Direct detection and prediction of all pneumococcal serogroups by target enrichment-based next-generation sequencing.

Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichment-based next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of Streptococcus pneumoniae, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci.

Selective equal-spin Andreev reflections induced by Majorana fermions.

In this work, we find that Majorana fermions induce selective equal spin Andreev reflections (SESARs), in which incoming electrons with certain spin polarization in the lead are reflected as counterpropagating holes with the same spin. The spin polarization direction of the electrons of this Andreev reflected channel is selected by the Majorana fermions. Moreover, electrons with opposite spin polarization are always reflected as electrons with unchanged spin. As a result, the charge current in the lead is spin polarized. Therefore, a topological superconductor which supports Majorana fermions can be used as a novel device to create fully spin-polarized currents in paramagnetic leads. We point out that SESARs can also be used to detect Majorana fermions in topological superconductors.

Evaluation of the LightCycler methicillin-resistant Staphylococcus aureus (MRSA) advanced test for detection of MRSA nasal colonization.

Rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization is crucial for the prevention and control of MRSA infections in health care settings. The LightCycler MRSA Advanced Test (Roche Diagnostics) is a commercially available real-time PCR assay for direct detection of MRSA nasal colonization by targeting of the staphylococcal cassette chromosome mec (SCCmec)-orfX junction. The diagnostic performance of the assay was compared with that of ChromID MRSA agar (bioMérieux) culture and an in-house duplex real-time PCR assay. Among 1,246 nasal swab specimens collected from 2 general hospitals in Hong Kong, 174 (14%) were considered true positive for MRSA. Chromogenic culture and the in-house real-time PCR assay identified 147 (84.5%) and 133 (76.4%) true-positive cases with specificities of 100% and 98.6%, respectively. Based on the target melting temperature (Tm) values (57.0 to 62.0 °C) defined by the manufacturer, the LightCycler MRSA Advanced Test identified only 85 (48.9%) true-positive specimens. Interestingly, an additional 60 (34.5%) true-positive specimens were detected despite atypical Tm values of 55 °C, providing overall sensitivity and specificity values of 83.3% and 99%, respectively. Among isolates with Tm values of 55 °C, most were typed as clonal complex 45 (CC45). By sequence analysis of the SCCmec-orfX junction, characteristic single-nucleotide polymorphisms (SNPs) were identified only in isolates with Tm values of 55°C and not in those with typical Tm values. It is conceivable that those SNPs were located inside the target region of the proprietary hybridization probes, which resulted in a Tm shift in the melting curve analysis. Our study highlights the importance of a global evaluation of commercial kits so that the interpretation algorithm covers different lineages of MRSA clones prevalent in various geographical regions.

Simultaneous quantum dash-well emission in a chirped dash-in-well superluminescent diode with spectral bandwidth >700 nm.

We report on the quantitative evidence of simultaneous amplified spontaneous emission from the AlGaInAs/InAs/InP-based quantum-well (Qwell) and quantum-dashes (Qdash) in a multistack dash-in-an-asymmetric-well superluminescent diode heterostructure. As a result, an emission bandwidth (full width at half-maximum) of >700 nm is achieved, covering entire O-E-S-C-L-U communication bands, and a maximum continuous wave output power of 1.3 mW, from this device structure. This demonstration paves a way to bridge entire telecommunication bands through proper optimization of device gain region, bringing significant advances and impact to a variety of cross-disciplinary field applications.

Detecting topological phases in cold atoms.

Chern insulators are band insulators which exhibit a gap in the bulk and gapless excitations in the edge. Detection of Chern insulators is a serious challenge in cold atoms since the Hall transport measurements are technically unrealistic for neutral atoms. By establishing a natural correspondence between the time-reversal invariant topological insulator and the quantum anomalous Hall system, we show for a class of Chern insulators that the topology can be determined by only measuring Bloch eigenstates at highly symmetric points of the Brillouin zone. Furthermore, we introduce two experimental schemes, including the spin-resolved Bloch oscillation, to carry out the measurement. These schemes are highly feasible under realistic experimental conditions. Our results may provide a powerful tool to detect topological phases in cold atoms.

