Dynamic dictionary matching and compressed suffix trees

Recent breakthrough in compressed indexing data structures has reduced the space for indexing a text (or a collection of texts) of length n from O(n log n) bits to O(n) bits, while allowing very efficient pattern matching. Yet the compressed nature of such indices also makes them difficult to update dynamically. This paper presents the first O(n)-bit representation of a suffix tree for a dynamic collection of texts whose total length is n, which supports insertion and deletion of a text T in O(|T| log2 n) time, as well as all suffix tree traversal operations, including forward and backward suffix links. This work can be regarded as a generalization of the compressed representation of static texts. Our new suffix tree representation serves as a core part in a compact solution for the dynamic dictionary matching problem, i.e., providing an O(d)-bit data structure for a dynamic collection of patterns of total length d that can support the dictionary matching query efficiently. When compared with the O(d log d)-bit suffix tree based solution of Amir et al., the compact solution increases the query time by roughly a factor of log d only. In the study of the above results, we also derive the first O(n)-bit representation for maintaining n pairs of balanced parentheses in O(log n/log log n) time per operation, matching the time complexity of the previous O(n log n)-bit solution.published_or_final_versio

Succinct Partial Sums and Fenwick Trees

We consider the well-studied partial sums problem in succint space where one is to maintain an array of n k-bit integers subject to updates such that partial sums queries can be efficiently answered. We present two succint versions of the Fenwick Tree - which is known for its simplicity and practicality. Our results hold in the encoding model where one is allowed to reuse the space from the input data. Our main result is the first that only requires nk + o(n) bits of space while still supporting sum/update in O(log_b n) / O(b log_b n) time where 2 <= b <= log^O(1) n. The second result shows how optimal time for sum/update can be achieved while only slightly increasing the space usage to nk + o(nk) bits. Beyond Fenwick Trees, the results are primarily based on bit-packing and sampling - making them very practical - and they also allow for simple optimal parallelization

Cache-oblivious index for approximate string matching

This paper revisits the problem of indexing a text for approximate string matching. Specifically, given a text T of length n and a positive integer k, we want to construct an index of T such that for any input pattern P, we can find all its k-error matches in T efficiently. This problem is well-studied in the internal-memory setting. Here, we extend some of these recent results to external-memory solutions, which are also cache-oblivious. Our first index occupies O((nlog kn)B) disk pages and finds all k-error matches with O((|P|+occ)B+log knloglog Bn) I/Os, where B denotes the number of words in a disk page. To the best of our knowledge, this index is the first external-memory data structure that does not require Ω (|P|+occ+poly(logn)) I/Os. The second index reduces the space to O((nlogn)B) disk pages, and the I/O complexity is O((|P|+occ)B+log k(k+1)nloglogn) . © 2011 Elsevier B.V. All rights reserved.postprin

Policy, legal and regulatory implications of a Europe-only cloud

This article explores key legal and regulatory issues arising from recent cloud localization initiatives, with a particular focus on calls to establish a Europe-only cloud. The analysis covers jurisdictional conflicts and extraterritoriality concerns, as well as the impact on fundamental rights such as privacy, data protection and freedom of expression

Phylodynamics of HIV-1 Subtype B among the Men-Having-Sex-with-Men (MSM) Population in Hong Kong

The men-having-sex-with-men (MSM) population has become one of the major risk groups for HIV-1 infection in the Asia Pacific countries. Hong Kong is located in the centre of Asia and the transmission history of HIV-1 subtype B transmission among MSM remained unclear. The aim of this study was to investigate the transmission dynamics of HIV-1 subtype B virus in the Hong Kong MSM population. Samples of 125 HIV-1 subtype B infected MSM patients were recruited in this study. Through this study, the subtype B epidemic in the Hong Kong MSM population was identified spreading mainly among local Chinese who caught infection locally. On the other hand, HIV-1 subtype B infected Caucasian MSM caught infection mainly outside Hong Kong. The Bayesian phylogenetic analysis also indicated that 3 separate subtype B epidemics with divergence dates in the 1990s had occurred. The first and latest epidemics were comparatively small-scaled; spreading among the local Chinese MSM while sauna-visiting was found to be the major sex partner sourcing reservoir for the first subtype B epidemic. However, the second epidemic was spread in a large-scale among local Chinese MSM with a number of them having sourced their sex partners through the internet. The epidemic virus was estimated to have a divergence date in 1987 and the infected population in Hong Kong had a logistic growth throughout the past 20 years. Our study elucidated the evolutionary and demographic history of HIV-1 subtype B virus in Hong Kong MSM population. The understanding of transmission and growth model of the subtype B epidemic provides more information on the HIV-1 transmission among MSM population in other Asia Pacific high-income countries

Safety Issues of Long-Term Glucose Load in Patients on Peritoneal Dialysis—A 7-Year Cohort Study

