Improving polygenic prediction with genetically inferred ancestry.

Genome-wide association studies (GWASs) have demonstrated that most common diseases have a strong genetic component from many genetic variants each with a small effect size. GWAS summary statistics have allowed the construction of polygenic scores (PGSs) estimating part of the individual risk for common diseases. Here, we propose to improve PGS-based risk estimation by incorporating genetic ancestry derived from genome-wide genotyping data. Our method involves three cohorts: a base (or discovery) for association studies, a target for phenotype/risk prediction, and a map for ancestry mapping; successively, (1) it generates for each individual in the base and target cohorts a set of principal components based on the map cohort-called mapped PCs, (2) it associates in the base cohort the phenotype with the mapped-PCs, and (3) it uses the mapped PCs in the target cohort to generate a phenotypic predictor called the ancestry score. We evaluated the ancestry score by comparing a predictive model using a PGS with one combining a PGS and an ancestry score. First, we performed simulations and found that the ancestry score has a greater impact on traits that correlate with ancestry-specific variants. Second, we showed, using UK Biobank data, that the ancestry score improves genetic prediction for our nine phenotypes to very different degrees. Third, we performed simulations and found that the more heterogeneous the base and target cohorts, the more beneficial the ancestry score is. Finally, we validated our approach under realistic conditions with UK Biobank as the base cohort and Swiss individuals from the CoLaus|PsyCoLaus study as the target cohort

A REAL TIME MONITORING MODEL OF THE CALCIUM CARBONATE FOULING INDUCTION PERIOD BASED ON THE CONDUCTANCE TITRATION

A new method has been developed to monitor the calcium carbonate fouling induction period (CCFIP) in real time. Based on the conductance titration, this paper investigated the forming process of CCFIP by a staticdynamic combined simulation experiment unit. With the help of titration analysis (that is titrimetry), an accurate definition of CCFIP and the corresponding real time monitoring model were built up. The investigation results show that the proposed model applies not only to measure the CCFIP in real time, but also applies to an investigation of the influence of various factors on the CCFIP

Effects of Sc and Zr on the texture and mechanical anisotropy of high strength Al - Zn - Mg alloy sheets

Texture, mechanical anisotropy and microstructure of aged Al–Zn–Mg, Al–Zn–Mg–0.1Sc–0.1Zr and Al–Zn–Mg–0.25Sc–0.1Zr (wt.%) alloy sheets were investigated by tensile tests and electron microscopy. Sc and Zr additions do not change the texture of homogenized and cold rolled alloys, but transfer the cube texture of the aged Al–Zn–Mg alloy into -fiber rolling texture. With increasing Sc and Zr additions, the strength significantly increases, and mechanical anisotropy is enhanced. The strength is highest parallel to the rolling direction, whereas it is lowest at a 45° angle to the rolling direction. The higher strength is mainly due to grain boundary strengthening and precipitation strengthening caused by Al₃ScxZr₁₋x nano-particles. The stronger mechanical anisotropy is ascribed to the rolling texture, due to the inhibitory effect of Al₃ScxZr₁₋x on recrystallization. A new model was successfully established to reveal the interrelation between Sc and Zr additions, texture and yield strength anisotropy of Al–Zn–Mg sheets

A rapid and cheap protocol for preparation of PCR templates in peanut

This paper describes a simple, low cost and reliable DNA template preparation protocol for polymerase chain reaction (PCR) using immature leaves from peanut seeds or leaves from field-grown plants. The technique may find wide utility in studies involving PCR-based molecular markers, rapid screening for transformants and gene cloning

Microbial modulation in the biomass and toxin production of a red-tide causing alga

The effect of S10, a strain of marine bacteria isolated from sediment in the Western Xiamen Sea, on the growth and paralytic shellfish poison (PSP) production in the alga Alexandrium tamarense (A. tamarense) was studied under controlled experimental conditions.The results of these experiments have shown that the growth of A. tamarense is obviously inhibited by S10 at high concentrations,however no evident effect on its growth was observed at low concentrations. Its PSP production was also inhibited by S10 at different concentrations, especially at low concentrations. The toxicity of this strain of A. tamarense is about (0.95– 12.14) • 10－6 MU/cell, a peak toxicity value of 12.14 • 10－6 MU/cell appeared on the 14th day, after which levels decreased gradually.The alga grew well in conditions of pH 6–8 and salinities of 20–34‰. The toxicity of the alga varied markedly at different pH and salinity levels. Toxicity decreased as pH increased, while it increased with salinity and reached a peak value at a salinity of 30‰,after which it declined gradually. S10 at a concentration of 1.02 • 109 cells/ml inhibited growth and the PSP production of A. tamarense at different pH and salinity levels. S10 had the strongest inhibitory function on the growth of A. tamarense under conditions of pH 7 and a salinity of 34‰. The best inhibitory effect on PSP production by A. tamarense was at pH 7, this inhibitory effect on PSP production did not relate to salinity. Interactions between marine bacteria and A. tamarense were also investigated using the flow cytometer technique (FCM) as well as direct microscope counting. S10 was identified as being a member of the genus Bacillus, the difference in 16S rDNA between S10 and Bacillus halmapalus was only 2%. The mechanism involved in the inhibition of growth and PSP production of A. tamarense by this strain of marine bacteria, and the prospect of using it and other marine bacteria in the biocontrol of red-tides was discussed

