Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes

Accurate determination of causalities between genes is a challenge in the inference of gene regulatory networks (GRNs) from the gene expression profile. Although many methods have been developed for the reconstruction of GRNs, most of them are insufficient in determining causalities or regulatory directions. In this work, we present a novel method, namely, DDTG, to improve the accuracy of causality determination in GRN inference by dissecting downstream target genes. In the proposed method, the topology and hierarchy of GRNs are determined by mutual information and conditional mutual information, and the regulatory directions of GRNs are determined by Taylor formula-based regression. In addition, indirect interactions are removed with the sparseness of the network topology to improve the accuracy of network inference. The method is validated on the benchmark GRNs from DREAM3 and DREAM4 challenges. The results demonstrate the superior performance of the DDTG method on causality determination of GRNs compared to some popular GRN inference methods. This work provides a useful tool to infer the causal gene regulatory network.

hUC-MSCs exosomal miR-451 alleviated acute lung injury by modulating macrophage M2 polarization via regulating MIF-PI3K-AKT signaling pathway

In the previous study, we have proved that exosomal miR-451 from human umbilical cord mesenchymal stem cells (hUC-MSCs) attenuated burn-induced acute lung injury (ALI). However, the mechanism of exosomal miR-451 in ALI remains unclear. Therefore, this study aimed to study the molecular mechanism of hUC-MSCs-derived exosomal miR-451 on ALI by regulating macrophage polarization. Exosomes were isolated and identified by transmission electron microscope (TEM) and nanoparticle tracking analysis (NTA). The expression of miR-451, macrophage migration inhibitory factor (MIF) and PI3K/AKT signaling pathway proteins were detected by qRT-PCR and western blot. Flow cytometry was used to detect the CD80 and CD206 positive cells. Severe burn rat model was established and HE was used to detect the inflammatory cell infiltration and inflammatory injury. Dual luciferase reporter system was used to detect the regulation of miR-451 to MIF. The contents of cytokines were detected by ELISA. The results showed that hUC-MSCs exosomes promoted macrophage M1 to M2 polarization. Furthermore, hUC-MSCs-derived exosomal miR-451 alleviated ALI development and promoted macrophage M1 to M2 polarization. Moreover, MIF was a direct target of miR-451. Downregulation of MIF regulated by miR-451 alleviated ALI development promoted macrophage M1 to M2 polarization. In addition, we found that MIF and hUC-MSCs-derived exosomal miR-451 participated in ALI by regulating PI3K/AKT signaling pathway. In conclusion, we indicated that hUC-MSCs-derived exosomal miR-451 alleviated ALI by modulating macrophage M2 polarization via regulating MIF-PI3K-AKT signaling pathway, which provided great scientific significance and clinical application value for the treatment of burn-induced ALI.

Non-Local Robust Quaternion Matrix Completion for Large-Scale Color Image and Video Inpainting

The image nonlocal self-similarity (NSS) prior refers to the fact that a local patch often has many nonlocal similar patches to it across the image and has been widely applied in many recently proposed machining learning algorithms for image processing. However, there is no theoretical analysis on its working principle in the literature. In this paper, we discover a potential causality between NSS and low-rank property of color images, which is also available to grey images. A new patch group based NSS prior scheme is proposed to learn explicit NSS models of natural color images. The numerical low-rank property of patched matrices is also rigorously proved. The NSS-based QMC algorithm computes an optimal low-rank approximation to the high-rank color image, resulting in high PSNR and SSIM measures and particularly the better visual quality. A new tensor NSS-based QMC method is also presented to solve the color video inpainting problem based on quaternion tensor representation. The numerical experiments on color images and videos indicate the advantages of NSS-based QMC over the state-of-the-art methods.

Influence of potential well thickness on the carrier transport characteristics of InGaAs quantum dot laser diodes

The characteristics of InGaAs quantum dot laser diodes have been investigated by inserting InGaAs wells of different thicknesses in the active zone.

