A Multiplex Recombinase-Aided qPCR Assay for Highly Sensitive and Rapid Detection of khe, blaKPC -2, and blaNDM -1 Genes in Klebsiella pneumoniae

OBJECTIVE

This study aimed to establish a highly sensitive and rapid single-tube, two-stage, multiplex recombinase-aided qPCR (mRAP) assay to specifically detect the khe, blaKPC-2, and blaNDM-1 genes in Klebsiella pneumoniae.

METHODS

mRAP was carried out in a qPCR instrument within 1 h. The analytical sensitivities of mRAP for khe, blaKPC-2, and blaNDM-1 genes were tested using recombinant plasmids and dilutions of reference strains. A total of 137 clinical isolates and 86 sputum samples were used to validate the clinical performance of mRAP.

RESULTS

mRAP achieved the sensitivities of 10, 8, and 14 copies/reaction for khe, blaKPC-2, and blaNDM-1 genes, respectively, superior to qPCR. The Kappa value of qPCR and mRAP for detecting khe, blaKPC-2, and blaNDM-1 genes was 1, 0.855, and 1, respectively (p < 0.05).

CONCLUSION

mRAP is a rapid and highly sensitive assay for potential clinical identification of khe, blaKPC-2, and blaNDM-1 genes in K. pneumoniae.

[Accumulation Characteristics, Sources, and Health Risks of Soil Lead of Urban Parks in Beijing]

Urban parks have multiple functions such as social culture, economy, and environmental services during urban development. The rapid development of cities and economy may lead to the accumulation of heavy metals in the soil of urban parks, which may threaten human health. A total of 140 soil samples were collected in 32 typical parks in Beijing. The accumulation characteristics of Pb in the soil of urban parks were analyzed using the single-factor pollution and geo-accumulation indices. The sources of Pb pollution in soils were quantitatively analyzed using the stable isotope of Pb, and the health risk was assessed using the probabilistic risk assessment method based on Monte Carlo simulation. The results showed that the geometric mean of Pb in soils of urban parks in Beijing was 38.63 mg·kg-1, which was 1.48 times the background value. However, it did not exceed the risk screening value(GB 36600-2018). The accumulation of soil Pb in urban parks increased with the increase in the proximity between the park and the central urban area and the increase in the establishment time. The soil Pb pollution index of 2 ring, 2-4 ring, and 4-6 ring parks were 0.16, 0.10, and 0.09, which did not reach the pollution level, and the geo-accumulation indices were 0.80, 0.07, and -0.31, respectively. Except for the no-moderate pollution level in ring 2 and ring 2 to ring 4, the other rings did not reach the pollution level. The sources of Pb pollution in urban parks were coal combustion, road dust, and paint, with the contributions of 45.4%, 19.6%, and 13.9%, respectively. The 95% quantiles of hazard index(HI) of soil Pb in the park for different age groups were 1.11E-01, 8.57E-02, 6.39E-02, 1.64E-02, 1.36E-02, 1.26E-02, 1.64E-02, and 1.78E-02, respectively, which indicated that there was no potential non-carcinogenic risk(HI<1). Exposure duration was the most sensitive to non-carcinogenic risks in people aged 0-18 years, and soil Pb concentration was the most sensitive to non-carcinogenic risks in people aged 18-80 years. The increase in body weight often reduced the non-carcinogenic risks. These results can provide theoretical basis for soil environmental risk control in urban parks.

Approaches to reconstruction of inferior vena cava by ex vivo liver resection and autotransplantation in 114 patients with hepatic alveolar echinococcosis

BACKGROUND

Hepatic alveolar echinococcosis (AE) is most commonly found in retrohepatic inferior vena cava (RHIVC). Ex vivo liver resection and autotransplantation (ELRA) can better realize the radical resection of end-stage hepatic AE with severely compromised hepatocaval confluences, and reconstruction of the affected vessels. Currently, there is a scarcity of information regarding RHIVC reconstruction in ELRA.

AIM

To propose reasonable RHICV reconstruction strategies for ex vivo liver resection and autotransplantation.

METHODS

We retrospectively summarized the clinical data of 114 patients diagnosed with hepatic AE who treated by ELRA in our department. A total of 114 patients were divided into three groups according to the different reconstruction methods of RHIVC: Group A with original RHIVC being repaired and reconstructed (n = 64), group B with RHIVC being replaced (n = 43), and group C with RHIVC being resected without reconstruction (n = 7). The clinical data of patients, including the operation time, anhepatic phase, intraoperative blood loss, complications and postoperative hospital stay, were analyzed and the patients were routinely followed up. The normally distributed continuous variables were expressed as means ± SD, whereas the abnormally distributed ones were expressed as median and analyzed by analysis of variance. Survival curve was plotted by the Kaplan-Meier method.

RESULTS

All patients were routinely followed up for a median duration of 52 (range, 12-125) mo. The 30 d mortality rate was 7.0% (8/114) and 7 patients died within 90 d. Among all subjects, the inferior vena cava (IVC)-related complication rates were 17.5% (11/63) in group A and 16.3% (7/43) in group B. IVC stenosis was found in 12 patients (10.5%), whereas thrombus was formed in 6 patients (5.3%). Twenty-two patients had grade III or higher complications, with the complication rates being 17.2%, 16.3%, and 57.1% in the three groups. The average postoperative hospital stay in the three groups was 32.3 ± 19.8, 26.7 ± 18.2, and 51.3 ± 29.4 d (P = 0.03), respectively.

CONCLUSION

ELRA can be considered a safe and feasible option for end-stage hepatic AE patients with RHIVC infiltration. The RHIVC reconstruction methods should be selected appropriately depending on the defect degree of AE lesions in IVC lumen. The RHIVC resection without any reconstruction method should be considered with caution.

Detection of low-load Epstein-Barr virus in blood samples by enriched recombinase aided amplification assay

Epstein-Barr virus (EBV), a common human γ-herpesvirus, infects more than 90% of adults worldwide. The purpose of this study was to establish a novel EBV detection method by combining the recombinase aided amplification (RAA) assay with an initial enrichment step that utilizes magnetic beads coated with a recombinant human mannan-binding lectin (rhMBL, M1 protein). An M1 protein–protein A magnetic bead complex (M1 beads) was prepared and used to achieve separation and enrichment of EBV from blood. After nucleic acid extraction, DNA was amplified by RAA. Using 388 whole blood samples and 1 serum sample, we explored the specificity, sensitivity and applicability of the newly developed detection method and compared it with commercial quantitative real-time polymerase chain reaction (qPCR) following M1 bead enrichment, traditional qPCR and traditional RAA. After enrichment, the positivity rate of EBV was increased from 15.94% to 17.74% by RAA (P < 0.05) and from 7.20% to 15.17% by qPCR (P < 0.05). The viral loads after enrichment were increased by 1.13 to 23.19-fold (P < 0.05). Our data demonstrates that an RAA assay incorporating M1 bead enrichment is a promising tool for detecting low EBV viral loads in blood samples that will facilitate an early response to EBV infection.

