Combined metabolomic and proteomic analysis of sepsis related acute liver injury and its pathogenesis research

BACKGROUND

Sepsis-induced acute liver injury is common in patients in intensive care units. However, the exact mechanism of this condition remains unclear. The purpose of this study was to investigate the roles and mechanisms of proteins and metabolites in the liver tissue of mice after sepsis and elucidate the molecular biological mechanisms of sepsis-related liver injury.

METHODS

First, a lipopolysaccharide (LPS)-induced sepsis mouse model was established. Then, according to alanine aminotransferase (ALT) and aspartate aminotransferase (AST) detection in mouse serum and liver histopathological examination (HE) staining, the septic mice were divided into two groups: acute liver injury after sepsis and nonacute liver injury after sepsis. Metabolomics and proteomic analyses were performed on the liver tissues of the two groups of mice to identify significantly different metabolites and proteins. The metabolomics and proteomics results were further analysed to identify the biological indicators and pathogenesis related to the occurrence and development of sepsis-related acute liver injury at the protein and metabolite levels.

RESULTS

A total of 14 differentially expressed proteins and 46 differentially expressed metabolites were identified. Recombinant Erythrocyte Membrane Protein Band 4.2 (Epb42) and adenosine diphosphate (ADP) may be the key proteins and metabolites responsible for sepsis-related acute liver injury, according to the correlation analysis of proteomics and metabolomics. The expression of the differential protein Epb42 was further verified by western blot (WB) detection.

CONCLUSIONS

Our study suggests that the differential protein Epb42 may be key proteins causing sepsis-associated acute liver injury, providing new and valuable information on the possible mechanism of sepsis-associated acute liver injury.

Gut microbiota composition and changes in patients with sepsis: potential markers for predicting survival

BACKGROUND

Sepsis can cause immune dysregulation and multiple organ failure in patients and eventually lead to death. The gut microbiota has demonstrated its precise therapeutic potential in the treatment of various diseases. This study aimed to discuss the structural changes of the gut microbiota in patients with sepsis and to analyze the differences in the gut microbiota of patients with different prognoses.

METHODS

We conducted a multicenter study in which rectal swab specimens were collected on the first and third days of sepsis diagnosis. A total of 70 specimens were collected, and gut microbiota information was obtained by 16S rRNA analysis.

RESULTS

The relative abundance of Enterococcus decreased in rectal swab specimens during the first three days of diagnosis in patients with sepsis, while the relative abundance of inflammation-associated Bacillus species such as Escherichia coli, Enterobacteriaceae, and Bacteroidetes increased. By comparing the differences in the flora of the survival group and the death group, we found that the abundance of Veillonella and Ruminococcus in the death group showed an increasing trend (p < 0.05), while the abundance of Prevotella_6 and Prevotella_sp_S4_BM14 was increased in surviving patients (p < 0.05).

CONCLUSIONS

The Firmicutes/Bacteroidetes ratio, reflecting overall gut microbial composition, was significantly lower on day three of sepsis diagnosis. Changes in the abundance of specific gut microbiota may serve as prognostic markers in patients with sepsis.

Early gut microbiological changes and metabolomic changes in patients with sepsis: a preliminary study

The gut microbiota is closely related to the development of sepsis. The aim of this study was to explore changes in the gut microbiota and gut metabolism, as well as potential relationships between the gut microbiota and environmental factors in the early stages of sepsis. Fecal samples were collected from 10 septic patients on the first and third days following diagnosis in this study. The results showed that in the early stages of sepsis, the gut microbiota is dominated by microorganisms that are tightly associated with inflammation, such as Escherichia-Shigella, Enterococcus, Enterobacteriaceae, and Streptococcus. On sepsis day 3 compared to day 1, there was a significant decrease in Lactobacillus and Bacteroides and a significant increase in Enterobacteriaceae, Streptococcus, and Parabacteroides. Culturomica_massiliensis, Prevotella_7 spp., Prevotellaceae, and Pediococcus showed significant differences in abundance on sepsis day 1, but not on sepsis day 3. Additionally, 2-keto-isovaleric acid 1 and 4-hydroxy-6-methyl-2-pyrone metabolites significantly increased on sepsis day 3 compared to day 1. Prevotella_7 spp. was positively correlated with phosphate and negatively correlated with 2-keto-isovaleric acid 1 and 3-hydroxypropionic acid 1, while Prevotella_9 spp. was positively correlated with sequential organ failure assessment score, procalcitonin and intensive care unit stay time. In conclusion, the gut microbiota and metabolites are altered during sepsis, with some beneficial microorganisms decreasing and some pathogenic microorganisms increasing. Furthermore, Prevotellaceae members may play different roles in the intestinal tract, with Prevotella_7 spp. potentially possessing beneficial health properties and Prevotella_9 spp. potentially playing a promoting role in sepsis.

PINK1 regulates apoptosis of osteosarcoma as the target gene of cisplatin

BACKGROUND

Osteosarcoma is a common primary bone malignancy prevalent among adolescents and young adults. PTEN-induced kinase 1 (PINK1) regulates Parkinson's disease, but its role in cancers is unknown.