[Clinical effects of vacuum sealing drainage in the treatment of alkali burn wounds]

Objective: To preliminarily observe the clinical effects of vacuum sealing drainage (VSD) in the treatment of alkali burn wounds. Methods: From June 2016 to March 2020, 60 male patients with alkali burns who met the inclusion criteria and hospitalized in the Affiliated Hospital of Jiangnan University were recruited in this prospectively randomized control study. According to the random number table, silver sulfadiazine group and VSD group were both allocated with 30 patients, aged (36±8) and (35±10) years respectively; with total burn area of (7.2±2.0) % and (8.5±3.0) % total body surface area respectively. After admission, patients in silver sulfadiazine group were treated with conventional silver sulfadiazine dressing change once a day after debridement; patients in VSD group were given continuous VSD treatment after debridement, with the negative pressure setting at -10.67 kPa, and the negative pressure materials were replaced every 6 to 8 days. On treatment day 1, 4, and 7, the exudate from the wounds of patients in silver sulfadiazine group and the wound drainage fluid of patients in VSD group were collected, the pH value was measured by a portable pH meter, and the volume of exudate/drainage fluid was measured. After 7, 14, and 21 days of treatment, the wound healing rates of patients were calculated in the two groups. Before treatment and 7 days after treatment, venous blood was collected from the patients in the two groups to detect the serum level of tumor necrosis factor α (TNF-α) and interleukin 8 (IL-8). Within treatment day 14, Visual Analogue Scale was used to assess the pain score of patients in the two groups during each time of dressing change. The medical costs and discharge satisfaction scores of patients in the two groups were recorded. Data were statistically analyzed with analysis of variance for repeated measurement, t test, and Bonferroni correction. Results: (1) On treatment day 1, 4, and 7, the pH values of the drainage fluid of patients in VSD group were 9.75±0.59, 9.01±0.46, and 8.13±0.28, respectively, which were significantly higher than 9.35±0.62, 8.18±0.18, and 7.58±0.09 of exudate of patients in silver sulfadiazine group (t=2.03, 6.80, 7.56, P<0.05 or P<0.01). On treatment day 1 and 4, the volumes of drainage fluid of patients in VSD group were (553±83) and (239±65) mL respectively, which were significantly higher than (440±77) and (175±49) mL of exudate of patients in silver sulfadiazine group (t=3.44, 2.24, P<0.05). On treatment day 7, the volume of drainage fluid of patients in VSD group was (21±8) mL, which was significantly lower than (149±44) mL of exudate of patients in silver sulfadiazine group (t=-12.61, P<0.01). (2) After 7, 14, and 21 days of treatment, the wound healing rates of patients in VSD group were (39±6) %, (74±10) %, and (92±3) %, respectively, which were significantly higher than (25±3) %, (59±6) %, and (77±6) % in silver sulfadiazine group (t=7.07, 5.59, 7.09, P<0.01). (3) Before treatment, the serum levels of TNF-α and IL-8 of patients in the two groups were similar. After 7 days of treatment, the serum levels of TNF-α and IL-8 of patients in VSD group were significantly lower than those in silver sulfadiazine group (t=-8.75, -8.04, P<0.01). (4) The pain score during dressing change and medical cost of patients in VSD group were significantly lower than those in silver sulfadiazine group (t=-4.28, -7.56, P<0.01), while the discharge satisfaction score of patients in VSD group was significantly higher than that in silver sulfadiazine group (t=10.91, P<0.05). Conclusions: The application of VSD technology in clinical alkali burn wounds can effectively promote the removal of residual lye, alleviate the further damage of lye to skin tissue, shorten the wound healing time, effectively remove inflammatory mediators, reduce the pain of dressing change, decrease the total cost of treatment, and enhance satisfaction of patient.