The RAA with an enrichment step that utilizes magnetic beads coated with M1 protein.

A very effective method for detecting low-load virus in blood samples.

The first report describing virus detection using this method.

Development of a duplex recombinase-aided amplification assay for direct detection of Mycoplasma pneumoniae and Chlamydia trachomatis in clinical samples

BACKGROUND

Pneumonia caused by Mycoplasma pneumoniae is common in the elderly and children, and pneumonia caused by Chlamydia trachomatis is prevalent in newborns. This study aimed to establish a rapid, sensitive, and simple method for the direct detection of M. pneumoniae and C. trachomatis in clinical samples without DNA extraction.

METHODS

We established a duplex recombinase-aided amplification (RAA) assay with the RNAseP gene as an internal control for detecting the P1 gene of M. pneumoniae and the ORF8 gene of C. trachomatis, respectively. The results were obtained at 39 °C within 15-20 min. A total of 130 clinical samples suspected of M. pneumoniae or C. trachomatis infection were collected and tested by duplex RAA and PCR. DNA extracted via a commercial kit or treated with a nucleic acid-releasing agent was used and compared, respectively. Standard recombinant plasmids were used to test the sensitivity of the duplex RAA assay. In addition, other similar common pathogens were used to verify the specificity of the duplex RAA assay.

RESULTS

The sensitivity of the duplex RAA assay for detecting M. pneumoniae and C. trachomatis was 10 copies/μL using recombinant plasmids. Compared with PCR, the sensitivity and specificity of duplex RAA assays for M. pneumoniae and C. trachomatis was 100% using clinical DNA samples extracted using a commercial kit and a nucleic acid-releasing agent, and the Kappa value was 1.

CONCLUSION

The advantages of this duplex RAA assay include high sensitivity and specificity, short duration, and simple extraction steps, with potential for use in the on-site detection of M. pneumoniae and C. trachomatis in resource-limited settings.

Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus

Vibrio parahaemolyticus (V. parahaemolyticus) is a widely distributed pathogen in the coastal areas, which causes food poisoning and leads to gastroenteritis and sepsis. Therefore, developing a simple, sensitive, and rapid detection method for V. parahaemolyticus is a major concern globally. This study established a sensitive and rapid technique based on recombinase aided amplification (RAA) to detect V. parahaemolyticus. The RAA reaction was carried out successfully at 39 °C within 30 min. The sensitivity of the RAA assay was 10¹ copies/μL using the recombinant plasmid and 10^-3 ng/μL using the V. parahaemolyticus strain. In addition, RAA directly detected 7 × 10³ CFU/mL of simulated fecal samples and 0.1 CFU/mL after enrichment for 4 h. The sensitivity and specificity of the RAA assay using fecal and fish samples were 100% similar to that of the real-time PCR. We conclude that the RAA assay is an ideal screening method for detecting V. parahaemolyticus due to its rapidity, high accuracy, and simplicity in operation.

[Effectiveness of the "14 plus 7 day quarantine" and "nucleic acid plus total antibody testing" strategy for screening imported patients with COVID-19 in Xiamen]

Objective: To analysis effectiveness of the "14 plus 7 day quarantine" and "nucleic acid plus total antibody testing" strategy (combined screening strategy) for screenin the imported patients with COVID-19 in Xiamen. Methods: The study populations were overseas travelers arriving in Xiamen from March 17 to December 31, 2020, and overseas travelers who had quarantine outside Xiamen for less than 21 days from July 18 to December 31, 2020. Data were collected and analyzed on the timing of detection, pathways, and test results of the imported patients with COVID-19 after implementing combined screening strategy. Results: A total of 304 imported patients with COVID-19 were found from 174 628 overseas travelers and 943 overseas travelers from other cities. A total of 163 cases (53.6%) were diagnosed by multitime, multisite intensive nucleic acid testing after positive finding in total antibody testing. Among them, 27 (8.9%) were first positive for nucleic acid in 14 plus 7 day quarantine and 136 were first positive for nucleic acid in 14-day quarantine. Only 8 of these individuals were tested positive for nucleic acid after positive total antibody testing. The other 128 individuals were tested positive for nucleic acid after being negative for average 2.3 times (maximum of 6 times). Aditional 155 cases might be detected by using the combined "14 plus 7 day quarantine" and " nucleic acid plus total antibody testing" strategy compared with "14-day quarantine and nucleic acid testing" strategy, accounting for 51.0% of the total inbound infections. So the combined screening strategy doubled the detection rate for imported patients with COVID-19. No second-generation case caused by overseas travelers had been reported in Xiamen as of February 26, 2021. Conclusions: Xiamen's combined screening strategy can effectively screen the imported patients with COVID-19 who were first positive for nucleic acid after 14 day quarantine. Compared with "14 day quarantine and nucleic acid testing", the combined screening strategy improved detection rate and further reduced the risk of the secondary transmission caused by the imported patients with COVID-19.

[Simultaneous combined radical surgery for hepatic and renal alveolar echinococcosis: an analysis of 10 clinical cases]

Objective: To examine the feasibility, safety and efficacy of simultaneous combined radical surgery for hepatic and renal alveolar echinococcosis (AE). Methods: Clinical dates of consecutive 10 hepatic and renal AE patients who accepted surgical treatment in the First Affiliated Hospital of Xinjiang Medical University during April 2013 to September 2019 were analyzed retrospectively. There were 8 males and 2 females, aged (42.5±10.3) years (range: 27 to 52 years). Seven of them had previously palliative surgical treatment with poor compliance to post-operative medication. All of the patients had hepatic-renal combined AE lesions, and two of them had left lateral and left renal lesions for each, which sized for (726.4±576.1)cm³ (range: 117.0 to 1 998.0 cm³). Extra-hepatic or renal lesions infiltrated to right diaphragm, inferior vena cava, right adrenal gland, abdominal wall, right psoas muscle, duodenum wall and right pulmonary lobe (respectively were 7, 7, 6, 2, 1, 1, 2 cases). Surgery were performed mainly with simultaneous combined surgery and vascular reconstruction techniques for this series. Hemi-hepatectomy or extended right lobectomy was applied in 8 patients, while 2 other patients received ex vivo liver resection and autotransplantation, additionally, one patient had partial hepatectomy for left lateral lobular lesion. Total right nephrectomy, partial right nephrectomy and partial left nephrectomy were respectively performed on 7, 3 and 1 patient(s). Additionally, extra-hepatic or renal lesions were eradicated followed by relevant repairments or reconstructions. Results: Surgeries went well and there was no intra-or post-operative liver or renal dysfunction occurred. During recovery period, 3 cases experienced with hydrothorax and managed well after drainage and supportive treatment, and one patient developed peri-renal urinary leakage and cured by "J" catheter. The subjects were followed-up for 6 to 81 months (median: 21 months), no death, organ dysfunction, chronic or acute kidney diseases occurred. One case encountered with abdominal hernia at post-operative 7^th month and was successfully managed with laparoscopic repair with artificial mesh. No disease recurrence in all patients, which reached clinical cure at last. Conclusion: When complied strictly to indications, simultaneous combined radical surgery could be a feasible, safe and efficient approach for patients with hepatic and renal AE, which is primary or relapsed from previous hepatic AE surgery or interventional therapies as well as neighboring organ AE invasions.

