Higher-order CIS codes

We introduce {\bf complementary information set codes} of higher-order. A binary linear code of length $tk$ and dimension $k$ is called a complementary information set code of order $t$ ($t$-CIS code for short) if it has $t$ pairwise disjoint information sets. The duals of such codes permit to reduce the cost of masking cryptographic algorithms against side-channel attacks. As in the case of codes for error correction, given the length and the dimension of a $t$-CIS code, we look for the highest possible minimum distance. In this paper, this new class of codes is investigated. The existence of good long CIS codes of order $3$ is derived by a counting argument. General constructions based on cyclic and quasi-cyclic codes and on the building up construction are given. A formula similar to a mass formula is given. A classification of 3-CIS codes of length $\le 12$ is given. Nonlinear codes better than linear codes are derived by taking binary images of $\Z_4$-codes. A general algorithm based on Edmonds' basis packing algorithm from matroid theory is developed with the following property: given a binary linear code of rate $1/t$ it either provides $t$ disjoint information sets or proves that the code is not $t$-CIS. Using this algorithm, all optimal or best known $[tk, k]$ codes where $t=3, 4, \dots, 256$ and $1 \le k \le \lfloor 256/t \rfloor$ are shown to be $t$-CIS for all such $k$ and $t$, except for $t=3$ with $k=44$ and $t=4$ with $k=37$.Comment: 13 pages; 1 figur

A new class of codes for Boolean masking of cryptographic computations

We introduce a new class of rate one-half binary codes: {\bf complementary information set codes.} A binary linear code of length $2n$ and dimension $n$ is called a complementary information set code (CIS code for short) if it has two disjoint information sets. This class of codes contains self-dual codes as a subclass. It is connected to graph correlation immune Boolean functions of use in the security of hardware implementations of cryptographic primitives. Such codes permit to improve the cost of masking cryptographic algorithms against side channel attacks. In this paper we investigate this new class of codes: we give optimal or best known CIS codes of length $<132.$ We derive general constructions based on cyclic codes and on double circulant codes. We derive a Varshamov-Gilbert bound for long CIS codes, and show that they can all be classified in small lengths $\le 12$ by the building up construction. Some nonlinear permutations are constructed by using $\Z_4$-codes, based on the notion of dual distance of an unrestricted code.Comment: 19 pages. IEEE Trans. on Information Theory, to appea

Network Code Design for Orthogonal Two-hop Network with Broadcasting Relay: A Joint Source-Channel-Network Coding Approach

This paper addresses network code design for robust transmission of sources over an orthogonal two-hop wireless network with a broadcasting relay. The network consists of multiple sources and destinations in which each destination, benefiting the relay signal, intends to decode a subset of the sources. Two special instances of this network are orthogonal broadcast relay channel and the orthogonal multiple access relay channel. The focus is on complexity constrained scenarios, e.g., for wireless sensor networks, where channel coding is practically imperfect. Taking a source-channel and network coding approach, we design the network code (mapping) at the relay such that the average reconstruction distortion at the destinations is minimized. To this end, by decomposing the distortion into its components, an efficient design algorithm is proposed. The resulting network code is nonlinear and substantially outperforms the best performing linear network code. A motivating formulation of a family of structured nonlinear network codes is also presented. Numerical results and comparison with linear network coding at the relay and the corresponding distortion-power bound demonstrate the effectiveness of the proposed schemes and a promising research direction.Comment: 27 pages, 9 figures, Submited to IEEE Transaction on Communicatio

Coding limits on the number of transcription factors

Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms. We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction. The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/BMCGenomics2006.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590034/ http://www.biomedcentral.com/1471-2164/7/23

Labor Markets in CIS Countries

This work is done as contribution to the Regional Human Development Report 2004 section 3.7 on “Labor Markets”. The paper focuses on discussing peculiarities of the labor market transition in CIS countries, features of unemployment, labor legislation, and role of the trade unions. The paper gathers information on the labor markets of CIS and Eastern European countries that was available by summer 2004, and draws policy recommendations based on comparison between these two groups of countries. The main conclusion is that the transformation of labor markets is not complete in any of the CIS countries; most of the problems that prevailed in the early 1990s remain. These include: centralized wage setting in five CIS countries – Belarus, Moldova, Tajikistan, Turkmenistan, and Uzbekistan; extensive unemployment and underemployment, much of which is hidden; ineffective systems of labor relations and social protection; large mismatches between the labor market skills supplied and the skills demanded by new market economies; inadequate official labor market data. Fortunately, the strong economic growth experienced by most CIS countries since 1999 has increased the demand for labor and is putting downward pressures on unemployment rates. This offers a window of opportunity for policy makers seeking to further transform labor markets, and to modernize labor relations and social protection systems. The above analysis suggests the policy recommendations to speed up further transformation.Labor markets of CIS (FSU) countries, labor market transition, unemployment, labor unions, labor protection, labor migration, labor law and labor market institutions, labor market policy in transition countries

A person-time analysis of hospital activity among cancer survivors in England.

BACKGROUND: There are around 2 million cancer survivors in the UK. This study describes the inpatient and day case hospital activity among the population of cancer survivors in England. This is one measure of the burden of cancer on the individual and the health service. METHODS: The national cancer registry data set for England (1990-2006) is linked to the NHS Hospital Episode Statistics (HES) database. Cohorts of survivors were defined as those people recorded in the cancer registry data with a diagnosis of breast, colorectal, lung or prostate cancer before 2007. The person-time of prevalence in 2006 for each cohort of survivors was calculated according to the cancer type, sex, age and time since diagnosis. The corresponding HES episodes of care in 2006 were used to calculate the person-time of admitted hospital care for each cohort of survivors. The average proportion of time spent in hospital by survivors in each cohort was calculated as the summed person-time of hospital activity divided by the summed person-time of prevalence. The analysis was conducted separately for cancer-related episodes and non-cancer-related episodes. RESULTS: Lung cancer survivors had the highest intensity of cancer-related hospital activity. For all cancers, cancer-related hospital activity was highest in the first year following diagnosis. Breast and prostate cancer survivors had peaks of cancer-related hospital activity in the relatively young and relatively old age groups. The proportion of time spent in hospital for non-cancer-related care was much lower than that for cancer-related care and increased gradually with age but was generally constant regardless of time since diagnosis. CONCLUSION: The person-time approach used in this study is more revealing than a simple enumeration of cancer survivors and hospital admissions. Hospital activity among cancer survivors is highest soon after diagnosis. The effect of age on the amount of hospital activity is different for each type of cancer

Oncogenic RET Kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans

To decipher the molecular basis for RET kinase activation and oncogenic deregulation, we defined the temporal sequence of RET autophosphorylation by label-free quantitative mass spectrometry. Early autophosphorylation sites map to regions flanking the kinase domain core, while sites within the activation loop only form at later time points. Comparison with oncogenic RET kinase revealed that late autophosphorylation sites become phosphorylated much earlier than wild-type RET, which is due to a combination of an enhanced enzymatic activity, increased ATP affinity, and surprisingly, by providing a better intermolecular substrate. Structural analysis of oncogenic M918T and wild-type RET kinase domains reveal a cis-inhibitory mechanism involving tethering contacts between the glycine-rich loop, activation loop, and αC-helix. Tether mutations only affected substrate presentation but perturbed the autophosphorylation trajectory similar to oncogenic mutations. This study reveals an unappreciated role for oncogenic RET kinase mutations in promoting intermolecular autophosphorylation by enhancing substrate presentation

Core promoter short tandem repeats as evolutionary switch codes for primate speciation

Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level. © 2014 Wiley Periodicals, Inc