A Professional Development Activity to Better Support International Graduate Teaching Assistants in Evaluating Scientific Writing

Graduate teaching assistants (GTAs) who are English language learners at American institutions often endure xenophobia, pressures to conform to American culture, and visa restrictions on working. Quantitative data we collected from the Introduction to Biology Laboratory course taught at a large R1 university indicate paper grading discrepancies between international and domestic GTAs. Qualitative data highlight international GTAs' concerns regarding grading load and language barriers. To alleviate the burden on international GTAs, we provide a professional development activity for professors to use in course planning meetings based on feedback from GTAs. Group reflection, discussion, and modification of a rubric are recommended in order to train GTAs in assessing scientific writing to collaboratively build expectations as a teaching team.

Improving the internal quantum efficiency of QD/QW hybrid structures by increasing the GaN barrier thickness

Three InGaN/GaN quantum well (QW) samples with different barrier thickness (Sample A: 15 nm, Sample B: 17.5 nm, and Sample C: 20 nm) were grown via a metal organic chemical vapor deposition (MOCVD) system. The InGaN/GaN QWs became QD/QW hybrid structures due to the high density of V-shaped pits (VPs), which cut the InGaN wells into InGaN quantum dots (QDs) and indium-rich (In-rich) QDs stemming from the indium phase separation. By increasing the thickness of GaN barriers, the interactions between InGaN wells are weakened; thus, the strain accumulation is relieved and the strain relaxation degree decreases. Abnormally, the residual internal strain first increased due to least VPs in B and then decreased for C. Lower internal strain weakens the strain-induced piezoelectric polarization effect and as a result, a higher electron–hole wave function overlap and radiative recombination efficiency are improved. Similarly, lower strain relaxation results in more homogeneous indium distribution, and accordingly, a slightly weaker carrier localization effect (CLE). The CLEs of the three samples are strong enough that carriers can be confined by localized states even at room temperature; thus, the slightly weaker CLE does not influence the internal quantum efficiency (IQE). More importantly, InGaN QDs or QWs with lower strain relaxation contain fewer stacking faults that can act as non-radiative recombination centers (NRRCs), improving the IQE. By analyzing the effects of strain-induced piezoelectric polarization, NRRCs and carrier localization on the IQE, it is found that less NRRCs are a major factor in improving the IQE of these QD/QW hybrid structures.

High-density V-shaped pits cause that InGaN/GaN multi-quantum well becomes QD/QW hybrid structure, and the internal quantum efficiency of the hybrid structure is improved by increasing the thickness of GaN barrier.

Understanding the Growth Mechanism of GaN Epitaxial Layers on Mechanically Exfoliated Graphite

The growth mechanism of GaN epitaxial layers on mechanically exfoliated graphite is explained in detail based on classic nucleation theory. The number of defects on the graphite surface can be increased via O-plasma treatment, leading to increased nucleation density on the graphite surface. The addition of elemental Al can effectively improve the nucleation rate, which can promote the formation of dense nucleation layers and the lateral growth of GaN epitaxial layers. The surface morphologies of the nucleation layers, annealed layers and epitaxial layers were characterized by field-emission scanning electron microscopy, where the evolution of the surface morphology coincided with a 3D-to-2D growth mechanism. High-resolution transmission electron microscopy was used to characterize the microstructure of GaN. Fast Fourier transform diffraction patterns showed that cubic phase (zinc-blend structure) GaN grains were obtained using conventional GaN nucleation layers, while the hexagonal phase (wurtzite structure) GaN films were formed using AlGaN nucleation layers. Our work opens new avenues for using highly oriented pyrolytic graphite as a substrate to fabricate transferable optoelectronic devices.

Morphologies and optical and electrical properties of InGaN/GaN micro-square array light-emitting diode chips

InGaN/GaN micro-square array light-emitting diode (LED) chips (micro-chips) have been prepared via the focused ion beam (FIB) etching technique, which can not only reduce ohmic contact degradation but also control the aspect ratio precisely in three-dimensional (3D) structure LED (3D-LED) device fabrication. The effects of FIB beam current and micro-square array depth on morphologies and optical and electrical properties of the micro-chips have been studied. Our results show that sidewall surface morphology and optical and electrical properties of the micro-chips degrade with increased beam current. After potassium hydroxide etching with different times, an optimal current-voltage and luminescence performance can be obtained. Combining the results of cathodoluminescence mappings and light output-current characteristics, the light extraction efficiency of the micro-chips is reduced as FIB etch depth increases. The mechanisms of micro-square depth on light extraction have been revealed by 3D finite difference time domain.