[Exhaustion of CD8+ T cell immune functions in spleen of mice with different doses of Echinococcus multilocularis infections]

OBJECTIVE

To examine the changes in the immune functions of CD8⁺ T cells in the spleen of mice following Echinococcus multilocularis infections at various doses and at different time points.

METHODS

The E. multilocularis protoscoleces were collected, and E. multilocularis infection was modeled in mice via the hepatic portal vein at doses of 50 (low-dose), 500 (medium-dose) and 2 000 protoscoleces (high-dose), while physiological saline served as controls. Mouse spleen was isolated 2 (earlystage), 12 (middle-stage) and 24 weeks post-infection (late-stage), and spleen lymphocytes were harvested. The phenotype of memory CD8⁺ T cells and 2B4 expression were quantified in the mouse spleen, and the secretion of interferon (IFN)-γ, tumor necrosis factor (TNF)-α, interleukin (IL)-17A and IL-10 was measured.

RESULTS

A central-memory phenotype was predominant in the CD8⁺ T cells in the spleen of mice at the early stage of high-dose protoscolece infections, and the proportion of central-memory CD8⁺ T cells was significantly greater in the high-dose group than in the control group (35.50% ± 2.00% vs. 25.90% ± 2.46%, P < 0.01), while a effector- memory phenotype was predominant in the CD8⁺ T cells in the spleen of mice at the late stage of medium- and high-dose protoscolece infections, and the proportions of effector-memory CD8⁺ T cells were significantly greater in the medium- (25.70% ± 4.12%) and high-dose group (28.40% ± 4.12%) than in the control group (10.50% ± 6.45%) (P < 0.05). The proportions of the central-memory CD8⁺ T cells were significantly higher in the high-dose group than at middle and late stages than at the early stage (P < 0.01), and the proportion of effector-memory CD8⁺ T cells was significantly greater in the high-dose group at the late stage than at early and middle stages (P < 0.05). The secretion of IFN-γ and IL-17A by spleen CD8⁺ T cells was elevated in the low- and medium-dose groups at the early stage of infection, and high-dose protoscolece infection promoted the secretion of IFN-γ and TNF-α by spleen CD8⁺ T cells; however, the levels of IFN-γ and TNF-α were significantly lower at the late stage than at the early and middle stages (P < 0.05). In addition, high 2B4 expression was detected in spleen CD8⁺ T cells in the middle- and high-dose groups at the late stage of infection, and the 2B4 expression was significantly higher in the medium(4.73% ± 1.56%) and high-dose groups (4.94% ± 1.90%) than in the low-dose group (2.49% ± 0.58%) and the control group (2.92% ± 0.60%) (P < 0.05).

CONCLUSIONS

E. multilocularis may be killed and eliminated through the host immune responses at the middle and late stages of low- and medium-dose protoscolece infections, while high-dose protoscolece infections may trigger the upregulation of 2B4 expression in mouse spleen CD8⁺ T cells at the late stage, which leads to immune exhaustion and the resultant chronic infections.

A highly sensitive one-tube nested quantitative real-time PCR assay for specific detection of Bordetella pertussis using the LNA technique

OBJECTIVES

Bordetella pertussis is a highly contagious respiratory agent and is the causative pathogen of pertussis, which primarily affects children. Current diagnostic techniques for this pathogen have a variety of limitations including a long culture time, low bacterial load, and lack of specificity.

METHODS

This article reports the development of a one-tube nested quantitative real-time PCR assay using the locked nucleic acid (LNA) technique (LNA-OTN-q-PCR), targeting the BP485 gene and using a simple inexpensive extraction method. A total of 130 clinical samples from patients with clinically suspected pertussis, collected from the Children's Hospital of Hebei, China, were tested by LNA-OTN-q-PCR assay. RT-PCR and two-step semi-nested PCR assays were performed in parallel for comparison.

RESULTS

Only strains of B. pertussis were identified as positive, whereas all of the remaining strains were appropriately identified as negative by the LNA-OTN-q-PCR assay. A single copy per reaction can be detected by the LNA-OTN-q-PCR assay. Additionally, the sensitivity of this method was 100 times that of the RT-PCR assay (100 copies per reaction). Sixty-three of the 130 clinical samples were detected positive by LNA-OTN-q-PCR assay; in contrast, RT-PCR was able to detect only 41 positive samples. Following this, all 63 samples were positively identified by two-step semi-nested PCR. Compared with the two-step semi-nested PCR assay, both the specificity and sensitivity of the LNA-OTN-q-PCR assay using purified DNA and crude extract were 100%.

CONCLUSIONS

This assay was able to detect B. pertussis infection with high sensitivity and specificity. This test shows great potential as a promising technique to detect B. pertussis in both clinical laboratories and public health settings.

Applicability of duplex real time and lateral flow strip reverse-transcription recombinase aided amplification assays for the detection of Enterovirus 71 and Coxsackievirus A16

BACKGROUND

Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are the two main etiological agents of Hand, Foot and Mouth Disease (HFMD). Simple and rapid detection of EV71 and CA16 is critical in resource-limited settings.

METHODS

Duplex real time reverse-transcription recombinase aided amplification (RT-RAA) assays incorporating competitive internal amplification controls (IAC) and visible RT-RAA assays combined with lateral flow strip (LFS) for detection of EV71 and CA16 were developed respectively. Duplex real time RT-RAA assays were performed at 42 °C within 30 min using a portable real-time fluorescence detector, while LFS RT-RAA assays were performed at 42 °C within 30 min in an incubator. Recombinant plasmids containing conserved VP1 genes were used to analyze the sensitivities of these two methods. A total of 445 clinical specimens from patients who were suspected of being infected with HFMD were used to evaluate the performance of the assays.

RESULTS

The limit of detection (LoD) of the duplex real time RT-RAA for EV71 and CA16 was 47 copies and 38 copies per reaction, respectively. The LoD of the LFS RT-RAA for EV71 and CA16 were both 91 copies per reaction. There was no cross reactivity with other enteroviruses. Compared to reverse transcription-quantitative PCR (RT-qPCR), the clinical diagnostic sensitivities of the duplex real time RT-RAA assay were 92.3% for EV71 and 99.0% for CA16, and the clinical diagnostic specificities were 99.7 and 100%, respectively. The clinical diagnostic sensitivities of the LFS RT-RAA assay were 90.1% for EV71 and 94.9% for CA16, and the clinical diagnostic specificities were 99.7 and 100%, respectively.

