Efficient fuzzy matching and intersection on private datasets

At Eurocrypt’04, Freedman, Nissim and Pinkas introduced a fuzzy private matching problem. The problem is defined as follows. Given two parties, each of them having a set of vectors where each vector has T integer components, the fuzzy private matching is to securely test if each vector of one set matches any vector of another set for at least t components where t < T. In the conclusion of their paper, they asked whether it was possible to design a fuzzy private matching protocol without incurring a communication complexity with the factor (T t ) . We answer their question in the affirmative by presenting a protocol based on homomorphic encryption, combined with the novel notion of a share-hiding error-correcting secret sharing scheme, which we show how to implement with efficient decoding using interleaved Reed-Solomon codes. This scheme may be of independent interest. Our protocol is provably secure against passive adversaries, and has better efficiency than previous protocols for certain parameter values.

Secure computation of the vector dominance problem

Suppose two parties, holding vectors A = (a 1,a 2,...,a n ) and B = (b 1,b 2,...,b n ) respectively, wish to know whether a i  > b i for all i, without disclosing any private input. This problem is called the vector dominance problem, and is closely related to the well-studied problem for securely comparing two numbers (Yao’s millionaires problem). In this paper, we propose several protocols for this problem, which improve upon existing protocols on round complexity or communication/computation complexity.

Random Gabor based templates for facial expression recognition in images with facial occlusion

Robust facial expression recognition (FER) under occluded face conditions is challenging. It requires robust algorithms of feature extraction and investigations into the effects of different types of occlusion on the recognition performance to gain insight. Previous FER studies in this area have been limited. They have spanned recovery strategies for loss of local texture information and testing limited to only a few types of occlusion and predominantly a matched train-test strategy. This paper proposes a robust approach that employs a Monte Carlo algorithm to extract a set of Gabor based part-face templates from gallery images and converts these templates into template match distance features. The resulting feature vectors are robust to occlusion because occluded parts are covered by some but not all of the random templates. The method is evaluated using facial images with occluded regions around the eyes and the mouth, randomly placed occlusion patches of different sizes, and near-realistic occlusion of eyes with clear and solid glasses. Both matched and mis-matched train and test strategies are adopted to analyze the effects of such occlusion. Overall recognition performance and the performance for each facial expression are investigated. Experimental results on the Cohn-Kanade and JAFFE databases demonstrate the high robustness and fast processing speed of our approach, and provide useful insight into the effects of occlusion on FER. The results on the parameter sensitivity demonstrate a certain level of robustness of the approach to changes in the orientation and scale of Gabor filters, the size of templates, and occlusions ratios. Performance comparisons with previous approaches show that the proposed method is more robust to occlusion with lower reductions in accuracy from occlusion of eyes or mouth.

Direct repression of MYB by ZEB1 suppresses proliferation and epithelial gene expression during epithelial-to-mesenchymal transition of breast cancer cells

Introduction Epithelial-to-mesenchymal transition (EMT) promotes cell migration and is important in metastasis. Cellular proliferation is often downregulated during EMT, and the reverse transition (MET) in metastases appears to be required for restoration of proliferation in secondary tumors. We studied the interplay between EMT and proliferation control by MYB in breast cancer cells. Methods MYB, ZEB1, and CDH1 expression levels were manipulated by lentiviral small-hairpin RNA (shRNA)-mediated knockdown/overexpression, and verified with Western blotting, immunocytochemistry, and qRT-PCR. Proliferation was assessed with bromodeoxyuridine pulse labeling and flow cytometry, and sulforhodamine B assays. EMT was induced with epidermal growth factor for 9 days or by exposure to hypoxia (1% oxygen) for up to 5 days, and assessed with qRT-PCR, cell morphology, and colony morphology. Protein expression in human breast cancers was assessed with immunohistochemistry. ZEB1-MYB promoter binding and repression were determined with Chromatin Immunoprecipitation Assay and a luciferase reporter assay, respectively. Student paired t tests, Mann–Whitney, and repeated measures two-way ANOVA tests determined statistical significance (P < 0.05). Results Parental PMC42-ET cells displayed higher expression of ZEB1 and lower expression of MYB than did the PMC42-LA epithelial variant. Knockdown of ZEB1 in PMC42-ET and MDA-MB-231 cells caused increased expression of MYB and a transition to a more epithelial phenotype, which in PMC42-ET cells was coupled with increased proliferation. Indeed, we observed an inverse relation between MYB and ZEB1 expression in two in vitro EMT cell models, in matched human breast tumors and lymph node metastases, and in human breast cancer cell lines. Knockdown of MYB in PMC42-LA cells (MYBsh-LA) led to morphologic changes and protein expression consistent with an EMT. ZEB1 expression was raised in MYBsh-LA cells and significantly repressed in MYB-overexpressing MDA-MB-231 cells, which also showed reduced random migration and a shift from mesenchymal to epithelial colony morphology in two dimensional monolayer cultures. Finally, we detected binding of ZEB1 to MYB promoter in PMC42-ET cells, and ZEB1 overexpression repressed MYB promoter activity. Conclusions This work identifies ZEB1 as a transcriptional repressor of MYB and suggests a reciprocal MYB-ZEB1 repressive relation, providing a mechanism through which proliferation and the epithelial phenotype may be coordinately modulated in breast cancer cells.