Effect of hydrogen treatment temperature on the properties of InGaN/GaN multiple quantum wells

InGaN/GaN multiple quantum wells (MQWs) were grown with hydrogen treatment at well/barrier upper interface under different temperatures. Hydrogen treatment temperature greatly affects the characteristics of MQWs. Hydrogen treatment conducted at 850 °C improves surface and interface qualities of MQWs, as well as significantly enhances room temperature photoluminescence (PL) intensity. In contrast, the sample with hydrogen treatment at 730 °C shows no improvement, as compared with the reference sample without hydrogen treatment. On the basis of temperature-dependent PL characteristics analysis, it is concluded that hydrogen treatment at 850 °C is more effective in reducing defect-related non-radiative recombination centers in MQWs region, yet has little impact on carrier localization. Hence, hydrogen treatment temperature is crucial to improving the quality of InGaN/GaN MQWs.

Surface Morphology Evolution Mechanisms of InGaN/GaN Multiple Quantum Wells with Mixture N2/H2-Grown GaN Barrier

Surface morphology evolution mechanisms of InGaN/GaN multiple quantum wells (MQWs) during GaN barrier growth with different hydrogen (H₂) percentages have been systematically studied. Ga surface-diffusion rate, stress relaxation, and H₂ etching effect are found to be the main affecting factors of the surface evolution. As the percentage of H₂ increases from 0 to 6.25%, Ga surface-diffusion rate and the etch effect are gradually enhanced, which is beneficial to obtaining a smooth surface with low pits density. As the H₂ proportion further increases, stress relaxation and H₂ over- etching effect begin to be the dominant factors, which degrade surface quality. Furthermore, the effects of surface evolution on the interface and optical properties of InGaN/GaN MQWs are also profoundly discussed. The comprehensive study on the surface evolution mechanisms herein provides both technical and theoretical support for the fabrication of high-quality InGaN/GaN heterostructures.

Measurement of spectacle lenses using wavefront aberration in real view condition

A wavefront aberration analysis method for measuring spectacle lenses in real-view condition is proposed and verified using experimental apparatus based on the eye-rotation model. Two strategies-feedback positioning and posture adjustment of incident beams and Hartmann-Shack wavefront-aberration sensor calibration at each measurement subarea-are applied to improve measurement accuracy. By simulating the real-view condition, wavefront aberration and user power on the vertex sphere can be obtained. Comparison experiments demonstrate the validity and accuracy of the proposed method and experimental apparatus. Freeform progressive addition lenses are also measured and the results analyzed. The findings provide a possible approach for optimizing the design of spectacle lenses and evaluating their manufacturing and imaging quality.

Effect of potential barrier height on the carrier transport in InGaAs/GaAsP multi-quantum wells and photoelectric properties of laser diode

The growth and strain-compensation behaviour of InGaAs/GaAsP multi-quantum wells, which were fabricated by metal-organic chemical vapor deposition, have been studied towards the application of these quantum wells in high-power laser diodes. The effect of the height of the potential barrier on the confined level of carrier transport was studied by incorporating different levels of phosphorus content into the GaAsP barrier. The crystal quality and interface roughness of the InGaAs/GaAsP multi-quantum wells with different phosphorus contents were evaluated by high resolution X-ray diffraction and in situ optical surface reflectivity measurements during the growth. The surface morphology and roughness were characterized by atomic force microscopy, which indicates the variation law of surface roughness, terrace width and uniformity with increasing phosphorus content, owing to strain accumulation. Moreover, the defect generation and structural disorder of the multi-quantum wells were investigated by Raman spectroscopy. The optical properties of the multi-quantum wells were characterized by photoluminescence, which shows that the spectral intensity increases as the phosphorus content increases. The results suggest that more electrons are well bound in InGaAs because of the high potential barrier. Finally, the mechanism of the effect of the height of the potential barrier on laser performance was proposed on the basis of simulation calculations and experimental results.