CONCLUSIONS

The developed duplex real time RT-RAA and LFS RT-RAA assays for detection of EV71 and CA16 are potentially suitable in primary clinical settings.

Dietary mannan oligosaccharide ameliorates cyclic heat stress-induced damages on intestinal oxidative status and barrier integrity of broilers

This study investigated protective effects of mannan oligosaccharide (MOS) inclusion on growth performance, intestinal oxidative status, and barrier integrity of cyclic heat-stressed broilers. A total of 240 one-day-old chicks were allocated into 3 treatments of 10 replicates each. Control broilers reared at a thermoneutral temperature were fed a basal diet, whereas broilers in heat stress and MOS groups raised at a cyclic high temperature (32 to 33°C for 8 h/d) were given the basal diet supplemented with 0 or 250 mg/kg MOS, respectively. Compared with control group, heat stress decreased (P < 0.05) average daily gain and feed conversion ratio during grower, finisher, and entire periods, average daily feed intake during finisher and entire periods, and ileal superoxide dismutase activity at 42 D, whereas increased (P < 0.05) rectal temperature at 21 and 42 D and jejunal malondialdehyde content at 42 D. Dietary MOS increased (P < 0.05) average daily gain, average daily feed intake, and feed conversion ratio during finisher and entire periods, but decreased (P < 0.05) jejunal malondialdehyde concentration of heat-stressed broilers at 42 D. Heat stress decreased (P < 0.05) jejunal villus height (VH) and claudin-3 gene expression at 21 D, and VH and VH: crypt depth (CD) ratio in jejunum and ileum as well as mRNA abundances of jejunal mucin 2 and occludin, and ileal mucin 2, zonula occludens-1, and occludin, and claudin-3 at 42 D, whereas increased (P < 0.05) serum D-lactate acid content at 21 and 42 D, and serum diamine oxidase activity and jejunal CD at 42 D. The MOS supplementation increased (P < 0.05) jejunal VH at 21 D, VH and VH: CD of jejunum and ileum at 42 D, mRNA abundances of jejunal occludin and ileal mucin 2, zonula occludens-1, and occludin at 42 D, whereas reduced (P < 0.05) ileal CD at 42 D. These results suggested that MOS improved growth performance, and oxidative status and barrier integrity in the intestine of broilers under cyclic heat stress.

Termination of a partial hydatidiform mole and coexisting fetus: A case report

BACKGROUND

We describe the treatment strategy for a patient who was found to have a partial hydatidiform mole and coexisting fetus (PHMCF) during the second trimester. The patient was a 38-year-old Chinese woman who had become pregnant following in vitro fertilization and embryo transplantation. We wanted to determine the safest therapeutic strategy to terminate the PHMCF during the second trimester.

CASE SUMMARY

In this case, we present a patient who was found to have a PHMCF complicated with serious continuous vaginal bleeding and pre-eclampsia during the second trimester. After careful evaluation, the pregnancy was considered to be unsustainable and was terminated via caesarean section (CS). An infant with weak vital signs and a partially cystic placenta measuring 110 mm × 95 mm × 35 mm were delivered by CS. The patient was discharged after 4 d. The serum levels of β-human chorionic gonadotropin decreased to within a normal range 5 wk after the operation, and no evidence of persistent trophoblastic disease or lung metastases was noticed at the 6-mo follow-up.

CONCLUSION

CS termination of PHMCF during the second trimester may be a relatively safe therapeutic strategy.

A rapid and sensitive recombinase aided amplification assay incorporating competitive internal control to detect Bordetella pertussis using the DNA obtained by boiling

OBJECTIVES

Pertussis is a highly transmissible acute respiratory infection caused by the bacterial pathogen Bordetella pertussis. The purpose of this study was to develop a rapid, simple and sensitive diagnostic test for detecting this pathogen.

METHODS

Here we present a recombinase aided amplification (RAA) assay incorporating competitive internal amplification control (IAC) to detect Bordetella pertussis using the DNA obtained by boiling. This assay was performed in a single closed tube at 39°C within 30min. A total of 115 clinical samples suspected of pertussis were collected and tested by the internally controlled RAA assay using both extracted DNA with the commercial kit and the DNA obtained by boiling. For comparison, the real-time PCR (RT-PCR) was also performed with DNA extraction in parallel.

RESULTS

The sensitivity of the internally controlled RAA assay was 10¹ copies or 10CFU/ml per reaction in detecting plasmid DNA or B. pertussis strain. The optimum concentration of the IAC plasmid was determined to be 100 copies, and the introduction of IAC effectively reduced the occurrence of false negatives. Compared to the RT-PCR, RAA results with DNA extraction obtained 100% sensitivity and specificity, and the RAA results with heat-treated DNA showed 85.96% sensitivity and 100% specificity.

CONCLUSION

With the advantages of 45min turn-around time and simple steps of DNA purification, this assay could become a useful diagnostic tool for Bordetella pertussis detection and is potentially suitable for point-of-care identification to guide prompt clinical treatment.

A multiplex one-tube nested real time RT-PCR assay for simultaneous detection of respiratory syncytial virus, human rhinovirus and human metapneumovirus

BACKGROUND

Respiratory syncytial virus (RSV), human Rhinovirus (HRV) and human Metapneumo Virus (HMPV) are important viral pathogens causing acute respiratory tract infections in the hospitalized patients. Sensitive and accurate detection of RSV, HRV and HMPV is necessary for clinical diagnosis and treatment.

RESULTS

A locked nucleic acid (LNA)-based multiplex closed one-tube nested real-time RT-PCR (mOTNRT-PCR) assay was developed for simultaneous detection of RSV, HRV and HMPV. The sensitivity, specificity, reproducibility and clinical performance of mOTNRT-PCR were evaluated and compared with individual real time PCR (RT-qPCR) assay using clinical samples. The analytical sensitivity of mOTNRT-PCR assay was 5 copies/reaction for RSV, HRV and HMPV, respectively, and no cross-reaction with other common respiratory viruses was observed. The coefficients of variation (CV) of intra-assay and inter-assay were between 0.51 to 3.67%. Of 398 nasopharyngeal aspirates samples tested, 109 (27.39%), 150 (37.69%) and 44 (11.06%) were positive for RSV, HRV and HMPV, respectively, whereas 95 (23.87%), 137 (34.42%) and 38 (9.55%) were positive for RSV, HRV and HMPV, respectively, by individual RT-qPCR assay. Thirty three samples that were positive by mOTNRT-PCR but negative by RT-qPCR were confirmed as true positives by sequencing using reported traditional two-step nested PCR assay.

