purpose

Microcatheterization is an important, but also difficult, technique used for the embolization of intracranial aneurysms. The purpose of this study was to investigate the application of three-dimensional (3D) printing technology in microcatheter shaping.

Methods

Nine cases of internal carotid artery posterior communicating artery aneurysm diagnosed by CT angiography were selected, and 3D printing technology was used to build a 3D model including the aneurysm and the parent artery. The hollow and translucent model had certain flexibility; it was immersed in water and the microcatheter was introduced into the water to the target position in the aneurysm, followed by heating the water temperature to 50°C. After soaking for 5 min, the microcatheter was taken out and the shaping was completed. After sterilization, the shaped microcatheter was used for arterial aneurysm embolization and evaluation was conducted.

Results

Nine cases of microcatheter shaping were satisfactory and shaping the needle was not necessary; no rebound was observed. The microcatheter was placed in an ideal position, and the stent-assisted method was used in three cases of wide-neck aneurysm. There were no complications related to surgery.

Conclusion

A new microcatheter shaping method using 3D printing technology makes intracranial artery aneurysm embolization more stable and efficient.

Graphene oxide-film-coated splitting ratio-adjustable Mach-Zehnder interferometer for relative humidity sensing

In this paper, a splitting ratio-adjustable Mach-Zehnder interferometer (MZI) for the measurement of relative humidity (RH) is proposed and experimentally demonstrated. The sensing head contains three sections of single mode fiber (SMF) and two sections of multimode fiber (MMF), in which the two MMFs are spliced among the three SMFs. The MMFs are corroded with hydrofluoric acid and act as mode couplers to split and recombine light owing to the core diameter mismatch with the SMF. A layer of graphene oxide (GO) is coated on the MMFs by dip-coating and natural evaporation. The effective refractive index of the GO will vary when it absorbs the water molecules. As a result, the intensity of the transmission light in the core and cladding of the single mode fiber can be adjusted. Thus, the intensity of the resonant dip will vary when the relative humidity changes. The experimental results show that a humidity sensitivity of 0.263 dB/RH% with a linear correlation coefficient of 99% can be achieved in a relative humidity range of 35% to 85%.

[Epidemiologic survey on the prevalence and distribution of infants' common gastrointestinal symptoms in 7 cities in China: a population-based study]

Objective: Regurgitation, infantile colic, and functional constipation are common gastrointestinal symptoms in childhood, the aim of this study was to explore the prevalence and distribution of these symptoms in China. Methods: A screening program in infants aged 0 to 3 years selected through stratified cluster random sampling was carried out in 7 cities in China. Questionnaires were filled, and then diagnosis were made according to Rome Ⅳ criteria. Areas, (urban-rural), age and gender distribution of prevalence of childhood common gastrointestinal symptoms were analyzed. Results: Totally, 20 932 effective questionnaires were returned. The total number of infants aged 0 to 1 years was 10 193. Regurgitation was diagnosed in 1 960 infants, with the prevalence of 19.2%, among infants aged 0 to 3 months that had highest prevalence (29.8%). The prevalence decreased with age, and differences among different age groups showed significant. For infantile colic, 4 470 infants aged 0 to 5 months were analyzed and the prevalence of infantile colic was 7.3%. The prevalence of infantile colic was the highest in infants aged 1 to 2 months (10.0%). Age specific difference was significant. Of all the infants, functional constipation was diagnosed in 1 755 infants with the prevalence of 8.4%, and the lowest prevalence was found in infants aged 0 to 3 months (6.2%), and the highest prevalence was in infants aged 30 to 36 months (10.0%). The differences in different age group were significant. Conclusion: Symptoms of regurgitation, infantile colic, and functional constipation are common in infants in China, with age specific difference in prevalence of the symptoms.

Silver-modified octahedral anatase particles as plasmonic photocatalyst

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Octahedral anatase particles (OAPs) modified with silver NPs by photodeposition.

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Ag/OAPs with enhanced photocatalytic activity under both UV and vis irradiation.

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Electron traps as nucleation sites for silver NPs.

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Polydispersity of silver NPs results in broad LSPR and thus enhanced vis activity.

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TRMC data correlate with photocatalytic activity.