OBJECTIVE

This study was designed to analyze the mechanism by which PINK1 affects osteosarcoma using bioinformatics and cell experiments.

MATERIALS AND METHODS

The gene expression profiles were downloaded from the TARGET database. Several online databases were used to analyze the expression and protein‒protein interaction networks. CCK-8 cell viability assays and cisplatin treatment were used to assess cell activity with or without cisplatin treatment. Acridine orange/ethidium bromide (AO/EB) fluorescence staining was used to calculate the percentage of apoptotic cells.

RESULTS

Through bioinformatics analysis, we found that high expression of PINK1 was associated with poor prognosis in patients with osteosarcoma, and PINK1 inhibited apoptosis and promoted proliferation pathways. Next, we found that both PINK1 mRNA and protein levels were upregulated in osteosarcoma tissues. Additionally, we found that PTEN was reduced, while FOXO3a was markedly increased in osteosarcoma, suggesting that FOXO3a and not PTEN induced the overexpression of PINK1. CCK-8 and clonogenic assays showed that the knockdown of PINK1 decreased the growth of U2OS osteosarcoma cells. Ki67 immunofluorescence staining revealed that reduced cell proliferation in U2OS cells resulted in the depletion of PINK1. In addition, our AO/EB staining results indicated that the knockdown of PINK1 resulted in an increase in apoptotic cells and increased the levels of cleaved caspase-3. Furthermore, our experiments revealed that cisplatin promotes OS cell apoptosis by downregulating PINK1.

CONCLUSION

Collectively, our findings demonstrate that PINK1 is crucially involved in osteosarcoma and suggests that it can promote the apoptosis of OS cells as the downstream target gene of cisplatin.

Changes in the microbiota in different intestinal segments of mice with sepsis

Introduction

The small intestine, as the main digestion and absorption site of the gastrointestinal tract, is often overlooked in studies, and the overall microbiota does not reflect the makeup of the microbiota in different segments of the intestine. Therefore, we aimed to exclude the influence of routine ICU treatment measures on sepsis patients and observed changes in the diversity and abundance of gut microbiota in different intestinal segments of septic mice.

Methods

The mice were randomly divided into the CLP6h group and the sham group. The contents of the colon and small intestine of the experimental group and the control group were collected after 6 h.

Results

After CLP, the number and structure of the gut microbiota in the colon changed most obviously, among which Bacteroidetes had the most significant changes. Akkermansia, D.Firmicutes_bacterium_M10_2, Blautia, Bifidobacterium, Lactobacillus, Candidatus_Arthromitus, and Muribaculaceae were changed in the colon. Lactobacillus, Bifidobacterium, Akkermansia, Blautia, Candidatus_Arthromitus, and Lachnospiraceae_NK4A136_group were changed in the small intestine.

Discussion

Our experiment found that there were different numbers of unique and common gut microbiota in the small intestine and colon after sepsis, and the gut microbiota of the colon changed more drastically after sepsis than the small intestine. Thus, we should focus on protective gut microbiota and mucin-degrading microbes. We hope that these results will provide help for sepsis treatment in the future.

Clinical characteristics and severity of beta and delta variants of SARS-CoV-2 and the effect of vaccine on delta variants

Background

The Delta variant of concern (VOC) is rapidly becoming the dominant strain globally. We report the clinical characteristics and severity of hospitalized patients infected with Delta and Beta VOCs during the local outbreak in Harbin, Heilongjiang Province, China, and the effect of vaccines on the Delta variant.

Methods

We collected a total of 735 COVID-19 patients from the First Affiliated Hospital of Harbin Medical University, including 96 cases infected with the Delta VOC and 639 cases infected with the Beta VOC. Demographic, clinical characteristic and laboratory findings were collected and compared.

Results

Differences in viral shedding, IgG and IgM levels, and the neutrophil-to-lymphocyte ratio were noted between the Delta and Beta VOCs (p < 0.05). Survival analysis of the two groups revealed longer viral shedding of the Delta VOC (p < 0.05). For the Delta VOC, the longer the vaccination period, the lower the IgG and IgM levels. IgM levels were higher in the convalescent plasma group, whereas lymphocyte counts were lower.

Conclusions

Delta VOC virus shedding was longer compared with Beta VOC shedding. Vaccination with inactivated vaccines can reduce the severe illness rate of the Delta VOC. IgG and IgM levels are reduced as the time period between the first and second vaccine doses increases.