CONCLUSION

mOTNRT-PCR assay reveals extremely higher sensitivity than that of RT-qPCR assay for detecting RSV, HRV and HMPV in clinical settings.

Selective interface transparency in graphene nanoribbon based molecular junctions

A clear understanding of electrode-molecule interfaces is a prerequisite for the rational engineering of future generations of nanodevices that will rely on single-molecule coupling between components. With a model system, we reveal a peculiar dependence on interfaces in all graphene nanoribbon-based carbon molecular junctions. The effect can be classified into two types depending on the intrinsic feature of the embedded core graphene nanoflake (GNF). For metallic GNFs with |N_A - N_B| = 1, good/poor contact transparency occurs when the core device aligns with the center/edge of the electrode. The situation is reversed when a semiconducting GNF is the device, where N_A = N_B. These results may shed light on the design of real connecting components in graphene-based nanocircuits.

Improved experimental model of hepatic cystic hydatid disease resembling natural infection route with stable growing dynamics and immune reaction

AIM

To investigate a safer way to set up the disease model of cystic echinococcosis without contamination risk and develop a novel experimental murine model of hepatic cystic echinococcosis.

METHODS

C57B/6 mice were injected with human protoscolices of three different concentrations via the portal vein. The mice were followed for 10 mo by ultrasound, gross anatomy, and pathological and immunological examinations. The protoscolex migration in the portal vein, hydatid cyst growth, host immune reaction, and hepatic histopathology were examined periodically.

RESULTS

The infection rates in the mice in the high, medium, and low concentration groups were 90%, 100%, and 63.6%, respectively. The protoscolices migrated in the portal vein with blood flow, settled in the liver, and developed into orthotopic hepatic hydatid cysts, resembling the natural infection route and course.

CONCLUSION

We have established an improved experimental model of hepatic cystic echinococcosis with low biohazard risk but stable growing dynamics and immune reaction. It is especially useful for new anti-parasite medication trials against hydatid disease.

Bevacizumab and gefitinib enhanced whole-brain radiation therapy for brain metastases due to non-small-cell lung cancer

Non-small-cell lung cancer (NSCLC) patients who experience brain metastases are usually associated with poor prognostic outcomes. This retrospective study proposed to assess whether bevacizumab or gefitinib can be used to improve the effectiveness of whole brain radiotherapy (WBRT) in managing patients with brain metastases. A total of 218 NSCLC patients with multiple brain metastases were retrospectively included in this study and were randomly allocated to bevacizumab-gefitinib-WBRT group (n=76), gefitinib-WBRT group (n=77) and WBRT group (n=75). Then, tumor responses were evaluated every 2 months based on Response Evaluation Criteria in Solid Tumors version 1.0. Karnofsky performance status and neurologic examination were documented every 6 months after the treatment. Compared to the standard WBRT, bevacizumab and gefitinib could significantly enhance response rate (RR) and disease control rate (DCR) of WBRT (P<0.001). At the same time, RR and DCR of patients who received bevacizumab-gefitinib-WBRT were higher than those who received gefitinib-WBRT. The overall survival (OS) rates and progression-free survival (PFS) rates also differed significantly among the bevacizumab-gefitinib-WBRT (48.6 and 29.8%), gefitinib-WBRT (36.7 and 29.6%) and WBRT (9.8 and 14.6%) groups (P<0.05). Although bevacizumab-gefitinib-WBRT was slightly more toxic than gefitinib-WBRT, the toxicity was tolerable. As suggested by prolonged PFS and OS status, bevacizumab substantially improved the overall efficacy of WBRT in the management of patients with NSCLC.

[The clinical practice of improvement the "Volume and Quality" of functional liver in autologous liver transplantation for the patients with alveolar echinococcosis]

Objective: To investigate the clinical significance of accurate assessment of "volume and quality" of functional liver in Autologous liver transplantation (ALT) in the treatment of the advanced hepatic alveolar echinococcosis (HAE). Methods: The clinical data of 12 patients with advanced HAE who underwent ALT at the First Affiliated Hospital of Xinjiang Medical University from May 2015 to July 2016 were retrospectively analyzed. Results: The preoperative hepatic functions of 12 patients were 8 Child-Pugh Grade A, 1 Grade B, and 3 Grade C. Three of the patients had moderate or severe jaundice. Three of the patients calculated functional liver graft volume (GV) and standard liver volume (SLV) ratio (GV/SLV) were <30%. After the protection of liver function, anti-infection, percutaneous transhepatic cholangiography drainage (PTCD), selective portal vein embolization (PVE), and staging liver resection, liver function Child-Pugh grade of 11 patients was raised to A grade, and the other patient was B grade, meanwhile the bilirubin was reduced to 2 times the normal value. The GV/SLV ratios of 3 patients with low GV/SLV ratio had reached 44.4%, 47.2% and 56.2% respectively. In this study, the GV/SLV ratios of the 12 patients were between 73.2% and 40.8% with an average of 55.6%. Operation time was 11.5-20.5 h, with an average of 12.3 h. Anhepatic phase time was 193-375 min with median 253.5 min. The red blood cell suspension was 0-6 U during the operation. The average hospitalization was 10-42 d, with the average 22.7 d. Total hospital costs were 121 600-434 800 Yuan, with the median cost of 174 400 Yuan. One patient died of septic shock a week after surgery. Conclusion: (1)ALT may provide feasibility for the advanced HAE. (2)Accurate assessment of functional liver "volume and quality" appeared as the key points to the ALT. (3)Precise surgery and individualized treatment could improve and protect the functional liver "volume and quality" .

[The causes and adjustment methods of prenatal anxiety disorder during the Han and Tang Dynasties]

Though the title of prenatal anxiety disorder didn't mentioned in the literature of the Han and Tang Dynasties, the effect of anxiety on the fetus and its delivery were already recognized. The causes of anxiety were mainly the physical discomfort caused by pregnancy, or the worries about fetus sex, health, appearance, and its fate etc., or the fear of delivery. Although the adjustment methods were often tainted with superstition, yet it could ease the anxiety of pregnant women to some extent.

Chloroplast analysis of Zelkova schneideriana (Ulmaceae): genetic diversity, population structure, and conservation implications

Zelkova schneideriana is endemic to China and belongs to the Ulmaceae. It is listed as a Near Threatened species in the China Biodiversity Red Data Book. We conducted a phylogeographical study of two chloroplast regions (psbA-trnH and trnG-trnM) in several Chinese Z. schneideriana populations, in order to examine the genetic diversity, population structure, and evolutionary history of the species. In all, 10 haplotypes were detected. The population from Sangzhi, Hunan, had the highest nucleotide diversity (π = 0.00653) and haplotype diversity (HD = 1.000), and should be considered the most suitable population to be protected under an in situ conservation strategy. Seed collections from as many individuals as possible in other populations would preserve the genetic diversity of Z. schneideriana.