Hong Kong experiences the 'Ultimate superbug': NDM-1 Enterobacteriaceae.

We report the second imported case of New Delhi metallo-beta-lactamase (NDM-1) Enterobacteriaceae encountered in Hong Kong soon after the patient's arrival in the territory for medical care. As NDM-1 is spreading throughout the world via international travel, being an international city, Hong Kong was always expected to encounter the same public health threat. This case also illustrates the importance of active surveillance of at-risk patients in preventing the spread of this 'superbug'.

Effect of the number of stacking layers on the characteristics of quantum-dash lasers.

A theoretical model is evaluated to investigate the characteristics of InAs/InP quantum dash (Qdash) lasers as a function of the stack number. The model is based on multimode carrier-photon rate equations and accounts for both inhomogeneous and homogeneous broadenings of the optical gain. The numerical results show a non monotonic increase in the threshold current density and a red shift in the lasing wavelength on increasing the stack number, which agrees well with reported experimental results. This observation may partly be attributed to an increase of inhomogeneity in the active region.

A double-blind randomised comparison of intravenous patient-controlled remifentanil with intramuscular pethidine for labour analgesia.

In a prospective, double-blind, randomised controlled trial, we compared the efficacy of patient-controlled analgesia using remifentanil (25-30 µg per bolus) with intramuscular pethidine (50-75 mg) for labour analgesia in 69 parturients. Parturients receiving patient-controlled analgesia reported less pain than those receiving intramuscular pethidine throughout the study period (p < 0.001), with maximal reduction in visual analogue pain score at 2 h after commencement of analgesia (mean (SD) 20 (17) in the patient-controlled analgesia group and 36 (22) in the intramuscular pethidine group. The median (95% CI) time to the first request for rescue analgesics was significantly longer with patient-controlled analgesia (8.0 (6.8-9.2) h) compared with intramuscular pethidine (4.9 (3.8-5.4) h, p < 0.001). Maternal satisfaction scores were also higher with remifentanil compared with intramuscular pethidine (p= 0.001). There was no report of sedation, aponea or oxygen desaturation in either group, and Apgar scores were similar between groups. We conclude that patient-controlled analgesia with remifentanil provides better labour analgesia and maternal satisfaction than intramuscular pethidine. At this dose, maternal and fetal side effects were uncommon.

Prevalence and risk factors for Chlamydia trachomatis infection among cross-border truck drivers in Hong Kong.

OBJECTIVES: To determine the prevalence and risk factors for chlamydial infection in cross-border truck drivers. METHODS: 225 Hong Kong-based cross-border truck drivers were screened for chlamydial infection. Associations between infection and potential risk factors were determined by questionnaire. RESULTS: 8.5% of drivers were positive for chlamydial infection. Of 62% of drivers reporting recent sex with commercial sex workers (CSW), 39% had not used condoms. 75% of drivers with extramarital sex partners (ESP) also frequented CSW and 47% of this group had not used condoms with CSW. 43.3% PCR-positive cases reported symptoms. No risk factor was associated with chlamydial infection after adjustment, although "had sex with ESP" approached significance. CONCLUSIONS: The prevalence of chlamydial infection among cross-border truck drivers was not strikingly high, although drivers engaged in sex with both ESP and CSW, with many admitting unprotected intercourse. The findings highlight the importance of promoting safe sex to truck drivers.

Majorana fermion induced resonant Andreev reflection.

We describe experimental signatures of Majorana fermion edge states, which form at the interface between a superconductor and the surface of a topological insulator. If a lead couples to the Majorana fermions through electron tunneling, the Majorana fermions induce resonant Andreev reflections from the lead to the grounded superconductor. The linear tunneling conductance is 0 (2e(2)/h) if there is an even (odd) number of vortices in the superconductor. Similar resonance occurs for tunneling into the zero mode in the vortex core. We also study the current and noise of a two-lead device.