High-throughput metabolomics using UPLC/Q-TOF-MS coupled with multivariate data analysis reveals the effect and mechanism of syringin against ovariectomized osteoporosis

Osteoporosis is an increasing public health problem in the worldwide and has caused socioeconomic burden. Natural products as candidates have the potential to promote bone formation and suppress bone resorption for osteoporosis treatment. Previously, syringin has showed the potent anti-osteoporosis activity, however the detailed mechanism of syringin against osteoporosis is still unclear. This study aimed to reveal the pharmacological effect and mechanism of syringin through the high-throughput metabolomics. In this study, metabolomics techniques were used to explore the metabolic biomarkers and profiles provides deep insights into the pharmacological effects and mechanism of syringin against osteoporosis. The metabolite biomarkers were monitored based on the high-resolution mass spectrometry. By the integration analysis of metabolomics technology, a total of 23 metabolic biomarkers were discovered and we found the highly relevant pathway involved in glycine and serine metabolism, butyrate metabolism, methionine metabolism, catecholamine biosynthesis, tyrosine metabolism, etc. Interestingly, synthesis and degradation of ketone bodies, phenylalanine, tyrosine and tryptophan biosynthesis, arachidonic acid metabolism, tyrosine metabolism, glycine, serine and threonine metabolism, butanoate metabolism, was related with efficacy of syringin. The present work showed that the metabolomics technology can provide novel strategies for revealing insights into the metabolic effects and action mechanism of drug.

lncRNA HAND2-AS1 is downregulated in osteoarthritis and regulates IL-6 expression in chondrocytes

BACKGROUND

Osteoarthritis (OA) is a leading cause of disability. The incidence of OA is progressively rising due to the diminishing levels of physical activity and ever-expanding aging population. However, the mainstay for OA treatment only can improve symptoms without delay the progression of this severe disease. This study aimed to explore the biological role and clinical function of lncRNA HAND2-AS1 in OA.

METHODS

Blood samples and synovial fluid were collected from OA patients and normal subjects. HAND2-AS1 expression was detected by qRT-PCR and IL-6 expression was detected by ELISA. The plasma levels of HAND2-AS1 were also detected in different ages, stages, and gender of OA patients and controls. Furthermore, the ROC curve was used to analyze whether HAND2-AS1 can distinguish OA patients from normal subjects. Also, Pearson correlation coefficient analysis was used to analyze the correlation between lncRNA HAND2-AS1 and IL-6. In addition, Western blot was used to detect the IL-6 level upon HAND2-AS1 over-expression in chondrocytes and qRT-PCR was used to detect the HAND2-AS1 level after endogenous IL-6 treatment.

RESULTS

HAND2-AS1 and IL-6 were dysregulated in plasma and synovial fluid of OA patients. The expression of HAND2-AS1 in plasma of OA patients was decreased with aging and progression. Furthermore, HAND2-AS1 downregulation effectively distinguished OA patients from the healthy controls. Over-expression of HAND2-AS1 inhibited IL-6 expression in chondrocytes, while treatment with exogenous IL-6 did not affect HAND2-AS1 expression.

CONCLUSION

HAND2-AS1 effectively distinguished OA patients from the healthy controls and regulates IL-6 expression in human chondrocytes.

TRIAL REGISTRATION

ChiCTR, ChiCTR2000038635 . Registered 11 February 2019.

High-Throughput Metabolomics Discovers Metabolic Biomarkers and Pathways to Evaluating the Efficacy and Exploring Potential Mechanisms of Osthole Against Osteoporosis Based on UPLC/Q-TOF-MS Coupled With Multivariate Data Analysis

Postmenopausal osteoporosis (PMOP) is the most common metabolic bone illness among the elderly especially in postmenopausal women resulting from a reduction in bone mineral density, but there is no effective drug at present. The study was aimed at evaluating efficacy of osthole against osteoporosis using high-throughput metabolomics method. The blood samples for illustrating the pathological mechanism of PMOP and exploring the efficacy of osthole treatment (ST) were collected to perform metabolites and metabolic profiles and pathways analysis using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) and pattern recognition methods. In addition, backbone weight, the bone density, and some vital biochemical indexes were also detected. A total of 28 metabolites were identified as biomarkers for ovariectomized-osteoporosis model, and ST could significantly regulate 19 of them including lysine, linoleic acid, 3-hydroxybutyric acid, prostaglandin F2a, taurocholic acid, LysoPC(15:0), l-carnitine, glucose, arginine, citric acid, corticosterone, ornithine, tryptophan, arachidonic acid, Cer(d18:0/18:0), glutamine, uric acid, 8-HETE, estriol, which mainly related with 13 metabolic pathways, such as linoleic acid metabolism, starch, and sucrose metabolism, arachidonic acid metabolism, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, citrate cycle (TCA cycle), and arginine biosynthesis. The ovariectomized model (OVX) rats display a significant decrease bone density, TGF-β1, NO, and NOS level, and a significant increase bone weight, IL-6, TNF-α, and Ca 2+ level. These parameters in the ST rats were evidently improved as compared to the OVX group. ST effectively mitigated ovariectomy-induced osteoporosis in rats by affecting endogenous metabolite-related metabolic mechanism and showed the natural alternative with potential for the treatment of PMOP.