Tailoring the transmission lineshape spectrum of zigzag graphene nanoribbon based heterojunctions via controlling their width and edge protrusions

We report a first-principles analysis of electron transport through narrow zigzag graphene nanoribbon (up to 2.2 nm) based wedge-shaped heterojunctions. We show that the width difference between the electrode and the scattering region and the edge protrusion of heterojunctions can be tuned to endow the system's transmission spectrum with distinctive features. In particular, transport through junctions with a one sided protrusion in the scattering region is always dominated by a Breit-Wigner-type resonance right at the Fermi level, regardless of the large or small width difference. On the other hand, a junction with protrusions on both sides of the scattering region shows insulating behaviour near the Fermi level for a large width difference but weak transmission channels are formed at the core of the scattering region for a small width difference. When the protrusion is absent in the junction, transmission functions display rather complex structures: double peaks situating nearly symmetrically away from the Fermi level and a strongly asymmetric profile in the vicinity of the Fermi level are observed for large and small width differences, respectively. These results may shed light on the design of real connecting components in nanocircuits.

Isolation and characterization of polymorphic microsatellite loci from Zelkova schneideriana Hand.-Mazz

Zelkova schneideriana is a highly valued hardwood species. An improved technique for isolating codominant compound microsatellite markers was used to develop simple sequence repeat markers for Z. schneideriana. A total of 12 microsatellite loci were identified. Overall, the number of alleles per locus ranged from 8-19, with an average of 11.75. Observed heterozygosity and expected heterozygosity values ranged from 0.109-0.709 and 0.832-0.929, respectively. Polymorphic information content is from 0.803-0.915, with an average of 0.854. These markers will be very important for future research related to the genetic diversity, population structure, patterns of gene flow, and mating system of this species.

Oxygen vacancy diffusion in bare ZnO nanowires

Oxygen vacancies (VO) are known to be common native defects in zinc oxide (ZnO) and to play important roles in many applications. Based on density functional theory, we present a study for the migration of oxygen vacancies in ultra-thin ZnO nanowires (NWs). We find that under equilibrium growth conditions VO has a higher formation energy (Ef) inside the wire than that at shallow sites and surface sites, with different geometric relaxations and structural reconstructions. The migration of VO has lower barriers in the NW than in the bulk and is found to be energetically favorable in the direction from the bulk to the surface. These results imply a higher concentration of VO at surface sites and also a relative ease of diffusion in the NW structure. Our results support the previous experimental observations and are important for the development of ZnO-based devices in photocatalysis and optoelectronics.

Superposed pulse amplitude modulation for visible light communication

We propose and experimentally demonstrate a novel modulation scheme called superposed pulse amplitude modulation (SPAM) which is low-cost, insensitive to non-linearity of light emitting diode (LED). Multiple optical pulses transmit parallelly from different spatial position in the LED array and overlap linearly in free space to realize SPAM. With LED arrangement, the experimental results show that using the modulation we proposed the data rate of 120 Mbit/s with BER 1 × 10(-3) can be achieved with an optical blue filter and RC post-equalization.

[Ecological risk assessment of bisphenol A in Chinese freshwaters]

Bisphenol A (BPA) has many toxic effects on aquatic organisms, of which the most obvious effect is the estrogenic effect. The data collected in the study were divided into two parts, based on the response of the tested organisms to the estrogenic effects of BPA and their exposed time, and the risk of BPA to Chinese aquatic water was assessed by using quotient method, quotient exponent and probability method, safety threshold value method and joint probability risk assessment, respectively. Similar results were derived from the above four methods. Aquatic organisms were more sensitive to the estrogenic effects of BPA than other toxic effects. The results of risk assessment from safety threshold value method were more accurate and confident than the other three methods. Using the chronic data of BPA's estrogenic effect on tested organisms as the endpoint for risk assessment in safety threshold value method, it was found that in 64.70% of the Chinese freshwaters more than 5% of aquatic organisms were affected by the estrogenic toxicity of BPA, and the maximum allowable concentration of BPA was 15.72 ng x L(-1). Using the acute data of such effects as endpoint in safety threshold value method, in about 20.43% volume of the Chinese freshwaters more than 5% of aquatic organisms were affected by the estrogenic toxicity of BPA, and the maximum allowable concentration was 2.24 x 10(2) ng x L(-1).

Rhizoctonia solani Identified as the Disease Causing Agent of Peanut Leaf Rot in China

Peanut (Arachis hypogaea L.) is one of the most economically important oil crops in the world. Since the 1990s, the peanut industry has developed rapidly in China. However, because of the use of high-yield varieties and increased plant density, a peanut leaf rot disease occurred in Laixi Experimental Fields in Shandong Province, China in 2007. Leaves had nearly circular, brown lesions that enlarged quickly developing yellow-brown halos at the edges of the lesions. High relative humidity under field conditions led to complete necrosis of the leaves with cotton wool-like mycelia observed followed by the development of sclerotia on the leaf surface. Symptomatic plants were observed between 2007 and 2010, and symptomatic leaf tissue was collected from the Laixi Experimental Fields. An isolate (designated YF-1) from symptomatic peanut leaves was isolated and purified on potato dextrose agar (PDA) and water agar (WA) medium. On PDA, the colony appeared initially as colorless and grew to the diameter of a 9-cm petri dish within 3 days. As the mycelium aged, the colony color gradually became light brown, and sclerotia developed on the surface of the colony. YF-1 was identified as Rhizoctonia solani Kühn based on the number of nuclei per cell ranging from 4 to 13 (average 6.1), hyphal diameter being 7.5 to 12.9 μm (average 8.3 μm), branching at right angles, a septum was present near each hyphal branch with a slight constriction, and no clamp connection structures or conidia were ever observed (4). To further confirm the identity of isolate YF-1, genomic DNA was extracted using the DNeasy Plant Mini DNA Extraction Kit (Shanghai Leifeng Biotechnol. Co., Ltd.), and the complete internal transcribed spacer (ITS) region of ribosomal DNA was amplified and sequenced with a pair of primers ITS1/ITS4 (2). A GenBank BLAST search produced an exact match for the sequences of R. solani (AY154301), with 100% sequence similarity. To estimate the mode of anastomosis, YF-1 was paired on WA medium with each reference strain belonging to anastomosis groups (AGs) 1 through 8 (provided by Shandong Agriculture University) (1,3). The results indicated that YF-1 belonged to group AG-1, subgroup AG-1-IA of R. solani. Pathogenicity tests were conducted by inoculating 10 peanut leaves using a colonized paper disc method (filter paper 1 cm in diameter suspended in the mycelia suspension). Ten control leaves received paper discs without mycelium. Inoculated and non-inoculated plants were kept in humid chambers for 24 h at 25°C. Three days after inoculation, the leaves developed typical brown lesions that were similar to those of naturally diseased plants. Koch's postulates were fulfilled by reisolation of R. solani from symptomatic leaves. No symptoms were observed on control leaves. To our knowledge, this is the first report of peanut leaf rot caused by R. solani. Occurrence of the disease in China is a new threat to the health of peanut. References: (1) Y. X. Chen et al. Acta Phytopathol. Sin. 3:139, 1985. (2) T. Misawa and S. Kuninaga. J. Gen. Plant Pathol. 76:310, 2010. (3) A. Ogoshi. Ann. Phytopathol. Soc. Jpn. 38:117, 1972. (4) J. R. Jr. Pameter and H. S. Whitmey. UC Press. 135, 1970.