Production of feedstock chemicals.

Renewable raw materials may be converted by biological means to feedstocks for the chemical industry. Glucose from cornstarch is the current choice as a substrate, although advances may enable the use of less expensive lignocellulosic materals. The production of oxychemicals and their derivatives from renewable resources could amount to about 100 billion pounds annually, or about half of the U.S. production of organic chemicals. Ethanol produced by fermentation is now cost-competitive with industral ethanol produced from fossil fuel. Biological routes to other oxychemicals exist and are expected to be important in the future. Several product recovery methods may be used, but new energy-conserving methods will be needed to make the engineering-biology combinations economical.

Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus.

1. Community-associated methicillin-resistant Staphylococcus aureus (MRSA) strains with diverse genetic backgrounds are emerging in Hong Kong. 2. Intra-familial spread of community-associated MRSA is common.

Community-associated methicillin-resistant Staphylococcus aureus skin and soft tissue infections in Hong Kong.

Community-associated methicillin resistant Staphylococcus aureus is an emerging cause of skin and soft tissue infections in Hong Kong, especially among certain ethnic minorities.

High responsivity GaNAsSb p-i-n photodetectors at 1.3 microm grown by radio-frequency nitrogen plasma-assisted molecular beam epitaxy.

GaNAsSb/GaAs p-i-n photo notdetectors with an intrinsic GaNAsSb photoabsorption layer grown at 350 degrees C, 400 degrees C, 440 degrees C and 480 degrees C, have been prepared using radio-frequency nitrogen plasma-assisted molecular beam epitaxy in conjunction with a valved antimony cracker source. The i-GaNAsSb photoabsorption layer contains 3.3% of nitrogen and 8% of antimony, resulting in DC photo-response up to wavelengths of 1350 nm. The device with i-GaNAsSb layer grown at 350 degrees C exhibits extremely high photoresponsivity of 12A/W at 1.3 microm. These photodetectors show characteristics which strongly suggest the presence of carrier avalanche process at reverse bias less than 5V.

Rapid detection of pathogenic Vibrio parahaemolyticus by a sensitive and specific duplex PCR-hybridization probes assay using LightCycler.

AIMS: To develop a real-time polymerase chain reaction (PCR) hybridization probe assay for rapid and specific detection of thermostable direct haemolysin-producing Vibrio parahaemolyticus. METHODS AND RESULTS: Primers and hybridization probes were designed to target the toxR and tdh2 genes. Mismatches were introduced in the tdh2 primers for specific amplification of the target. The 3' ends of donor probes for both genes were labelled with fluorescein. The 5' ends of recipient probes for tdh2 and toxR were labelled with LC Red 640 and LC Red 705, respectively. The real-time assay was evaluated against conventional biochemical tests and the KAP-RPLA kit (Kanagawa phenomenon detection kit by reverse passive latex agglutination). toxR and tdh2 were detected in 100% and 91% of clinical V. parahaemolyticus isolates (n = 118), respectively. Specificity and sensitivity of the real-time assay for toxR and tdh2 were 100%, respectively. Dynamic range of detection for toxR was 10(7)-10(1) CFU ml(-1) and that for tdh2 was 10(7)-10(4) CFU ml(-1). CONCLUSIONS: The LightCycler assay described is sensitive and highly specific for detection of pathogenic V. parahaemolyticus in a single reaction tube within 80 min. SIGNIFICANCE AND IMPACT OF THE STUDY: The assay developed allows accurate detection of pathogenic V. parahaemolyticus, which is valuable for rapid tracing of infection source during outbreaks.

Self-planarized quantum-disks-in-nanowires ultraviolet-B emitters utilizing pendeo-epitaxy.

