SiPM joint likelihood reception for mobile LED-optical communication under pointing errors.

Light-emitting diode (LED)-optical communication is a novel spectrum communication with wide field of view (FOV), light weight, and long-distance free-space capabilities. Due to atmospheric turbulence attenuation and pointing errors caused by long-distance communication, this Letter proposes a multi-pixel channel joint maximum likelihood (JML) reception method using a highly sensitive silicon photomultiplier (SiPM). To evaluate the performance of the SiPM under mobile terminal jittering communication, we analyze the effect of optical transmitting power, pointing errors, and signal-to-noise ratio (SNR) gain on optical communication by comparing JML with signal channel using the maximum likelihood (ML) algorithm. Both simulation analysis and experimental results demonstrate that the proposed JML algorithm to process signals received from SiPM multi-pixel channels can effectively mitigate the impact of pointing errors on the bit error rate (BER) of optical communications by two orders of magnitude at large jitter radians and SNR.

Carrier rate of thalassemia among 25,910 high school students in Shaoguan area, China.

OBJECTIVES: As one of the most common hereditary diseases, thalassemia affects a large number of people in China. The aim of this study was to investigate the feasibility of a method based on next-generation sequencing (NGS) for screening of thalassemia carriers among high school students in the Shaoguan area. MATERIALS AND METHODS: The NGS-based method was performed using 25,910 high school students recruited from 38 schools. The screening yield was systematically analyzed. Before screening, a lecture on how the disease is inherited, the symptoms of thalassemia, and how to prevent it was given to 28,780 students. RESULTS: Implying successful delivery of information on the disease, 90.03% (25,910 of 28,780) of the students agreed to join this program for thalassemia screening. A thalassemia carrier rate of 15.99% (4144 of 25,910) was found. Also, 69 rare genotypes (28 of α-thalassemia and 41 of ß-thalassemia) and 9 novel variants were identified. CONCLUSIONS: This NGS-based method provided a feasible platform for high school population thalassemia screening. Combined with a clinical follow-up strategy, it could help eventually to prevent the births of affected children.

Integrated physical-layer secure visible light communication and positioning system based on polar codes.

Visible light communication (VLC) with physical-layer security can provide information-theoretic security for the optical wireless channel based on the characteristics of the channel instead of encryption algorithms and secret keys at application layer. Since precise location information of communication parties is crucial for estimating channel states and designing secure communication schemes, this paper proposes an integrated visible light communication and positioning system which provides triple functionalities of high-accuracy indoor positioning, physical-layer secure visible light communication, and flicker mitigation illumination. A heterogeneous signal hybrid line coding scheme is proposed for the transmitter to converge the high-speed communication data signals and the low-speed positioning data signals, and a hybrid heterogeneous signal extraction scheme is proposed for the receiver to separate the hybrid heterogeneous signals with a high-bandwidth photodetector and a low-pass complementary metal-oxide-semiconductor (CMOS) image sensor. Based on the positioning information and the communication scheme, a polar codes-based forward error correction coding scheme is designed to achieve physical-layer security and transmission reliability simultaneously. Numerical results show that the proposed system can reach a secrecy code rate of 0.76 for a single-input single-output indoor VLC channel and a transmission efficiency of 0.38 without perceivable flicker. Experimental results show that the proposed system can achieve an average positioning accuracy of 3.35 cm and decrease the bit error rate of a legitimate receiver to a near error-free level (lower than 10-7) while keeping the bit error rate of an eavesdropper at 0.4887 (nearly 0.5) with a transmission data rate of 1 Mbps, resulting in near-zero suppression of the eavesdropped information and a high secrecy capacity of 0.9994.

Improved polar-code-based efficient post-processing algorithm for quantum key distribution.

Combined with one-time pad encryption scheme, quantum key distribution guarantees the unconditional security of communication in theory. However, error correction and privacy amplification in the post-processing phase of quantum key distribution result in high time delay, which limits the final secret key generation rate and the practicability of quantum key distribution systems. To alleviate this limitation, this paper proposes an efficient post-processing algorithm based on polar codes for quantum key distribution. In this algorithm, by analyzing the channel capacity of the main channel and the wiretap channel respectively under the Wyner's wiretap channel model, we design a codeword structure of polar codes, so that the error correction and privacy amplification could be completed synchronously in a single step. Through combining error correction and privacy amplification into one single step, this efficient post-processing algorithm reduces complexity of the system and lower the post-processing delay. Besides, the reliable and secure communicaiton conditions for this algorithm has been given in this paper. Simulation results show that this post-processing algorithm satisfies the reliable and secure communication conditions well.