Expression of a bacterial xylanase in Trichoderma reesei under the egl2 and cbh2 glycosyl hydrolase gene promoters

Expression vectors were constructed for Trichoderma reesei using the promoters, secretion signals and the modular structure of the efficiently expressed and secreted cellulase enzymes EGL2 (Cel5A) and CBH2 (Cel6A) as a prelude to establishing a platform where a gene of interest can be expressed under several promoters simultaneously. The designs featured (i) EGL2sigpro (egl2 promoter and secretion signal), (ii) EGL2cbmlin (egl2 promoter, secretion signal, EGL2 cellulose binding module and linker), (iii) CBH2sigpro (cbh2 promoter and secretion signal) and (iv) CBH2cbmlin (cbh2 promoter, secretion signal, CBH2 cellulose binding module and linker). Recombinant vectors were introduced individually into the high protein-secreting T. reesei RUT-C30 strain to generate single-promoter transformants expressing the Dictyoglomus thermophilum xynB gene that encodes a thermophilic xylanase enzyme (XynB). Ten transformants producing XynB representing each of the four different types of vectors were selected for further testing and the highest XynB production was achieved from a transformant containing 1–2 copies of the EGL2cbmlin vector. Best xylanase producers did not show any particular pattern in terms of the number of gene copies and their mode of integration into the chromosomal DNA. Transformants generated with the cbmlin-type vectors produced multiple forms of XynB which were decorated with various N- and O-glycans. One of the O-glycans was identified as hexuronic acid, whose presence had not been observed previously in the glycosylation patterns of T. reesei.

pGreen : a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation

Binary Ti vectors are the plasmid vectors of choice in Agrobacterium-mediated plant transformation protocols. The pGreen series of binary Ti vectors are configured for ease-of-use and to meet the demands of a wide range of transformation procedures for many plant species. This plasmid system allows any arrangement of selectable marker and reporter gene at the right and left T-DNA borders without compromising the choice of restriction sites for cloning, since the pGreen cloning sites are based on the well-known pBluescript general vector plasmids. Its size and copy number in Escherichia coli offers increased efficiencies in routine in vitro recombination procedures. pGreen can replicate in Agrobacterium only if another plasmid, pSoup, is co-resident in the same strain. pSoup provides replication functions in trans for pGreen. The removal of RepA and Mob functions has enabled the size of pGreen to be kept to a minimum. Versions of pGreen have been used to transform several plant species with the same efficiencies as other binary Ti vectors. Information on the pGreen plasmid system is supplemented by an Internet site (http://www.pgreen.ac.uk) through which comprehensive information, protocols, order forms and lists of different pGreen marker gene permutations can be found.

A transient assay for recombination demonstrates that Arabidopsis SNM1 and XRCC3 enhance non-homologous recombination

Replacement of endogenous genes by homologous recombination is rare in plants; the majority of genetic modifications are the result of transforming DNA molecules undergoing random genomic insertion by way of non-homologous recombination. Factors that affect chromatin remodeling and DNA repair are thought to have the potential to enhance the frequency of homologous recombination in plants. Conventional tools to study the frequencies of genetic recombination often rely on stable transformation-based approaches, with these systems being rarely capable of high-throughput or combinatorial analysis. We developed a series of vectors that use chemiluminescent (LUC and REN) reporter genes to assay the relative frequency of homologous and non-homologous recombination in plants. These transient assay vectors were used to screen 14 candidategenes for their effects on recombination frequencies in Nicotiana benthamiana plants. Over-expression of Arabidopsis genes with sequence similarity to SNM1 from yeast and XRCC3 from humans enhanced the frequency of non-homologous recombination when assayed using two different donor vectors. Transient N. benthamiana leaf systems were also used in an alternative assay for preliminary measurements of homologous recombination frequencies, which were found to be enhanced by over-expression of RAD52, MIM and RAD51 from yeast, as well as CHR24 from Arabidopsis. The findings for the assays described here are in line with previous studies that analyzed recombination frequencies using stable transformation. The assays we report have revealed functions in non-homologous recombination for the Arabidopsis SNM1 and XRCC3 genes, so the suppression of these genes' expression offers a potential means to enhance the gene targeting frequency in plants. Furthermore, our findings also indicate that plant gene targeting frequencies could be enhanced by over-expression of RAD52, MIM, CHR24, and RAD51 genes.