[Uncertainty characterization approaches for ecological risk assessment of polycyclic aromatic hydrocarbon in Taihu Lake]

Probabilistic approaches, such as Monte Carlo Sampling (MCS) and Latin Hypercube Sampling (LHS), and non-probabilistic approaches, such as interval analysis, fuzzy set theory and variance propagation, were used to characterize uncertainties associated with risk assessment of sigma PAH8 in surface water of Taihu Lake. The results from MCS and LHS were represented by probability distributions of hazard quotients of sigma PAH8 in surface waters of Taihu Lake. The probabilistic distribution of hazard quotient were obtained from the results of MCS and LHS based on probabilistic theory, which indicated that the confidence intervals of hazard quotient at 90% confidence level were in the range of 0.000 18-0.89 and 0.000 17-0.92, with the mean of 0.37 and 0.35, respectively. In addition, the probabilities that the hazard quotients from MCS and LHS exceed the threshold of 1 were 9.71% and 9.68%, respectively. The sensitivity analysis suggested the toxicity data contributed the most to the resulting distribution of quotients. The hazard quotient of sigma PAH8 to aquatic organisms ranged from 0.000 17 to 0.99 using interval analysis. The confidence interval was (0.001 5, 0.016 3) at the 90% confidence level calculated using fuzzy set theory, and the confidence interval was (0.000 16, 0.88) at the 90% confidence level based on the variance propagation. These results indicated that the ecological risk of sigma PAH8 to aquatic organisms were low. Each method has its own set of advantages and limitations, which was based on different theory; therefore, the appropriate method should be selected on a case-by-case to quantify the effects of uncertainties on the ecological risk assessment. Approach based on the probabilistic theory was selected as the most appropriate method to assess the risk of sigma PAH8 in surface water of Taihu Lake, which provided an important scientific foundation of risk management and control for organic pollutants in water.

Enhanced removal of chemical oxygen demand, nitrogen and phosphorus using the ameliorative anoxic/anaerobic/oxic process and micro-electrolysis

Synthetic wastewater was treated using a novel system integrating the reversed anoxic/anaerobic/oxic (RAAO) process, a micro-electrolysis (ME) bed and complex biological media. The system showed superior chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) removal rates. Performance of the system was optimised by considering the influences of three major controlling factors, namely, hydraulic retention time (HRT), organic loading rate (OLR) and mixed liquor recirculation (MLR). TP removal efficiencies were 69, 87, 87 and 83% under the HRTs of 4, 8, 12 and 16 h. In contrast, HRT had negligible effects on the COD and TN removal efficiencies. COD, TN and TP removal efficiencies from synthetic wastewater were 95, 63 and 87%, respectively, at an OLR of 1.9 g/(L·d). The concentrations of COD, TN and TP in the effluent were less than 50, 15 and 1 mg/L, respectively, at the controlled MLR range of 75-100%. In this system, organics, TN and TP were primarily removed from anoxic tank regardless of the operational conditions.

Molecule-substrate interaction channels of metal-phthalocyanines on graphene on Ni(111) surface

Molecule-substrate interaction channels of metal-phthalocyanines (MPcs, including NiPc, CuPc, ZnPc, FePc, and CoPc) on graphene on Ni(111) were investigated by employing high-resolution electron energy loss spectroscopy (HREELS). Except the expected IR-active modes, some Raman-active modes were also observed in all of MPcs, which are considered in this study. From the origination of the Raman-active features, it was deduced that MPcs are coupled with the substrate mainly through their central metal atom. The Raman-active modes appear as symmetric peaks in the HREELS in the case of MPcs with Ni, Cu, and Zn, whereas they are asymmetric and appear as a Fano line shape in the case of MPcs with Fe and Co. This spectroscopic difference indicates that the molecule-substrate coupling is completely different in the two cases mentioned above. The molecule-substrate interaction strength is considerably weak and comparable with the π-π interaction between molecules in the case of MPcs with Ni, Cu, and Zn, whereas it is much stronger in the case of MPcs with Fe and Co. From the HREELS observations, it can be suggested that the whole molecule can be effectively decoupled from the underneath Ni(111) by inserting a single layer of graphene between them in the case of MPcs with Ni, Cu, and Zn, whereas only benzene rings can be completely decoupled in the case of MPcs with Fe and Co.

Electron Transport Suppression from Tip-π State Interaction on Si(100)-2 × 1 Surfaces

We investigate the electron transport between a scanning tunneling microscope tip and Si(100)-2 × 1 surfaces with four distinct configurations by performing calculations using density functional theory and the nonequilibrium Green's function method. Interestingly, we find that the conducting mechanism is altered when the tip-surface distance varies from large to small. At a distance larger than the critical value of 4.06 Å, the conductance is increased with a reduction in distance owing to the π state arising from the silicon dimers immediately under the tip; this in turn plays a key role in facilitating a large transmission probability. In contrast, when the tip is closer to the substrate, the conductance is substantially decreased because the π state is suppressed by the interaction with the tip, and its contribution in the tunneling channels is considerably reduced.

Tunable electrical properties of silicon nanowires via surface-ambient chemistry

p-Type surface conductivity is a uniquely important property of hydrogen-terminated diamond surfaces. In this work, we report similar surface-dominated electrical properties in silicon nanowires (SiNWs). Significantly, we demonstrate tunable and reversible transition of p(+)-p-i-n-n(+) conductance in nominally intrinsic SiNWs via changing surface conditions, in sharp contrast to the only p-type conduction observed on diamond surfaces. On the basis of Si band energies and the electrochemical potentials of the ambient (pH value)-determined adsorbed aqueous layer, we propose an electron-transfer-dominated surface doping model, which can satisfactorily explain both diamond and silicon surface conductivity. The totality of our observations suggests that nanomaterials can be described as a core-shell structure due to their large surface-to-volume ratio. Consequently, controlling the surface or shell in the core-shell model represents a universal way to tune the properties of nanostructures, such as via surface-transfer doping, and is crucial for the development of nanostructure-based devices.