Variation in greater trochanteric lateroversion: a risk factor for femoral stem varus in total hip arthroplasty

INTRODUCTION

Correct implant positioning is required to achieve adequate biomechanics. The greater trochanter is more medially or laterally positioned in some patients, known as trochanteric lateroversion. However, studies have not identified correlations between postoperative coronal alignment and variation in greater trochanteric lateroversion. The purpose of this study was to identify the effects of variation in greater trochanteric lateroversion on postoperative stem coronal alignment and to investigate other factors related to stem coronal alignment.

METHODS

A total of 213 hips in 149 patients who underwent total hip arthroplasty were included in this prospective study. The greater trochanters were categorised into 5 groups according to the degree of variation in greater trochanteric lateroversion, and the stem coronal alignment angle and stem fit were measured on anteroposterior radiographs.

RESULTS

Postoperative stem varus was positively correlated with greater trochanteric lateroversion (r = 0.26065, p = 0.0001) and negatively correlated with the stem fit (r = -0.16568, p = 0.0155).

DISCUSSION

Excessive variation in greater trochanteric lateroversion was a risk factor for femoral stem varus, and the stem varus position was always accompanied by inadequate canal filling. When the tip of the trochanteric overhang exceeded the centreline of the femoral canal, the influence of lateroversion of the greater trochanter on the femoral stem remarkably increased. Appropriate measures should be implemented to avoid a stem varus position and inappropriate stem fit.

Serum Homocysteine Levels Had Important Associations with Activity and Quality of Daily Living in Chinese Centenarians

BACKGROUND

Population aging is an important problem worldwide, with activity and quality of daily living commonly reduced in elderly people. leading to increased hospitalization and mortality rates, and substantial individual and social burdens.

OBJECTIVE

This study was designed to investigate the associations of serum homocysteine levels with activity and quality of daily living in Chinese centenarians for the first time.

PARTICIPANTS

The China Hainan Centenarian Cohort Study was performed in 18 cities and counties of Hainan Province.

MAIN MEASURES

Home interview, physical examination and blood analysis were performed in 787 centenarians following standard procedures.

KEY RESULTS

The median age was 102 years, ranging between 100 and 115 years. There were 634 females (80.6%) and 153 males (19.4%) in all. The median level of serum homocysteine was 23.80 (18.80-29.90) umol/L, whereas median values of Barthel Index and EuroQol 5 Dimensions were 85(60-95) and 0.661(0.558-0.766), respectively. The centenarians with serum homocysteine levels ≥23.8μmol/L were more likely to had lower values of Barthel Index and EuroQol 5 Dimensions than those with serum homocysteine levels <23.8μmol/L (P<0.05 for all). In multivariate linear regression analyses, serum homocysteine levels were significantly associated with Barthel Index and EuroQol 5 Dimensions (P<0.05 for all).

CONCLUSIONS

Serum homocysteine levels had important associations with activity and quality of daily living in Chinese centenarians. Future research should focus on the value of intervening in serum homocysteine levels by supplying folic acid (vitamin B9) and vitamin B12 on improving activity and quality of daily living in elderly people.

Sex, Residence and Fish Intake Predict Vitamin D Status in Chinese Centenarians

OBJECTIVES

This study aims to investigate the prevalence of vitamin D deficiency in Chinese centenarians and to identify the factors associated with vitamin D deficiency.

DESIGN

Cross-sectional population-based study.

SETTING

Hainan province in the south of China.

PARTICIPANTS

943 subjects aged 100 years old and older.

METHODS

Details on sociodemographics and lifestyle characteristics were collected using a structured questionnaire. Anthropometrics and blood samples were obtained. Vitamin D deficiency was defined as serum 25-hydroxyvitamin D concentration < 20ng/mL (50nmol/L).

RESULTS

The overall prevalence of vitamin D deficiency among these 943 centenarians was 39.9% (376 subjects) and the mean serum vitamin D concentrations were 22.7±9.5 (ng/mL). Female centenarians had higher prevalence of vitamin D deficiency than male (44.0% vs. 21.7%, P <0.001). Multivariate logistic regression analyses showed that being female, urban residency, lower body mass index, higher serum parathyroid hormone levels, no fish consumption, and less sun exposure time were all significant and independent determinants of vitamin D deficiency. No significant associations of vitamin D deficiency with ethnic, education, geographic location, tea drinking, alcohol use, or smoking were found in this study.

CONCLUSION

Vitamin D deficiency was common in Chinese centenarians, especially in women. Given that vitamin D deficiency is linked to numerous adverse health outcomes, dietary, outdoor activities and other intervention measures are needed to correct vitamin D deficiency in this population.

Relationships of Sex Hormone Levels with Activity of Daily Living in Chinese Female Centenarians

BACKGROUND

Activity of daily living declines in female elderly, which not only increases hospitalization and mortality rates, but also aggravates individual and societal burden. Large samples are needed to elucidate the relationships of plasma sex hormone levels with activity of daily living in Chinese female centenarians to better understand the effects of hormone-replacing therapy.

OBJECTIVE

As the first time in the world, the current study was designed to investigate the relationships of plasma sex hormone levels with activity of daily living in Chinese female centenarians.