Multi-shot person re-identification via relational stein divergence

Person re-identification is particularly challenging due to significant appearance changes across separate camera views. In order to re-identify people, a representative human signature should effectively handle differences in illumination, pose and camera parameters. While general appearance-based methods are modelled in Euclidean spaces, it has been argued that some applications in image and video analysis are better modelled via non-Euclidean manifold geometry. To this end, recent approaches represent images as covariance matrices, and interpret such matrices as points on Riemannian manifolds. As direct classification on such manifolds can be difficult, in this paper we propose to represent each manifold point as a vector of similarities to class representers, via a recently introduced form of Bregman matrix divergence known as the Stein divergence. This is followed by using a discriminative mapping of similarity vectors for final classification. The use of similarity vectors is in contrast to the traditional approach of embedding manifolds into tangent spaces, which can suffer from representing the manifold structure inaccurately. Comparative evaluations on benchmark ETHZ and iLIDS datasets for the person re-identification task show that the proposed approach obtains better performance than recent techniques such as Histogram Plus Epitome, Partial Least Squares, and Symmetry-Driven Accumulation of Local Features.

Characterising the spatial dynamics of sympatric Aedes aegypti and Aedes albopictus populations in the Philippines

Entomological surveillance and control are essential to the management of dengue fever (DF). Hence, understanding the spatial and temporal patterns of DF vectors, Aedes (Stegomyia) aegypti (L.) and Ae. (Stegomyia) albopictus (Skuse), is paramount. In the Philippines, resources are limited and entomological surveillance and control are generally commenced during epidemics, when transmission is difficult to control. Recent improvements in spatial epidemiological tools and methods offer opportunities to explore more efficient DF surveillance and control solutions: however, there are few examples in the literature from resource-poor settings. The objectives of this study were to: (i) explore spatial patterns of Aedes populations and (ii) predict areas of high and low vector density to inform DF control in San Jose village, Muntinlupa city, Philippines. Fortnightly, adult female Aedes mosquitoes were collected from 50 double-sticky ovitraps (SOs) located in San Jose village for the period June-November 2011. Spatial clustering analysis was performed to identify high and low density clusters of Ae. aegypti and Ae. albopictus mosquitoes. Spatial autocorrelation was assessed by examination of semivariograms, and ordinary kriging was undertaken to create a smoothed surface of predicted vector density in the study area. Our results show that both Ae. aegypti and Ae. albopictus were present in San Jose village during the study period. However, one Aedes species was dominant in a given geographic area at a time, suggesting differing habitat preferences and interspecies competition between vectors. Density maps provide information to direct entomological control activities and advocate the development of geographically enhanced surveillance and control systems to improve DF management in the Philippines.

Oncogene-induced basement membrane invasiveness in human mammary epithelial cells

Expression of the intermediate filament protein vimentin, and loss of the cellular adhesion protein uvomorulin (E-cadherin) have been associated with increased invasiveness of established human breast cancer cell lines in vitro and in vivo. In the current study, we have further examined these relationships in oncogenically transformed human mammary epithelial cells. A normal human mammary epithelial strain, termed 184, was previously immortalized with benzo[a]pyrene, and two distinct sublines were derived (A1N4 and 184B5). These sublines were infected with retroviral vectors containing a single or two oncogenes of the nuclear, cytoplasmic, and plasma membrane-associated type (v-rasH, v-rasKi, v -mos, SV40T and c -myc). All infectants have been previously shown to exhibit some aspects of phenotypic transformation. In the current study, cellular invasiveness was determined in vitro using Matrigel, a reconstituted basement membrane extract. Lineage-specific differences were observed with respect to low constitutive invasiveness and invasive changes after infection with ras, despite similar ras-induced transformation of each line. Major effects on cellular invasiveness were observed after infection of the cells with two different oncogenes (v-rasH + SV40T and v -rasH + v -mos). In contrast, the effects of single oncogenes were only modest or negligible. All oncogenic infectants demonstrated increased attachment to laminin, but altered secretion of the 72 kDa and 92 kDa gelatinases was not associated with any aspect of malignant progression. Each of the two highly invasive double oncogene transformants were vimentinpositive and uvomorulin-negative, a phenotype indicative of the epithelial-mesenchymal transition (EMT) previously associated with invasiveness of established human breast cancer cell lines. Weakly invasive untransformed mammary epithelial cells in this study were positive for both vimentin and uvomorulin, suggesting that uvomorulin may over-ride the otherwise vimentin-associated invasiveness.