Collimation of high current fast electrons in dense plasmas with a tightly focused precursor intense laser pulse

High-current fast electrons at the mega-ampere level provide a unique way to generate high-energy density states of matter, which are related to many applications. However, the large divergence angle of fast electrons typically over 50 degrees is a significant disadvantage. The guiding effect of the self-generated azimuthal magnetic fields on fast electron current is found to be very limited due to the cone-shaped spatial structure of the fields. In this work, we present a new understanding of the collimation conditions of fast electrons under such a magnetic field structure. It is shown that the transverse peak position of the magnetic field layer plays a more crucial role in collimating the fast electrons than its magnitude. Based upon this, a new two-pulse collimating scheme is proposed, where a guiding precursor pulse is adopted to form proper azimuthal magnetic fields and the main pulse is for fast electron generation as usual. The present scheme can be implemented relatively easily with the precursor lasers at the 10 TW level with a duration of 200 femtoseconds, with which the divergence angle of fast electrons driven by the main pulse can be confined within a few degrees. Practical applications of our scheme can be found in high-energy density science

Derivatization of estrogens enhances specificity and sensitivity of analysis of human plasma and serum by liquid chromatography tandem mass spectrometry

AbstractEstrogens circulate at concentrations less than 20pg/mL in men and postmenopausal women, presenting analytical challenges. Quantitation by immunoassay is unreliable at these low concentrations. Liquid chromatography tandem mass spectrometry (LC–MS/MS) offers greater specificity and sometimes greater sensitivity, but ionization of estrogens is inefficient. Introduction of charged moieties may enhance ionization, but many such derivatives of estrogens generate non-specific product ions originating from the “reagent” group. Therefore an approach generating derivatives with product ions specific to individual estrogens was sought.Estrogens were extracted from human plasma and serum using solid phase extraction and derivatized using 2-fluoro-1-methylpyridinium-p-toluenesulfonate (FMP-TS). Electrospray in positive mode with multiple reaction monitoring using a QTrap 5500 mass spectrometer was used to quantify “FMP” derivatives of estrogens, following LC separation.Transitions for the FMP derivatives of estrone (E1) and estradiol (E2) were compound specific (m/z 362→238 and m/z 364→128, respectively). The limits of detection and quantitation were 0.2pg on-column and the method was linear from 1–400pg/sample. Measures of intra- and inter-assay variability, precision and accuracy were acceptable (<20%). The derivatives were stable over 24h at 10°C (7–9% degradation). Using this approach, E1 and E2, respectively were detected in human plasma and serum: pre-menopausal female serum (0.5mL) 135–473, 193–722pmol/L; male plasma (1mL) 25–111, 60–180pmol/L and post-menopausal female plasma (2mL), 22–78, 29–50pmol/L.Thus FMP derivatization, in conjunction with LC–MS/MS, is suitable for quantitative analysis of estrogens in low abundance in plasma and serum, offering advantages in specificity over immunoassay and existing MS techniques

