Private genome analysis through homomorphic encryption

Background: The rapid development of genome sequencing technology allows researchers to access large genome datasets. However, outsourcing the data processing o the cloud poses high risks for personal privacy. The aim of this paper is to give a practical solution for this problem using homomorphic encryption. In our approach, all the computations can be performed in an untrusted cloud without requiring the decryption key or any interaction with the data owner, which preserves the privacy of genome data. Methods: We present evaluation algorithms for secure computation of the minor allele frequencies and chi(2) statistic in a genome-wide association studies setting. We also describe how to privately compute the Hamming distance and approximate Edit distance between encrypted DNA sequences. Finally, we compare performance details of using two practical homomorphic encryption schemes -the BGV scheme by Gentry, Halevi and Smart and the YASHE scheme by Bos, Lauter, Loftus and Naehrig. Results: The approach with the YASHE scheme analyzes data from 400 people within about 2 seconds and picks a variant associated with disease from 311 spots. For another task, using the BGV scheme, it took about 65 seconds to securely compute the approximate Edit distance for DNA sequences of size 5K and figure out the differences between them. Conclusions: The performance numbers for BGV are better than YASHE when homomorphically evaluating deep circuits (like the Hamming distance algorithm or approximate Edit distance algorithm). On the other hand, it is more efficient to use the YASHE scheme for a low-degree computation, such as minor allele frequencies or chi(2) test statistic in a case-control study

Differential expression of microRNAs during fiber development between fuzzless- lintless mutant and its wild-type allotetraploid cotton

Cotton is one of the most important textile crops but little is known how microRNAs regulate cotton fiber development. Using a well-studied cotton fiberless mutant Xu-142-fl, we compared 54 miRNAs for their expression between fiberless mutant and its wildtype. In wildtype Xu-142, 26 miRNAs are involved in cotton fiber initiation and 48 miRNAs are related to primary wall synthesis and secondary wall thickening. Thirty three miRNAs showed different expression in fiber initiation between Xu-142 and Xu- 142-fl. These miRNAs potentially target 723 protein-coding genes, including transcription factors, such as MYB, ARF, and LRR. ARF18 was newly predicted targets of miR160a, and miR160a was expressed at higher level in −2DPA of Xu-142-fl compared with Xu-142. Furthermore, the result of Gene Ontology- based term classification (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows that miRNA targets were classified to 222 biological processes, 64 cellular component and 42 molecular functions, enriched in 22 KOG groups, and classified into 28 pathways. Together, our study provides evidence for better understanding of miRNA regulatory roles in the process of fiber development, which is helpful to increase fiber yield and improve fiber quality

MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development

The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield

Spin reorientation effect in neutron reflection from ferromagnetic films

We demonstrate that the magnetic state of a thin magnetic film can be probed using polarized neutron reflection even when the magnetization in the film plane is at 90° to the polarization direction of the incident neutron beam. For this special case, no magnetic interaction is expected classically, thus the effect is entirely quantum mechanical in origin. We show both theoretically and experimentally that it arises from the independent interaction of each spin component with the magnetization in the film. We demonstrate this effect for a single Co/GaAs(001) film and discuss its application to magnetic measurements using an unpolarized neutron beam. © 1995 The American Physical Society

Thickness dependence of the total magnetic moment per atom in the Ni/Cu/Si(001) system

Systematic measurements of the magnetic moment per Ni atom in Cu/Ni/Cu/Si(001) structures have been made using polarized neutron reflection (PNR) for Ni thicknesses in the range 30Å, , perpendicular anisotropy strength, and surface in-plane Ni lattice constant, respectively, during epitaxial growth. RHEED measurements show that the in-plane lattice constant falls by 1.7% in the Ni thickness range 30 Å, , and total moment per atom versus Ni thickness as found for the total moment by PNR. Polar MOKE measurements confirmed the transition from a perpendicular easy axis towards an in-plane magnetic easy axis as has already been extensively studied in the literature. Comparison of the PNR results with RHEED measurements reveal a striking correlation between the increase of in-plane strain and reduction in magnetic moment per atom with decreasing Ni thickness. While a direct strain-induced variation of the moment based on bulk phase calculations cannot account for the magnitude of the moment variations we observe, we show that the results cannot be attributed to sample contamination, interdiffusion, or a reduction of the Curie temperature with decreasing Ni thickness. Furthermore, the presence of a magnetically dead layer in the samples is not consistent with the PNR results. The strong moment variation partially explains the large thickness range for which perpendicular anisotropy is observed in this system

Magnetic properties of bcc Co films

The magnetic properties of epitaxial bcc Co films of thickness 10-100 Å have been investigated using the surface magneto-optic Kerr effect (SMOKE), polarized neutron reflection (PNR), and nuclear magnetic resonance (NMR). The in-plane coercivity is found to vary strongly with thickness and a large magnetocrystalline anisotropy develops in-plane at 60 Å which is maintained in thicker films. PNR measurements on a Au-coated 100-Å bcc Co film at 300 K are consistent with a layer averaged magnetic moment per atom of 1.4 μB and a magnetization profile within 50 Å of the GaAs interface. NMR measurements on a 75-Å bcc Co film at 4.2 K yield the center frequency consistent with a moment per atom of 1.4 μB

SANS measurements with polarised neutrons on FeAg magnetic granular samples: compositional and magnetic morphology

We have performed small angle neutron scattering measurements with polarised and non-polarised neutrons on FeAg magnetic systems prepared by plasma sputtering deposition with the co-sputtering method. We have prepared various samples withan iron content ranging from 10% to 30% and for iron concentration up to 20% they display a superparamagnetic behaviour. Particular attention has been dedicated to these systems, in order to investigate the evolution of granular phase morphology with iron content. The data collected with polarised neutrons can be interpreted in terms of the presence of nanosized particles surrounded by non-magnetic regions. Our data also indicate that samples ‘‘magnetic’’ morphology is greatly affected by iron percentage while the compositional shows negligible modifications