Flying supercapacitors as power smoothing elements in wind generation

This paper presents a capacitor-clamped three-level inverter-based supercapacitor direct integration scheme for wind energy conversion systems. The idea is to increase the capacitance of clamping capacitors with the use of supercapacitors and allow their voltage to vary within a defined range. Even though this unique approach eliminates the need of interfacing dc-dc converters for supercapacitors, the variable voltage operation brings about several challenges. The uneven distribution of space vectors is the major modulation challenge. A space vector modulation method is proposed in this paper to address this issue and to generate undistorted currents even in the presence of dynamic changes in supercapacitor voltages. A supercapacitor voltage equalization algorithm is also presented. Moreover, control strategies of the proposed system are discussed in detail. Simulation and experimental results are presented to verify the efficacy of the proposed system in suppressing short-term wind power fluctuations.

Direct integration of battery energy storage systems in distributed power generation

In this paper, a wind energy conversion system interfaced to the grid using a dual inverter is proposed. One of the two inverters in the dual inverter is connected to the rectified output of the wind generator while the other is directly connected to a battery energy storage system (BESS). This approach eliminates the need for an additional dc-dc converter and thus reduces power losses, cost, and complexity. The main issue with this scheme is uncorrelated dynamic changes in dc-link voltages that results in unevenly distributed space vectors. A detailed analysis on the effects of these variations is presented in this paper. Furthermore, a modified modulation technique is proposed to produce undistorted currents even in the presence of unevenly distributed and dynamically changing space vectors. An analysis on the battery charging/discharging process and maximum power point tracking of the wind turbine generator is also presented. Simulation and experimental results are presented to verify the efficacy of the proposed modulation technique and battery charging/discharging process.

The effect of the histological properties of tumors on transfection efficiency of electrically assisted gene delivery to solid tumors in mice

Uniform DNA distribution in tumors is a prerequisite step for high transfection efficiency in solid tumors. To improve the transfection efficiency of electrically assisted gene delivery to solid tumors in vivo, we explored how tumor histological properties affected transfection efficiency. In four different tumor types (B16F1, EAT, SA-1 and LPB), proteoglycan and collagen content was morphometrically analyzed, and cell size and cell density were determined in paraffin-embedded tumor sections under a transmission microscope. To demonstrate the influence of the histological properties of solid tumors on electrically assisted gene delivery, the correlation between histological properties and transfection efficiency with regard to the time interval between DNA injection and electroporation was determined. Our data demonstrate that soft tumors with larger spherical cells, low proteoglycan and collagen content, and low cell density are more effectively transfected (B16F1 and EAT) than rigid tumors with high proteoglycan and collagen content, small spindle-shaped cells and high cell density (LPB and SA-1). Furthermore, an optimal time interval for increased transfection exists only in soft tumors, this being in the range of 5-15 min. Therefore, knowledge about the histology of tumors is important in planning electrogene therapy with respect to the time interval between DNA injection and electroporation.

Cheating immune secret sharing

We consider secret sharing with binary shares. This model allows us to use the well developed theory of cryptographically strong boolean functions. We prove that for given secret sharing, the average cheating probability over all cheating and original vectors, i.e., ρ ¯= 1 n ⋅ 2 −n ∑ n c=1 ∑ α∈Vn ρ c,α , satisfies ρ ¯⩾ 1 2 , and the equality holds ⇔ ρc,α satisfies ρc,α = 1/2 for every cheating vector δc and every original vector α. In this case the secret sharing is said to be cheating immune. We further establish a relationship between cheating-immune secret sharing and cryptographic criteria of boolean functions. This enables us to construct cheating-immune secret sharing.

On cheating immune secret sharing

The paper addresses the cheating prevention in secret sharing. We consider secret sharing with binary shares. The secret also is binary. This model allows us to use results and constructions from the well developed theory of cryptographically strong boolean functions. In particular, we prove that for given secret sharing, the average cheating probability over all cheating vectors and all original vectors, i.e., 1/n 2n ∑c=1...n ∑α∈V n ρc,α , denoted by ρ, satisfies ρ ≥ ½, and the equality holds if and only if ρc,α satisfies ρc,α= ½ for every cheating vector δc and every original vector α. In this case the secret sharing is said to be cheating immune. We further establish a relationship between cheating-immune secret sharing and cryptographic criteria of boolean functions.This enables us to construct cheating-immune secret sharing.