Real-time display camera communication system based on LED displays and smartphones.

Visible light communication based on display and camera can simultaneously provide the functionalities of display and invisible information transmission. There are widely potential applications in information broadcasting, stealth advertising, etc. In this paper, a real-time display camera communication system based on LED displays and smartphones is proposed. To solve the rate mismatch problem and the symbol unsynchronization problem between the LED display panel with a relatively high frame rate and the smartphones' camera with a relatively low frame rate, we propose an Alternate Bit-flipping Repeat Coding scheme for adjustable frame rate matching and symbol synchronization with the advantage of eliminating flickers perceivable to human eyes. Fast image processing algorithms are also designed to decrease the computational complexity of extracting information from the captured video frames in real-time. An experimental system was implemented on a 16×16 points LED display panel with a refresh rate of 150 fps and a commercial Android smartphone with an 8 megapixels camera working at 30 fps and a self-developed Android APP. The experimental results show that the real-time LED display camera communication system can achieve a data transmission rate of 30 bps for one LED display point and a maximum distance of 80 cm, and the computational time on the Android smartphone for data receiving is only 11.827 ms.

Quartz-enhanced photoacoustic spectroscopy exploiting a fast and wideband electro-mechanical light modulator.

A quartz-enhanced photoacoustic spectroscopy (QEPAS) gas sensor exploiting a fast and wideband electro-mechanical light modulator was developed. The modulator was designed based on the electro-mechanical effect of a commercial quartz tuning fork (QTF). The laser beam was directed on the edge surface of the QTF prongs. The configuration of the laser beam and the QTF was optimized in detail in order to achieve a modulation efficiency of ∼100%. The L-band single wavelength laser diode and a C-band tunable continuous wave laser were used to verify the performance of the developed QTF modulator, respectively, realizing a QEPAS sensor based on amplitude modulation (AM). As proof of concept, the AM-based QEPAS sensor demonstrated a detection limit of 45 ppm for H2O and 50 ppm for CO2 with a 1 s integration time respectively.

SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles.

BACKGROUND: The human leukocyte antigen (HLA) gene family plays a key role in the immune response and thus is crucial in many biomedical and clinical settings. Utilizing Sanger sequencing, the golden standard technology for HLA typing enables accurate identification of HLA alleles in high-resolution. However, only the commercial software, such as uTYPE, SBT-Assign, and SBTEngine, and very few open-source tools could be applied to perform HLA typing based on Sanger sequencing. RESULTS: We developed a user-friendly, cross-platform and open-source desktop application, known as SOAPTyping, for Sanger-based typing in HLA class I and II alleles. SOAPTyping can produce accurate results with a comprehensible protocol and featured functions. Moreover, SOAPTyping supports a more advanced group-specific sequencing primers (GSSP) module to solve the ambiguous typing results. We used SOAPTyping to analyze 36 samples with known HLA typing from the University of California Los Angeles (UCLA) International HLA DNA Exchange platform and 100 anonymous clinical samples, and the HLA typing results from SOAPTyping are identical to the golden results and 5.5 times faster than commercial software uTYPE, which shows the usability of SOAPTyping. CONCLUSIONS: We introduce the SOAPTyping as the first open-source and cross-platform HLA typing software with the capability of producing high-resolution HLA typing predictions from Sanger sequence data.

Real-time visible light positioning supporting fast moving speed.

Real-time capability is a key factor which affects the practicality of an indoor positioning system significantly. While visible light positioning (VLP) is widely studied since it can provide indoor positioning functionality with LED illumination, the existing VLP systems still suffer from the high positioning latency and are not practical for mobile units with high moving speed. In this paper, a real-time VLP system with low positioning latency and high positioning accuracy is proposed. With the lightweight image processing algorithm, the proposed system can be implemented on low-cost embedded system and support real-time accurate indoor positioning for mobile units with a fast moving speed. Experimental results show that the proposed system implemented on a Raspberry Pi can achieve a positioning accuracy of 3.93 cm and support the moving speed up to 38.5 km/h.