PARTICIPANTS

China Hainan Centenarian Cohort Study was carried out in 18 cities and counties of Hainan Province.

MAIN MEASURES

Home interview, physical examination and blood analysis were carried out in 583 female centenarians following standard procedures. Barthel Index was used to assess the activity of daily living.

KEY RESULTS

Median age of all female centenarians was 102 years, with the range from 100 to 115 years. Median values of Barthel Index were 85(60-90). In multivariate linear regression analyses, Barthel Index values were inversely associated with plasma luteinizing hormone (LH), follicle-simulating hormone (FSH), testosterone, progesterone and estradiol levels (P<0.05 for all).

CONCLUSION

Plasma sex hormone levels, including LH, FSH, testosterone, progesterone and estradiol, had significant relationships with activity of daily living in Chinese female centenarians.

Digital Assessment of the Implantation Angle of Proximal Femoral Nail Antirotation Helical Blade Using CT Three-dimensional Reconstruction

OBJECTIVES

To facilitate simple and safe manipulation during proximal femoral nail antirotation (PFNA) operation, we studied the range of safe implantation angle of the helical blade of the PFNA system by using a digital-based three-dimensional reconstruction model of CT images.

METHODS

Thirty-five healthy volunteers were recruited. Original multilayer helical CT scan data of the left femur were collected and imported into Mimics software. Anatomic features of the femur, including the safe implantation angle, anterior and posterior angle, were measured. Differences in each angle between male and female subjects were compared using Student's t test, and the determinants of each angle were analyzed by linear regression.

RESULTS

The mean safe implantation angle was 30.09° ± 4.73°, the mean anterior angle was 15.82° ± 2.07°, and the mean posterior angle was 14.27° ± 3.19°. All the three angles were greater in males than females (P < 0.05). Neck shaft angle and the diameter of the femoral neck and head were linearly correlated with the safe implantation angle, the anterior and posterior angle, respectively. Femoral neck diameter was a significant determinant of the safe implantation angle and posterior angle, respectively. Moreover, femoral neck diameter and femoral head diameter were significant determinants of the anterior angle.

CONCLUSIONS

The study has introduced and delineated a novel parameter, the safe implantation angle, for FPNA surgery, which may help orthopedic surgeons in deciding a safe range of PFNA operation and improve the accuracy of PFNA helical blade implantation.

Overexpression of the CmACS-3 gene in melon causes abnormal pollen development

Sexual diversity expressed by the Curcurbitaceae family is a primary example of developmental plasticity in plants. Most melon genotypes are andromonoecious, where an initial phase of male flowers is followed by a mixture of bisexual and male flowers. Over-expression of the CmACS-3 gene in melon plants showed an increased number of flower buds, and increased femaleness as demonstrated by a larger number bisexual buds. Transformation of CmACS-3 in melons showed earlier development of and an increased number of bisexual buds that matured to anthesis but also increased the rate of development of the bisexual buds to maturity. Field studies showed that CmACS-3-overexpressing melons had earlier mature bisexual flowers, earlier fruit set, and an increased number of fruits set on closely spaced nodes on the main stem.

Fiber-integrated 780 nm source for visible parametric generation

We report the development of a fully fiber-integrated pulsed master oscillator power fibre amplifier (MOPFA) source at 780 nm, producing 3.5 W of average power with 410 ps pulses at a repetition rate of 50 MHz. The source consists of an intensity modulated 1560 nm laser diode amplified in an erbium fiber amplifier chain, followed by a fiber coupled periodically poled lithium niobate crystal module for frequency doubling. The source is then used for generating visible light through four-wave mixing in a length of highly nonlinear photonic crystal fiber: 105 mW at 668 nm and 95 mW at 662 nm are obtained, with pump to anti-Stokes conversion slope efficiencies exceeding 6% in both cases.

Role of ligand-based drug design methodologies toward the discovery of new anti- Alzheimer agents: futures perspectives in Fragment-Based Ligand Design

Alzheimer's disease (AD), a degenerative disease affecting the brain, is the single most common source of dementia in adults. The cause and the progression of AD still remains a mystery among medical experts. As a result, a cure has not yet been discovered, even after decade's worth of research that started since 1906, when the disease was first identified. Despite the efforts of the scientific community, several of the biological receptors associated with AD have not been sufficiently studied to date, limiting in turn the design of new and more potent anti-AD agents. Thus, the search for new drug candidates as inhibitors of different targets associated with AD constitutes an essential part towards the discovery of new and more efficient anti-AD therapies. The present work is focused on the role of the Ligand-Based Drug Design (LBDD) methodologies which have been applied for the elucidation of new molecular entities with high inhibitory activity against targets related with AD. Particular emphasis is given also to the current state of fragment-based ligand approaches as alternatives of the Fragment-Based Drug Discovery (FBDD) methodologies. Finally, several guidelines are offered to show how the use of fragment-based descriptors can be determinant for the design of multi-target inhibitors of proteins associated with AD.