The growth of self-assembled, vertically oriented and uniform nanowires (NWs) has remained a challenge for efficient light-emitting devices. Here, we demonstrate dislocation-free AlGaN NWs with spontaneous coalescence, which are grown by plasma-assisted molecular beam epitaxy on an n-type doped silicon (100) substrate. A high density of NWs (filling factor >95%) was achieved under optimized growth conditions, enabling device fabrication without planarization using ultraviolet (UV)-absorbing polymer materials. UV-B (280-320 nm) light-emitting diodes (LEDs), which emit at ∼303 nm with a narrow full width at half maximum (FWHM) (∼20 nm) of the emission spectrum, are demonstrated using a large active region ("active region/NW length-ratio" ∼50%) embedded with 15 stacks of AlxGa1-xN/AlyGa1-yN quantum-disks (Qdisks). To improve the carrier injection, a graded layer is introduced at the AlGaN/GaN interfaces on both p- and n-type regions. This work demonstrates a viable approach to easily fabricate ultra-thin, efficient UV optoelectronic devices on low-cost and scalable silicon substrates.

Evaluation of a new transcutaneous bilirubinometer in Chinese newborns.

OBJECTIVE: To evaluate the use of a new transcutaneous bilirubinometer (JM-103 Minolta Airshields) for detection of hyperbilirubinaemia in term or near-term healthy Chinese newborns. METHODS: Transcutaneous bilirubin (TcB) was used to screen for severe hyperbilirubinaemia in newborn infants. Blood was taken for total serum bilirubin (TSB) measurement if the initial TcB level was higher than the 40th centile in Bhutani's nomogram. Paired TcB and TSB results were then reviewed over 6 months. The correlation as well as the mean difference between the two methods were calculated. The clinical application of TcB with Bhutani's nomogram in the prediction of severe hyperbilirubinaemia in low-risk, medium-risk and high-risk thresholds for phototherapy was also analysed. RESULTS: 997 paired TcB and TSB measurements were evaluated in term or near-term newborns. TcB was significantly correlated with TSB, with a correlation coefficient of 0.83 (p<0.001). Their mean difference was 21.7 micromol/l (SD 21.2, p<0.001), with the 95% limits of agreement between -19.9 and 63.3 micromol/l. In both low-risk and medium-risk thresholds for phototherapy, using the 75th centile of Bhutani's nomogram as threshold, TcB could identify all cases and had a sensitivity and negative predictive value of 100% each, a specificity of 56% and positive predictive value of 23%. For high-risk cases, using the 75th centile as cut-off, the sensitivity and negative predictive value were reduced to 86.7% and 97.0%, respectively. CONCLUSION: An accurate point-of-care bilirubin analyser facilitates bilirubin screening and avoids unnecessary blood tests. Although using the transcutaneous bilirubinometer JM-103 might result in a significant difference between TcB and TSB measured in Chinese newborns, combining the use of TcB and the 75th centile in Bhutani's nomogram as the cut-off level can identify all cases of significant hyperbilirubinaemia.

Retrospective prevalence of snakebites from Hospital Kuala Lumpur (HKL) (1999-2003).

A hospital based retrospective study of the prevalence of snakebite cases at Hospital Kuala Lumpur was carried out over a five-year period from 1999 to 2003. A total of 126 snakebite cases were recorded. The highest admission for snakebites was recorded in 2001 (29 cases). The majority of cases were admitted for three days or less (79%). Most of the snakebite cases were reported in the 11-30 years age group (52%). The male:female ratio was 3:1. The majority of cases were Malaysians (80%, 101 cases). Of the non-Malaysians, Indonesians constituted the most (56%, 14 cases). Bites occurred most commonly on the lower limbs (49%), followed by upper limbs (45%) and on other parts of the body (6%). No fatal cases were detected and complications were scarce. In 60% (70 cases) the snake could not be identified. Of the four species of snakes that were identified, cobra (both suspected and confirmed) constituted the largest group (25%), followed by viper (10%), python (4%) and sea snake (1%). The most common clinical presentations were pain and swelling, 92% (116 cases). All patients were put on snakebite charts and their vital signs were monitored. Of the snakebite cases, 48% (61 cases) were treated with cloxacillin and 25% (32 cases) were given polyvalent snake antivenom.