Residual thickness enhanced core-removed D-shaped single-mode fiber and its application for VOC evaporation monitoring.

A core-removed D-shaped structure with different residual thickness (RT) was manufactured on a single mode silica fiber (SMF) to enhance the sensitivity by using of ultra-precise polishing technology. With six different RTs ranging from ∼55 µm to ∼28 µm, the RT enhancement effect in a D-shaped SMF was researched in detail. The influence of the RT on its transmission spectra was investigated both theoretically and experimentally. Considering a compromise between the multimode interference efficiency and optical power loss, an optimum RT value of 34.09 µm was achieved. The obtained refractive index (RI) sensitivity was 10243 nm/RIU in the RI range of 1.430-1.444, corresponding to a RI resolution of 1.9×10-6 RIU. A high-performance all-fiber sensor was developed to monitor the evaporation process volatile organic compounds (VOCs) based on the RT-enhanced D-shaped SMF. As proof of concept, a 2-hour continuous monitoring was carried to monitor the chloroform and alcohol mixture. As a result, the evaporation of alcohol and chloroform were clearly identified and monitored. The developed RT-enhanced D-shaped fiber sensor provides an alternative way for chemical process monitoring and industrial applications.

Quartz-enhanced photoacoustic spectroscopy employing pilot line manufactured custom tuning forks.

Pilot line manufactured custom quartz tuning forks (QTFs) with a resonance frequency of 28 kHz and a Q value of >30, 000 in a vacuum and ∼ 7500 in the air, were designed and produced for trace gas sensing based on quartz enhanced photoacoustic spectroscopy (QEPAS). The pilot line was able to produce hundreds of low-frequency custom QTFs with small frequency shift < 10 ppm, benefiting the detecting of molecules with slow vibrational-translational (V-T) relaxation rates. An Au film with a thickness of 600 nm were deposited on both sides of QTF to enhance the piezoelectric charge collection efficiency and reduce the environmental electromagnetic noise. The laser focus position and modulation depth were optimized. With an integration time of 84 s, a normalized noise equivalent absorption (NNEA) coefficient of 1.7 × 10-8 cm-1∙W∙Hz-1/2 was achieved which is ∼10 times higher than a commercially available QTF with a resonance frequency of 32 kHz.

Next-generation sequencing improves molecular epidemiological characterization of thalassemia in Chenzhou Region, P.R. China.

OBJECTIVES: Thalassemia is a highly prevalent monogenic inherited disease in southern China. It is important to collect epidemiological data comprehensively for proper prevention and treatment. METHODS: In this study, blood samples collected from 15 807 residents of Chenzhou were primarily screened by hematological tests. A total of 3973 samples of suspected thalassemia carriers were further characterized by combined next-generation sequencing (NGS) and Gap-PCR. RESULTS: In total, 1704 subjects were diagnosed as thalassemia carriers with a total prevalence rate of 10.78%, including 943 α-thalassemia carriers, 708 ß-thalassemia carriers, and 53 composite α and ß-thalassemia carriers. The prevalence rates of α-thalassemia, ß-thalassemia, and composite α and ß-thalassemia were 5.97%, 4.48%, and 0.34%, respectively. Meanwhile, we characterized 19 α-thalassemia variations and 21 ß-thalassemia variations in thalassemia carriers. Approximately 2.88% of thalassemia carriers would be missed by traditional genetic analysis. In addition, four novel thalassemia mutations and one novel abnormal hemoglobin mutation were identified. CONCLUSIONS: Our data suggest a high prevalence of thalassemia and a diverse spectrum of thalassemia-associated variations in Chenzhou. Also, combined NGS and Gap-PCR is an effective thalassemia screening method. Our findings might be helpful for prevention and treatment of thalassemia in this region.

High-sensitivity humidity sensing of side-polished optical fiber with polymer nanostructure cladding.