Optical phase conjugation by an As(2)S(3) glass planar waveguide for dispersion-free transmission of WDM-DPSK signals over fiber

We report the first demonstration of optical phase conjugation (OPC) transmission of phase encoded and wavelength-division multiplexed (WDM) signals by the Kerr effect in a planar structured waveguide. The phase conjugated electric field of the signal is produced by four wave mixing pumped by a CW laser during co-propagating with the signal in a highly nonlinear waveguide fabricated in As(2)S(3) glass. Experiments demonstrate the capability of the device to perform dispersion-free transmission through up to 225 km of standard single mode fiber for a 3 × 40 Gb/s WDM signal, with its channels encoded as return-to-zero differential phase shift keying and spaced either 100 or 200 GHz apart. This work represents an important milestone towards demonstrating advanced signal processing of high-speed and broadband optical signals in compact planar waveguides, with the potential for monolithic optical integration.

Simultaneous multi-impairment monitoring of 640 Gb/s signals using photonic chip based RF spectrum analyzer

We report the first demonstration of simultaneous multi-impairment monitoring at ultrahigh bitrates using a THz bandwidth photonic-chip-based radio-frequency (RF) spectrum analyzer. Our approach employs a 7 cm long, highly nonlinear (gamma approximately 9900 /W/km), dispersion engineered chalcogenide planar waveguide to capture the RF spectrum of an ultrafast 640 Gb/s signal, based on cross-phase modulation, from which we numerically retrieve the autocorrelation waveform. The relationship between the retrieved autocorrelation trace and signal impairments is exploited to simultaneously monitor dispersion, in-band optical signal to noise ratio (OSNR) and timing jitter from a single measurement. This novel approach also offers very high OSNR measurement dynamic range (> 30 dB) and is scalable to terabit data rates.

Hepatitis B virus protein preS2 potentially promotes HCC development via its transcriptional activation of hTERT

BACKGROUNDS AND AIMS

Telomerase is significantly reactivated in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC). Our previous studies showed that the transactivation unit of HBV surface (S) gene, preS2, could upregulate human telomerase reverse transcriptase (hTERT) expression and telomerase activity of HepG2 cells. Here, we aim to explore the functions, and the underlying mechanisms, of this preS2-mediated hTERT upregulation during HCC development.

METHODS

An antisense blocking assay was performed on HBV-integrated HepG2.2.15 cells. The expression of hTERT was examined in clinical samples to test the role of the preS2-mediated hTERT upregulation in HCC development in vivo. In order to explore the mechanisms of preS2-mediated hTERT upregulation, co-transfection, reporter assays and electrophoretic mobility shift assays (EMSA) were performed.

RESULTS

Blocking preS2 expression reduced hTERT expression, telomerase activity, cell proliferation and tumorigenicity of HepG2.2.15. A region located between -349 and -329 bp upstream of the transcription initiation site of hTERT was identified as responsible for the preS2-mediated effect. preS2 interacted with the preS2-responsible region (PRR) and activated the hTERT promoter. Importantly, hTERT was also highly expressed in preS2-positive human HCC samples. All these findings strongly suggest that preS2 may promote HCC development via hTERT activation.

CONCLUSIONS

HBV protein preS2 upregulates hTERT via the PRR element in promoting HCC development.

Characterization of picosecond pulse nonlinear propagation in chalcogenide As(2)S(3) fiber

We characterize the nonlinear propagation of picosecond pulses in chalcogenide As(2)S(3) single-mode fiber using a pump-probe technique. The cross-phase modulation (XPM)-induced sideband broadening and stimulated Raman scattering (SRS)-induced sideband amplification are measured in order to map out the Raman gain spectrum of this glass across the C-band. We extract the Raman response function from the Raman gain spectrum and determine the power and polarization dependence of the SRS. In contrast to previous work using As(2)Se(3) fiber, we find that the As(2)S(3) fiber does not suffer from large two-photon absorption (TPA) in the wavelength range of the telecommunications band. We achieved a 20 dB peak Raman gain at a Stokes shift of 350 cm(-1) in a 205 mm length of As(2)S(3) single-mode fiber. The Raman gain coefficient is estimated to be 4.3x10(-12) m/W and the threshold pump peak power is estimated to be 16.2 W for the 205 mm As(2)S(3) fiber. We also demonstrate that we can infer the dispersion of the As(2)S(3) fiber and justify the Raman response function by comparing simulation and experimental results.

Terahertz bandwidth RF spectrum analysis of femtosecond pulses using a chalcogenide chip

We report the first demonstration of the use of an RF spectrum analyser with multi-terahertz bandwidth to measure the properties of femtosecond optical pulses. A low distortion and broad measurement bandwidth of 2.78 THz (nearly two orders of magnitude greater than conventional opto-electronic analyzers) was achieved by using a 6 cm long As(2)S(3) chalcogenide waveguide designed for high Kerr nonlinearity and near zero dispersion. Measurements of pulses as short as 260 fs produced from a soliton-effect compressor reveal features not evident from the pulse's optical spectrum. We also applied an inverse Fourier transform numerically to the captured data to re-construct a time-domain waveform that resembled pulse measurement obtained from intensity autocorrelation.