Wireless transmission of biosignals for hyperbaric chamber applications

[EN] This paper presents a wireless system to send biosignals outside a hyperbaric chamber avoiding wires going through the chamber walls. Hyperbaric chambers are becoming more and more common due to new indications of hyperbaric oxygen treatments. Metallic walls physically isolate patients inside the chamber, where getting a patient's vital signs turns into a painstaking task. The paper proposes using a ZigBee-based network to wirelessly transmit the patient's biosignals to the outside of the chamber. In particular, a wearable battery supported device has been designed, implemented and tested. Although the implementation has been conducted to transmit the electrocardiography signal, the device can be easily adapted to consider other biosignals.The authors would like to thanks the University of Balearic Islands (UIB), the Miguel Hernandez University (UMH), MEDIBAROX unit of the Perpetuo Socorro Hospital and the "Catedra de Medicina Hiperbarica" (UMH) for their support allowing the use of its facilities for this work. The authors would also like to thank Borja Mas Boned for his help designing the LabVIEW application. This research has been carried out with funding and promotion of "Catedra de Medicina Hiperbarica" of the Miguel Hernandez University. http://nbio.umh.es/es/2010/12/01/catedra-de-medicina-hiperbarica-medibarox/.Perez-Vidal, C.; Gracia Calandin, LI.; Carmona, C.; Alorda, B.; Salinas, A. (2017). Wireless transmission of biosignals for hyperbaric chamber applications. PLoS ONE. 12(3):1-19. https://doi.org/10.1371/journal.pone.0172768S119123Sureda, A., Batle, J. M., Martorell, M., Capó, X., Tejada, S., Tur, J. A., & Pons, A. (2016). Antioxidant Response of Chronic Wounds to Hyperbaric Oxygen Therapy. PLOS ONE, 11(9), e0163371. doi:10.1371/journal.pone.0163371Branco, B. H. M., Fukuda, D. H., Andreato, L. V., Santos, J. F. da S., Esteves, J. V. D. C., & Franchini, E. (2016). The Effects of Hyperbaric Oxygen Therapy on Post-Training Recovery in Jiu-Jitsu Athletes. PLOS ONE, 11(3), e0150517. doi:10.1371/journal.pone.0150517Xu, Y., Ji, R., Wei, R., Yin, B., He, F., & Luo, B. (2016). The Efficacy of Hyperbaric Oxygen Therapy on Middle Cerebral Artery Occlusion in Animal Studies: A Meta-Analysis. PLOS ONE, 11(2), e0148324. doi:10.1371/journal.pone.0148324Lin, B.-S., Lin, B.-S., Chou, N.-K., Chong, F.-C., & Chen, S.-J. (2006). RTWPMS: A Real-Time Wireless Physiological Monitoring System. IEEE Transactions on Information Technology in Biomedicine, 10(4), 647-656. doi:10.1109/titb.2006.874194Hu, S., Wei, H., Chen, Y., & Tan, J. (2012). A Real-Time Cardiac Arrhythmia Classification System with Wearable Sensor Networks. Sensors, 12(9), 12844-12869. doi:10.3390/s120912844Burns, A., Greene, B. R., McGrath, M. J., O’Shea, T. J., Kuris, B., Ayer, S. M., … Cionca, V. (2010). SHIMMER™ – A Wireless Sensor Platform for Noninvasive Biomedical Research. IEEE Sensors Journal, 10(9), 1527-1534. doi:10.1109/jsen.2010.2045498Gil, Y., Wu, W., & Lee, J. (2012). A Synchronous Multi-Body Sensor Platform in a Wireless Body Sensor Network: Design and Implementation. Sensors, 12(8), 10381-10394. doi:10.3390/s120810381Chin-Teng Lin, Kuan-Cheng Chang, Chun-Ling Lin, Chia-Cheng Chiang, Shao-Wei Lu, Shih-Sheng Chang, … Li-Wei Ko. (2010). An Intelligent Telecardiology System Using a Wearable and Wireless ECG to Detect Atrial Fibrillation. IEEE Transactions on Information Technology in Biomedicine, 14(3), 726-733. doi:10.1109/titb.2010.2047401W. Y. Chung, Y. D. Lee, and S. J. Jung, &apos;A Wireless Sensor Network Compatible Wearable U-Healthcare Monitoring System Using Integrated Ecg, Accelerometer and Spo2&apos;, Conf Proc IEEE Eng Med Biol Soc, 2008 (2008), 1529–32.ZigBee Alliance; http://www.zigbee.org/Mahmood, A., Javaid, N., & Razzaq, S. (2015). A review of wireless communications for smart grid. Renewable and Sustainable Energy Reviews, 41, 248-260. doi:10.1016/j.rser.2014.08.036J.S. Lee, Y.W. Su, and C.C. Shen, &quot;A comparative study of wireless protocols: Bluetooth, UWB, ZigBee, and Wi-Fi, 33rd Annual Conference of the IEEE Industrial Electronics Society (IECON), 2007, pp. 46–51.P.P. Parikh, M.G. Kanabar, and T.S. Sidhu, &quot;Opportunities and challenges of wireless communication technologies for smart grid applications, IEEE PES General Meeting, 2010, pp. 1–7.Fadlullah, Z. M., Fouda, M. M., Kato, N., Takeuchi, A., Iwasaki, N., & Nozaki, Y. (2011). Toward intelligent machine-to-machine communications in smart grid. IEEE Communications Magazine, 49(4), 60-65. doi:10.1109/mcom.2011.5741147A.C. Olteanu, G.D. Oprina, N. Tapus, and S. Zeisberg, &quot;Enabling mobile devices for home automation using ZigBee, 19th IEEE International Conference on Control Systems and Computer Science, 2013, pp. 189–195.Shang, Y. (2014). Vulnerability of networks: Fractional percolation on random graphs. Physical Review E, 89(1). doi:10.1103/physreve.89.012813R. Barea-Navarro. Biomedical Instrumentation. Chapter 3. University of Alcala

Single Spin Asymmetry ANA_N in Polarized Proton-Proton Elastic Scattering at s=200\sqrt{s}=200 GeV

We report a high precision measurement of the transverse single spin asymmetry $A_N$ at the center of mass energy $\sqrt{s}=200$ GeV in elastic proton-proton scattering by the STAR experiment at RHIC. The $A_N$ was measured in the four-momentum transfer squared $t$ range $0.003 \leqslant |t| \leqslant 0.035$ \GeVcSq, the region of a significant interference between the electromagnetic and hadronic scattering amplitudes. The measured values of $A_N$ and its $t$-dependence are consistent with a vanishing hadronic spin-flip amplitude, thus providing strong constraints on the ratio of the single spin-flip to the non-flip amplitudes. Since the hadronic amplitude is dominated by the Pomeron amplitude at this $\sqrt{s}$, we conclude that this measurement addresses the question about the presence of a hadronic spin flip due to the Pomeron exchange in polarized proton-proton elastic scattering.Comment: 12 pages, 6 figure