Octahedral anatase particles (OAPs) were modified with silver nanoparticles (NPs) by photodeposition method. The properties of OAPs influenced the properties of silver deposits, and thus the photocatalytic activity of the obtained silver-modified OAPs. Photocatalytic activities were tested under UV and vis irradiation for oxidative decomposition of acetic acid and oxidation of 2-propanol, respectively. The properties of silver-modified OAPs were investigated by XRD, STEM, DRS, XPS and time-resolved microwave conductivity (TRMC) method. It was found that electron traps (ETs) worked as nucleation sites for silver, resulting in formation of smaller silver NPs on smaller OAPs with larger content of ETs. The modification with silver resulted in enhanced photocatalytic activity under both UV and vis irradiation. It was found that larger crystallite size of silver NPs, and thus larger polydispersity of silver deposits resulted in broad and intense plasmon resonance peak causing enhanced visible activity. The correlation between photocatalytic activity and TRMC data, e.g., slower decay of TRMC signal for more active samples, allowed discussion on property-governed photocatalytic activities of silver-modified titania.

Characteristics and formation of typical winter haze in Handan, one of the most polluted cities in China

Handan, a city within the North China Plain (NCP) region, is a typical city influenced by regional particulate matter (PM) pollution. One-year hourly semi-continuous observation was carried out in 2015 in Handan with the aim of identifying the chemical composition and variations in PM_2.5. Moreover, the concentration of aerosol precursors, meteorological factors, and secondary transformations are considered. The results demonstrate that the annual average PM_2.5 concentration in Handan is 122.35μgm^-3, approximately 3.5 times higher than the Chinese National Ambient Air Quality Standard (NAAQS) (35μgm^-3), and only 12days were below the guideline. As expected, PM concentrations are highest in winter, especially in December. In addition, we measure the concentrations of five species commonly found in PM, nitrate, sulfate, ammonium, inorganic carbon, and organic carbon. Of these, nitrate and sulfate account for the largest proportion of PM_2.5; during periods when the PM_2.5 concentration was below 400μgm^-3, nitrate dominates, while above this concentration, sulfate dominate. This is likely related to the nitrogen and sulfur oxidation ratios, which are in turn, especially the sulfur oxidation ratio, driven by high relative humidity (>60%). In addition, haze events are driven by other meteorological conditions, wind speed and direction, where low wind speeds from the south and southwest enable pollutant accumulation, which are infrequently interspersed with brief periods with high wind speeds that promote pollutant dispersal. Even though Handan is among the ten most polluted cities in China with regard to air pollution, few studies beyond model simulations have analyzed air pollutant concentrations in this city. Therefore, this study makes a significant contribution to understanding air pollution in Handan, which can further be used to improve our understanding of regional pollution in the highly populated North China Plain. These results have implications for the creation of policies and legislation, as well as other pollution control measures.

Risk Factors Analysis and Death Prediction in Some Life-Threatening Ailments Using Chi-Square Case-Based Reasoning (χ2 CBR) Model

A wealth of data are available within the health care system, however, effective analysis tools for exploring the hidden patterns in these datasets are lacking. To alleviate this limitation, this paper proposes a simple but promising hybrid predictive model by suitably combining the Chi-square distance measurement with case-based reasoning technique. The study presents the realization of an automated risk calculator and death prediction in some life-threatening ailments using Chi-square case-based reasoning (χ² CBR) model. The proposed predictive engine is capable of reducing runtime and speeds up execution process through the use of critical χ² distribution value. This work also showcases the development of a novel feature selection method referred to as frequent item based rule (FIBR) method. This FIBR method is used for selecting the best feature for the proposed χ² CBR model at the preprocessing stage of the predictive procedures. The implementation of the proposed risk calculator is achieved through the use of an in-house developed PHP program experimented with XAMP/Apache HTTP server as hosting server. The process of data acquisition and case-based development is implemented using the MySQL application. Performance comparison between our system, the NBY, the ED-KNN, the ANN, the SVM, the Random Forest and the traditional CBR techniques shows that the quality of predictions produced by our system outperformed the baseline methods studied. The result of our experiment shows that the precision rate and predictive quality of our system in most cases are equal to or greater than 70%. Our result also shows that the proposed system executes faster than the baseline methods studied. Therefore, the proposed risk calculator is capable of providing useful, consistent, faster, accurate and efficient risk level prediction to both the patients and the physicians at any time, online and on a real-time basis.

Laugier-Hunziker syndrome: A case report

Laugier-Hunziker syndrome (LHS) is a rare, benign, acquired pigmentary condition mainly affecting lips, oral mucosa and acral area, frequently associated with longitudinal melanonychia. Herein, we reported a 45-year-old female case with LHS. The clinical, dermoscopic, histopathologic features of LHS were reviewed and the important differential diagnosis was discussed.