BACKGROUND: Effects of long-term glucose load on peritoneal dialysis (PD) patient safety and outcomes have seldom been reported. This study demonstrates the influence of long-term glucose load on patient and technique survival. METHODS: We surveyed 173 incident PD patients. Long-term glucose load was evaluated by calculating the average dialysate glucose concentration since initiation of PD. Risk factors were assessed by fitting Cox's models with repeatedly measured time-dependent covariates. RESULTS: We noted that older age, higher glucose concentration, and lower residual renal function (RRF) were significantly associated with a worse patient survival. We found that female gender, absence of diabetes, lower glucose concentration, use of icodextrin, higher serum high density lipoprotein cholesterol, and higher RRF were significantly associated with a better technique survival. CONCLUSIONS: Long-term glucose load predicted mortality and technique failure in chronic PD patients. These findings emphasize the importance of minimizing glucose load in PD patients

FOXA1 repression is associated with loss of BRCA1 and increased promoter methylation and chromatin silencing in breast cancer

FOXA1 expression correlates with the breast cancer luminal subtype and patient survival. RNA and protein analysis of a panel of breast cancer cell lines revealed that BRCA1 deficiency is associated with the downregulation of FOXA1 expression. Knockdown of BRCA1 resulted in the downregulation of FOXA1 expression and enhancement of FOXA1 promoter methylation in MCF-7 breast cancer cells, whereas the reconstitution of BRCA1 in Brca1-deficent mouse mammary epithelial cells (MMECs) promoted Foxa1 expression and methylation. These data suggest that BRCA1 suppresses FOXA1 hypermethylation and silencing. Consistently, the treatment of MMECs with the DNA methylation inhibitor 5-aza-2'-deoxycitydine induced Foxa1 mRNA expression. Furthermore, treatment with GSK126, an inhibitor of EZH2 methyltransferase activity, induced FOXA1 expression in BRCA1-deficient but not in BRCA1-reconstituted MMECs. Likewise, the depletion of EZH2 by small interfering RNA enhanced FOXA1 mRNA expression. Chromatin immunoprecipitation (ChIP) analysis demonstrated that BRCA1, EZH2, DNA methyltransferases (DNMT)1/3a/3b and H3K27me3 are recruited to the endogenous FOXA1 promoter, further supporting the hypothesis that these proteins interact to modulate FOXA1 methylation and repression. Further co-immunoprecipitation and ChIP analysis showed that both BRCA1 and DNMT3b form complexes with EZH2 but not with each other, consistent with the notion that BRCA1 binds to EZH2 and negatively regulates its methyltransferase activity. We also found that EZH2 promotes and BRCA1 impairs the deposit of the gene silencing histone mark H3K27me3 on the FOXA1 promoter. These associations were validated in a familial breast cancer patient cohort. Integrated analysis of the global gene methylation and expression profiles of a set of 33 familial breast tumours revealed that FOXA1 promoter methylation is inversely correlated with the transcriptional expression of FOXA1 and that BRCA1 mutation breast cancer is significantly associated with FOXA1 methylation and downregulation of FOXA1 expression, providing physiological evidence to our findings that FOXA1 expression is regulated by methylation and chromatin silencing and that BRCA1 maintains FOXA1 expression through suppressing FOXA1 gene methylation in breast cancer.Oncogene advance online publication, 22 December 2014; doi:10.1038/onc.2014.421.published_or_final_versio

Outcome of infants with acute lymphoblastic leukemia treated with the Chinese Children's Cancer Group Acute Lymphoblastic Leukemia 2015 study protocol

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Competing jurisdictions: data privacy across the borders

Borderless cloud computing technologies are exacerbating tensions between European and other existing approaches to data privacy. On the one hand, in the European Union (EU), a series of data localisation initiatives are emerging with the objective of preserving Europe’s digital sovereignty, guaranteeing the respect of EU fundamental rights and preventing foreign law enforcement and intelligence agencies from accessing personal data. On the other hand, foreign countries are unilaterally adopting legislation requiring national corporations to disclose data stored in Europe, in this way bypassing jurisdictional boundaries grounded on physical data location. The chapter investigates this twofold dynamics by focusing particularly on the current friction between the EU data protection approach and the data privacy model of the United States (US) in the field of cloud computing

Proteomic Analysis of the Cyst Stage of Entamoeba histolytica

We used tandem mass spectrometry to identify E. histolytica cyst proteins in 5 cyst positive stool samples. We report the identification of 417 non-redundant E. histolytica proteins including 195 proteins that were not identified in existing trophozoite derived proteome or EST datasets, consistent with cyst specificity. Because the cysts were derived directly from patient samples with incomplete purification, a limited number of proteins were identified (N = 417) that probably represent only a partial proteome. Nevertheless, the study succeeded in identifying proteins that are likely to be abundant in the cyst stage of the parasite. Several of these proteins may play roles in E. histolytica stage conversion or cyst function. Proteins identified in this study may be useful markers for diagnostic detection of E. histolytica cysts. Overall, the data generated in this study promises to aid the understanding of the cyst stage of the parasite which is vital for disease transmission and pathogenesis in E. histolytica