QSPR analysis of air-to-blood distribution of volatile organic compounds

Quantitative structure property relationship (QSPR) models for the prediction of human blood:air partition coefficient (log K(blood)) of volatile organic compounds (VOCs) has been developed based on the linear heuristic method (HM) and non-linear radial basis function neural networks (RBFNNs). Molecular descriptors that are calculated from the structures alone were used to represent the characteristics of the compounds. HM was used both to pre-select the whole descriptor sets and to build the linear model. RBFNN was performed to obtain more accurate models. Both the linear and the non-linear models can give very satisfactory prediction results: the correlation coefficient R was 0.964 and 0.979, and the root-mean-square (RMS) error was 0.3303 and 0.2542 for the whole data set, respectively. The prediction result of the non-linear model is better than that obtained by the linear model. In addition, this paper provides an effective method for predicting log K(blood) from its structures and gives some insight into the structural features related to the solubility of VOCs in human blood.

High bit rate all-optical signal processing in a fiber photonic wire

We report the first demonstration of high bit rate signal processing by a fiber-based photonic wire. We achieve 160 Gb/s demultiplexing via four wave mixing in a 1.9 microm diameter photonic wire tapered from As(2)S(3) chalcogenide glass single mode fibre, with very low pump power requirements ( < 20 mW average power, 0.45 W peak power), enabled by a very high nonlinearity (gamma approximately 7850 W(-1) km (-1) ) and greatly reduced dispersion.

ZHX2 is a repressor of alpha-fetoprotein expression in human hepatoma cell lines

The zinc-fingers and homeoboxes 2 (ZHX2) protein was shown previously to be involved in postnatal repression of α-fetoprotein (AFP) in mice. More recently, loss of ZHX2 expression was often found in human hepatcellular carcinoma (HCC), where AFP is frequently reactivated. Using HepG2 and HepG2.2.15, which express high AFP levels, we show that ZHX2 overexpression significantly decreases of AFP secretion in a dose dependent manner. Furthermore, using LO2 and SMMC7721 cells, which express low AFP levels, we use siRNA inhibition to show that AFP is de-repressed when ZHX2 levels are reduced. This represents the first direct evidence that ZHX2 represses AFP. Co-transfections of ZHX2 and AFP-luciferase reporter genes demonstrate ZHX2 repression is governed by the AFP promoter and requires intact HNF1 binding sites. These data support the idea that ZHX2 contributes to AFP repression in the liver after birth and may also be involved in AFP reactivation in liver cancer.

Classification of estrogen receptor-β ligands on the basis of their binding affinities using support vector machine and linear discriminant analysis

Classification models of estrogen receptor-beta ligands were proposed using linear and nonlinear models. The data set was divided into active and inactive classes on the basis of their binding affinities. The two-class problem (active, inactive) was firstly explored by linear classifier approach, linear discriminant analysis (LDA). In order to get a more accurate prediction model, the nonlinear novel machine learning technique, support vectors machine (SVM), was subsequently used to investigate. The heuristic method (HM) was used to pre-select the whole descriptor sets. The model containing eight descriptors founded by SVM, showed better predictive ability than LDA. The accuracy in prediction for the training, test and overall data sets are 92.9%, 85.8% and 91.4% for SVM, 83.1%, 76.1% and 81.9% for LDA, respectively. The results indicate that SVM can be used as a powerful modeling tool for QSAR studies.

Prediction of atmospheric degradation data for POPs by gene expression programming

Quantitative structure-activity relationship models for the prediction of the mean and the maximum atmospheric degradation half-life values of persistent organic pollutants were developed based on the linear heuristic method (HM) and non-linear gene expression programming (GEP). Molecular descriptors, calculated from the structures alone, were used to represent the characteristics of the compounds. HM was used both to pre-select the whole descriptor sets and to build the linear model. GEP yielded satisfactory prediction results: the square of the correlation coefficient r(2) was 0.80 and 0.81 for the mean and maximum half-life values of the test set, and the root mean square errors were 0.448 and 0.426, respectively. The results of this work indicate that the GEP is a very promising tool for non-linear approximations.

Tunable enhancement of a soliton spectrum using an acoustic long-period grating

We demonstrate a scheme for tunable shaping of a soliton spectrum. Specifically, we show a local enhancement of 6 dB in the pulse spectrum by propagating the pulse through a fiber containing micro-bends generated by a flexural acoustic wave - an acoustic long-period grating (LPG) - followed by nonlinear propagation through uniform fiber. The location of the enhancement peak can be tuned by external control of the acoustic frequency of the LPG. We discuss the potential application of this scheme to tunable supercontinuum sources.