The morphologies and optical properties of three-dimensional GaN nano-cone arrays

Three-dimensional GaN nanostructures with well-aligned nano-cones were fabricated via laser interference lithography + inductively coupled plasma etching techniques.

Mechanical characterization of stomach tissue under uniaxial tensile action

In this article, the tensile properties of gastric wall were investigated by using biomechanical test and theoretical analysis. The samples of porcine stomach strips from smaller and greater curvature of the stomach were cut in longitudinal and circumferential direction, respectively. The loading-unloading, stress relaxation, strain creep, tensile fracture tests were performed at mucosa-submucosa, serosa-muscle and intact layer, respectively. Results showed that the biomechanical properties of the porcine stomach depended on the layers, orientations and locations of the gastric wall and presented typical viscoelastic, nonlinear and anisotropic mechanical properties. During loading-unloading test, the stress of serosa-muscle layer in the longitudinal direction was 15-20% more than that in the circumferential direction at 12% stretch ratio, while it could reach about 40% for the intact layer and 50% for the mucosa-submucosa layer. The results of stress relaxation and strain creep showed that the variation degree was obviously faster in the circumferential direction than that in the longitudinal direction, and the ultimate residual values were also different for the different layers, orientations and locations. In the process of fracture test, the serosa-muscle layer fractured firstly followed by the mucosa-submucosa layer when the intact layer was tested, the longitudinal strips firstly began to fracture and the required stress value was about twice as much as that in the circumferential strips. The anisotropy and heterogeneity of mechanical characterization of the porcine stomach were related to its complicated geometry, structure and functions. The results would help us to understand the biomechanics of soft organ tissue.

The evolution of a GaN/sapphire interface with different nucleation layer thickness during two-step growth and its influence on the bulk GaN crystal quality

The role of the nucleation layer thickness on the GaN crystal quality grown by metal organic chemical vapor deposition is explored.

Gene expression profiling of human kidneys undergoing laparoscopic donor nephrectomy

BACKGROUND AND OBJECTIVES

The objective was to compare gene expression profiles of 6 kidneys from open donor nephrectomy with 6 kidneys removed after laparoscopic donor nephrectomy and several hours of carbon dioxide pneumoperitoneum with DNA microarrays and identify small-molecule drugs.

METHODS

The gene expression profile GSE3297 was downloaded from the Gene Expression Omnibus database, and the differentially expressed genes were identified by a bioinformatics approach. First, Osprey software was used to construct a differentially expressed gene associated network. Then, DAVID (Database for Annotation, Visualization, and Integrated Discovery) and FuncAssociate were used to perform functional analyses. Finally, the Connectivity Map was used to screen for small-molecule drugs.

RESULTS

A total of 285 differentially expressed genes were identified, including 148 down-regulated genes and 137 up-regulated genes. In addition, the differentially expressed genes in the most significant Gene Ontology term were CASP6, KRAS, SOCS1, ESR1, TSHB, COL1A1, and MMP14. Furthermore, several differentially expressed genes, including STAT1, STAT6, SOS2, and SOCS1, participated in the most remarkable Janus kinase-signal transducer and activator of transcription signaling pathway. Finally, luteolin--with the highest score (0.887)--was identified as the small-molecule drug.

CONCLUSIONS

Our data show an altered renal transcriptome induced by several hours of carbon dioxide pneumoperitoneum and laparoscopic surgery characterized by up-regulation of genes associated with acute inflammation, apoptosis, and immune injury, which could potentially result in renal injury and an enhanced immune response in the recipient after transplant.