This paper presented a high-sensitivity humidity sensor comprised of a side-polished fiber with polymer nanostructure cladding, which was constructed by dehydrating dichromate gelatin film on the polished surface. Due to the intermodal interference of the core mode and cladding mode, two main transmission dips were observed at 1184.4 nm and 1325.6 nm. These two transmission dips showed significant sensitivity to humidity. The position of transmission dip at 1325.6 nm shifted 22 nm while the relative humidity (RH) changed from 30% RH to 50% RH. The humidity sensitivity was up to 1.12 nm/% RH, and its linear correlation was 98.45%. The humidity sensing characteristic of nanostructure cladding fiber was successfully demonstrated. This novel sensor is compatible with optical fiber systems and has high potential in optical sensing applications.

High performance all-fiber temperature sensor based on coreless side-polished fiber wrapped with polydimethylsiloxane.

A novel fiber structure, coreless side-polished fiber (CSPF) that is wrapped by polydimethylsiloxane (PDMS), is demonstrated to be highly sensitive to temperature because of the high refractive index sensitivity of the CSPF and the large thermal optic coefficient of the PDMS. Our numerical and experimental results show that the several dips in the transmitted spectra of PDMSW-CSPF is originated from the multimode interference (MMI) in the CSPF and will blueshift with the increase of temperature. Furthermore, for such a PDMSW-CSPF, we investigate its temperature sensing characteristics and the influences of residual thickness (RT) and dip wavelength on the sensitivity both numerically and experimentally. In the temperature range of 30~85°C, the PDMSW-CSPF with RT = 43.26 µm exhibits a high temperature sensitivity of -0.4409 nm/°C, the high linearity of 0.9974, and the high stability with low standard deviation of 0.141 nm. Moreover, in the cycle experiments, where the environmental temperature was set to automatically increase and then decrease, the PDMSW-CSPF exhibits a low relative deviation of sensitivity (RSD) of down to ± 0.068%. Here, the RSD is defined as the ratio of sensitivity deviation to the average sensitivity measured in the heating/cooling cycle experiments. The lower RSD indicates that PDMSW-CSPF has better reversibility than other fiber structure. The investigations also show that the sensitivity of the PDMSW-CSPF could be enhanced further by reducing the residual thickness and choosing the dip at a longer wavelength.

Association Analysis of the MHC in Lupus Nephritis.

Lupus nephritis (LN) is one of the most prevalent and serious complications of SLE, with significant effects on patient and renal survival. Although a large number of genetic variants associated with SLE have been identified, biomarkers that correlate with LN are extremely limited. In this study, we performed a comprehensive sequencing analysis of the whole MHC region in 1331 patients with LN and 1296 healthy controls and validated the independent associations in another 950 patients with LN and 1000 controls. We discovered five independent risk variants for LN within the MHC region, including HLA-DRß1 amino acid 11 (Pomnibus<0.001), HLA-DQß1 amino acid 45 (P<0.001; odds ratio, 0.58; 95% confidence interval, 0.52 to 0.65), HLA-A amino acid 156 (Pomnibus<0.001), HLA-DPß1 amino acid 76 (Pomnibus<0.001), and a missense variant in PRRC2A (rs114580964; P<0.001; odds ratio, 0.38; 95% confidence interval, 0.30 to 0.49) at genome-wide significance. These data implicate aberrant peptide presentation by MHC classes 1 and 2 molecules and sex hormone modulation in the development of LN.

An improved parameter estimation scheme for image modification detection based on DCT coefficient analysis.

Most of the existing image modification detection methods which are based on DCT coefficient analysis model the distribution of DCT coefficients as a mixture of a modified and an unchanged component. To separate the two components, two parameters, which are the primary quantization step, Q1, and the portion of the modified region, α, have to be estimated, and more accurate estimations of α and Q1 lead to better detection and localization results. Existing methods estimate α and Q1 in a completely blind manner, without considering the characteristics of the mixture model and the constraints to which α should conform. In this paper, we propose a more effective scheme for estimating α and Q1, based on the observations that, the curves on the surface of the likelihood function corresponding to the mixture model is largely smooth, and α can take values only in a discrete set. We conduct extensive experiments to evaluate the proposed method, and the experimental results confirm the efficacy of our method.