High nonlinearity glass photonic crystal nanowires

Soft glass photonic crystal fibers (PCFs) have been fabricated for the first time with the stack and draw process. The same SF6-PCFs have been successfully tapered using a brush flame method. The transverse structure of the PCF does not collapse in the tapering process and core dimensions of the fabricated photonic nanowire has been measured to be 400 nm in diameter. Supercontinuum radiation in excess of one octave has been generated in both the untapered and tapered PCF and, in the latter case, pulse energy thresholds of 65 picojoules at a pump wavelength of 1550 nm were observed.

All solid photonic bandgap fiber based on an array of oriented rectangular high index rods

We report the fabrication, characterization and modeling of an all-solid photonic bandgap fiber (PBGF) based on an array of oriented rectangular rods. Observed near-field patterns of cladding modes clearly identify the cut-off rod modes at the bandgap edges. The bend losses in this fiber depend on the bend direction, and can be understood by the directional coupling properties of the different rod modes and the modeled density of cladding states.

Energy exchange between colliding solitons in photonic crystal fibers

Collisions of femtosecond solitons in silica core photonic crystal fibers are investigated experimentally and theoretically. Clear spectral signatures of the significant energy exchange between the interacting pulses are reported. Two primary and competing effects causing energy exchange are interpulse Raman scattering, which is insensitive to the phase difference of the colliding solitons, and the phase sensitive interaction via the Kerr nonlinearity.

Polarization instability of solitons in photonic crystal fibers

We present experimental and numerical results demonstrating the existence of polarization instability of femtosecond solitons in small core photonic crystal fibers. The frequency of the solitons in our setup shifts rapidly with propagation along the dispersion curve due to the Raman effect. This process can cause initially stable solitons to become unstable, or vice versa depending on the parameters.

An improved photonic bandgap fiber based on an array of rings

We describe the modeling, fabrication and characterization of a silica-core photonic bandgap fiber based on a 2-d array of raised-index cladding rings. The use of rings to form the cladding is shown to re-order the cladding modes in such a way as to broaden the photonic band gaps and reduce bend sensitivity. We compare the performance of the ring fiber with that of a similar fiber made using solid rods.

Bend loss in all-solid bandgap fibres

Experimental measurements of all-solid photonic bandgap fibres with an array of high-index rods in a low-index background revealed an unexpected variation of bend loss across different bandgaps. This behaviour was confirmed by calculations of photonic band structure, and explained with reference to the differing field distributions of the modes of the cladding rods. Our understanding was confirmed by further experiments, leading to proposals for the improvement of these fibres.

Hybrid photonic crystal fiber

We present a hybrid photonic crystal fiber in which a guided mode is confined simultaneously by modified total internal reflection from an array of air holes and antiresonant reflection from a line of high-index inclusions. Experimental results demonstrate that this fiber shares properties of both index-guided and photonic bandgap structures.

Photonic bandgap with an index step of one percent

Early work suggested that very large refractive index contrasts would be needed to create photonic bandgaps in two or three dimensionally periodic photonic crystals. It was then shown that in two-dimensionally periodic structures (such as photonic crystal fibres) a non-zero wavevector component in the axial direction permits photonic bandgaps for much smaller index contrasts. Here we experimentally demonstrate a photonic bandgap fibre made from two glasses with a relative index step of only 1%.

All-solid photonic bandgap fiber

We describe the design and fabrication of a photonic bandgap fiber formed with two different glasses. As in a hollow-core fiber, light is guided in a low-index core region because of the antiresonances of the high-index strands in the fiber cladding. The structure described represents an ideal bandgap fiber that exhibits no interface modes and guides over the full width of multiple bandgaps.

Femtosecond soliton pulse delivery at 800nm wavelength in hollow-core photonic bandgap fibers

We describe delivery of femtosecond solitons at 800nm wavelength over five meters of hollow-core photonic bandgap fiber. The output pulses had a length of less than 300fs and an output pulse energy of around 65nJ, and were almost bandwidth limited. Numerical modeling shows that the nonlinear phase shift is determined by both the nonlinearity of air and by the overlap of the guided mode with the glass.

Soliton Self-Frequency Shift Cancellation in Photonic Crystal Fibers

We report the cancellation of the soliton self-frequency shift in a silica-core photonic crystal fiber with a negative dispersion slope. Numerical and experimental results show that stabilization of the soliton wavelength is accompanied by exponential amplification of the red-shifted Cherenkov radiation emitted by the soliton. The spectral recoil from the radiation acts on the soliton to compensate for the Raman frequency shift. This phenomenon may find applications in the development of a family of optical parametric amplifiers.

Properties of a hollow-core photonic bandgap fiber at 850 nm wavelength

We describe a hollow-core photonic bandgap fiber designed for use in the 850 nm wavelength region. The fiber has a minimum attenuation of 180dB/km at 847nm wavelength. The low-loss mode has a quasi- Gaussian intensity profile. The group-velocity dispersion of this mode passes through zero around 830nm, and is anomalous for longer wavelengths. The polarization beat length varies from 4 mm to 13 mm across the band gap. We expect this fiber to be useful for delivery of high-energy ultrashort optical pulses.