Effects of exogenous spermidine on subcellular distribution and chemical forms of cadmium in Typha latifolia L. under cadmium stress

The effects of foliar spraying with spermidine (Spd) on the subcellular distribution and chemical speciation of Cd in Typha latifolia L. in hydroponic system were investigated. Increased Cd concentration in the medium caused an increase of Cd concentration in all tissues and all subcellular fractions, with the highest Cd level occurring in roots, followed by rhizomes and leaves and the greatest accumulation was in cell walls, soluble fraction and organelle containing fractions ranked next, respectively. The greatest amount of Cd was found in the extraction of 1 mol.L(-1) NaCl, followed by 2% HAC, deionized water, 80% ethanol, residues and the least in 0.6 mol.L(-1) HCl. The subcellular distribution and different chemical forms of Cd both decreased after Spd application and were more inhibited by 0.25 than 0.50 mmol.L(-1) Spd, especially in roots at 0.10 mmol.L(-1) Cd treatment. It could be suggested that the retention of Cd in roots, cell walls binding with metal, metal ion compartmentation in vacuoles and Cd forms existing in undissolved and integrated with pectates and protein play an important role in Cd detoxification and Spd could enhance the tolerance of cattail to Cd stress.

Unique electronic band structures of hydrogen-terminated [Formula: see text] silicon nanowires

Band structure mutation from an indirect to a direct gap is a well-known character of small hydrogen-terminated [Formula: see text] and [Formula: see text] silicon nanowires (SiNWs), and suggests the possible emission of silicon. In contrast, we show that hydrogen-terminated [Formula: see text] SiNWs consistently present indirect band gaps even at an extremely small size, according to our calculations using density functional theory. Interestingly, the band gap of [Formula: see text] SiNWs shows a quasi-direct feature as the wire size increases, suggesting the possibility of using medium SiNWs in optoelectronic devices. This result also indicates that the electronic structures of SiNWs are strongly orientation dependent.

Signature of nanodiamond in Raman spectra: a density functional theoretical study

Nanocrystalline diamond (NCD) has attracted great attention both experimentally and theoretically in the past few years. The identification of the presence and the amount of NCD in amorphous carbon film has been a challenging issue. Although Raman spectroscopy has become a standard tool for the characterization of various carbon phases, a simple criterion for identifying NCD has not yet been well-established. In the present work, a theoretical study of the Raman spectra of the model compounds of NCD is presented on the basis of the density functional calculations. The reliability of the computational approach has been tested by comparing the predicated Raman spectra of several reference molecules to those obtained experimentally. To show the unique Raman spectrum of a NCD phase, a series of the model compounds of various carbon materials including tetrahedral and hexagonal clusters, and trans-polyacetylene fragments, were considered, and subsequently their Raman spectra below 2000 cm(-1) were calculated and compared with each other. The calculated results indicate that the relatively stronger broad peak at about 480 cm(-1) could be used as the signature of a NCD phase in the sample.

Possible Gas-Phase Reactions of H2/CH4/Tetramethylsilane in Diamond/β-SiC Nanocomposite Film Deposition: An Ab-Initio Study

The Si-C bond breakings in tetramethylsilane (TMS) when interacting with H/H2 and the successive H abstractions from SiH4/CH4 in the gas mixture of H2/ CH4/TMS were studied at the CCSD(T)/6-311+G**//MP2/6-31+G** level of theory. Their rate constants between 1500 and 2500 K were estimated using a conventional transition state theory. The results indicate that (i) it is mainly the H radical that causes the Si-C bond breaking in TMS, and (ii) the successive H abstractions from SiH4 are much easier and faster than those from CH4. At low temperatures the differences of rate constants among the four types of the reactions are large, but generally reduced at high temperatures. The reaction rates show no selectivity over the pressure as verified at P = 0.00025, 0.025, 1, and 100 atm, respectively. Our results could provide the following microscopic level understanding of reactions in the synthesis of diamond/beta-SiC nanocomposite films. Although the Si content is smaller than that of C in the precursor gases, the gas mixture activated by microwave plasma technique could provide Si sources with a higher rate. The produced Si sources with excellent rigidity in sp3 hybridization competitively occupy the space on the substrate together with C sources, resulting in the deposition of diamond/beta-SiC nanocomposite films.

Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory

We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.

Density functional theory study of geometrical structures and electronic properties of silica nanowires

Silica nanowires are expected to possess structural diversity like bulk silica. We modeled three silica nanowires based on the side-shared two-membered rings, spiro-united two-membered rings, and three-membered rings, respectively. By performing density functional theory calculations, we studied their geometrical structures and electronic properties with and without the presence of external electric field. It is found that the stability of silica nanowires increases with length and diameter. As indicated by calculated large HOMO-LUMO gaps, silica nanowires are expected to be good insulating materials. The energy gaps, however, gradually decrease with applied electronic field and finally close, resulting in the breakdown of the insulating nanowires. Moreover, it is shown that the breakdown threshold remarkably increases with the nanowire diameter. These significant findings from the present calculations for the simplest silica nanowires will provide relevant insight into the structures and properties of much more complicated real silica nanowires.

Dimensionality Dependence of Optical Properties and Quantum Confinement Effects of Hydrogenated Silicon Nanostructures

The excited state properties of linear, planar, and spherical hydrogenated silicon nanostructures are studied systematically with use of a time-dependent Hartree-Fock (TDHF) approach with a semiempirical Hamiltonian. The calculated optical gaps decrease significantly from linear, planar, to spherical silicon structures, showing that the optical gap is dimensionality dependent and hence it can be varied by solely managing the shape of the nanostructures. Remarkably, the calculated exciton sizes of the lowest dipole-allowed excited states for both silicon chains and planes are approximately 26 A, revealing that the quantum confinement effect should be significantly enhanced when the sizes of silicon nanostructures are smaller than this value but not dependent on the dimensionality. A similar trend is also observed for hydrogenated silicon spherical clusters.

Geometric and Excited-State Properties of 1,4-Bis(benzothiazolylvinyl)benzene Interacting with 2,2‘,2‘ ‘-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] Studied by a Density-Functional Tight-Binding Method

The energetics and luminescent property of a guest molecule, 1,4-bis(benzothiazolylvinyl)benzene (BT), interacting with a host molecule, 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] (TPBI), in organic light-emitting diodes are studied by performing excited-state calculations using a time-dependent density-functional tight-binding method complemented with dispersion energy. It is found that the overlap between the TPBI emission and the BT absorption spectra shows an efficient energy transfer from the host molecule to the guest molecule when they are excited. The planar BT molecule becomes distorted when it is mixed with TPBI, resulting in a blue luminescence around 475 nm. The separation of the TPBI + BT mixture on a graphite surface is found to be energetically favorable, consistent with experimental observation.