Integrated gene network analysis and text mining revealing PIK3R1 regulated by miR-127 in human bladder cancer

BACKGROUND

Cancer is the result of a complex multistep process that involves the accumulation of sequential alterations of several genes, including those encoding microRNAs (miRNAs) that have critical roles in the regulation of gene expression.In this study, we aimed to predict potential mechanisms of bladder cancer related miRNAs and target genes by bioinformatics analyses.

METHODS

Here we used the method of text mining to identify nine miRNAs in bladder cancer and adopted protein-protein interaction analysis to identify interaction sites between these miRNAs and related-target genes.

RESULTS

There are two relationship types between bladder cancer and its related miRNAs: causal and unspecified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment test showed that there were three pathways related to four miRNA targeted genes. The remaining five miRNAs annotated to disease are not enriched in the KEGG pathways. Of these, PIK3R1 is the overlapping gene among 38 genes in the cancer and bladder cancer pathways.

CONCLUSIONS

These findings provide new insights into the role of miRNAs in the pathway of cancer and give us a hypothesis that miR-127 might play a similar role in regulation and control of PIK3R1.

[Intraoperative radiotherapy of unresectable pancreatic carcinoma]

During the period from 1986 to 1991, 33 patients with unresectable carcinoma of the pancreas received intraoperative radiotherapy (IORT). Abdominal and back pain which tormented all patients before IORT totally disappeared in 18 patients (54%) and was allevrited in 13 patients (40%). The average survival time of 6.5 months for patients treated with IORT was not statistically different from that of 30 patients with resectable pancreatic cancers undergoing resection. IORT hence is a good palliative therapy for unresectable carcinoma of the pancreas.

[Analysis of serum levels of selenium, zinc, and copper in 132 patients with malignant tumors]

Since March 1987 to December 1988, serum levels of selenium, zinc, and copper were determined in 132 patients with malignant tumors and in a control group of 43 patients with benign disease. The mean level of selenium in 132 patients with malignant tumors was 0.074 microgram/ml, it was lower than in the control group (P less than 0.01). Zinc was 0.814 microgram/ml, it was low compared to the control group (P less than 0.05). Copper was 1.27 microgram/ml, it was significantly increased (P less than 0.05). Cu/Zn was higher than in the control group (P less than 0.01). An analysis of all the readings showed that the lowest levels of selenium and zinc are associated with advanced gastrointestinal cancer.

[Cystadenoma of the pancreas]

Cystadenoma of the pancreas is a rare tumor, which usually occurs in young women. In this paper, 8 patients are reported. The common clinical symptom was upper abdominal mass or discomfort. The tumor was located by ultrasonography and CT scan. Impression and displacement of the duodenum and stomach were showed by barium meal examination of the upper gastrointestinal tract. Macroscopically, the tumor was encapsulated. Its section showed cystic and multilocular structures. Microscopically, the tumor cells were in papillary arrangement. Six of these 8 patients were misdiagnosed as pseudocyst of the pancreas and cystojejunostomy was performed. Three of 6 underwent malignant change, which was finally diagnosed by fine needle aspiration cytology. This tumor, even after malignant change, is prone to local invasion and less likely towards distant metastasis. Resection, including pancreatoduodenectomy, is the best treatment.

[CT-guided percutaneous fine needle aspiration cytodiagnosis of pancreatic and periampullary tumors]

CT guided percutaneous fine needle aspiration cytodiagnosis was performed on 30 patients with pancreatic and periampullary tumors in China-Japan Friendship Hospital from November 1984 to January 1986. In our series, 9 pancreatic head cancers, 4 pancreatic body and tail cancers, 5 ampullary cancers had positive cytodiagnosis (100%-18/18). 2 of 3 (67%) duodenal cancers and 6 of 7 (86%) the distal common bile duct cancers were positive by cytodiagnosis. 2 pancreatitis were negative (100%). The positive rate by CT guided diagnosis was 93.3% (28/30). In the same period, ultrasonically guided percutaneous fine needle aspiration cytodiagnosis was performed on 30 patients with pancreatic and periampullary tumors, a correction rate of diagnosis was 67%. CT guided procedure is more accurate than that ultrasonically guided.