A Heuristic Algorithm for Multiple Sequence Alignment Based on Blocks

Blocked multiple sequence alignment refers to the construction of multiple alignment by first aligning conserved regions into what we call blocks and then aligning the regions between successive blocks to form a final alignment. Instead of starting from low order pairwise alignments we propose a new way to form blocks by searching for closely related regions in all input sequences, allowing internal spaces in blocks as well as some degree of mismatch. We address the problem of semi-conserved patterns (patterns that do not appear in all input sequences) by introducing into the process two similarity thresholds that are adjusted dynamically according to the input. A method to control the number of blocks is also presented to deal with the situation when input sequences have so many similar regions that it becomes impractical to form blocks by trying every combination. BMA is an implementation of this approach, and our experimental results indicatethat this approach is efficient, particularly on large numbers of long sequences with well-conserved regions.     

Overlapping subsampling and invariance to initial conditions

This article studies the use of the overlapping blocking scheme in unit root autoregression. When the underlying process is that of a random walk, the blocks’ initial conditions are not fixed, but are equal to the sum of all the previous observations’ error terms. When non overlapping subsamples are used, these initial conditions do not disappear asymptotically. In this article, we show that a simple way of overcoming this issue is to use overlapping blocks. By doing so, the effect of these initial conditions vanishes asymptotically. An application of these findings to jackknife estimators indicates that an estimator based on moving blocks is able to provide obvious reductions to the mean square error. Also results are shown to be robust to local-to-unity frameworks, when the autoregressive parameter is unknown.     

Efficiency of tests based on weighted rankings for randomized blocks when the alternatives have an a prior1 ordering

Salama and Quade (1981) proposed a family of nonparametric tests based on a method of weighted within-block rankings, for testing the hypothesis of no treatment effects against a postulated ranking of the treatments in a complete randomized blocks layout.

These tests and others are compared with respect to asymptotic efficiency.     

Analysis of multiple sets of incomplete rankings

The L statistic is extended to allow incomplete or partial rankings within groups. As a special case of these extensions, tests for ofered alternatives analogous to the page test are provided for other than complete rankings. A two group illustration is provided by an alternative analysis of the Bradley and Terry taste-testing experiment on pork-roasts.     

Matrix–geometric analysis of the discrete time Gi/G/1 system

In this paper, we show that the discrete GI/G/1 system can be analysed as a QBD process with infinite blocks. Most importantly, we show that Matrix–geometric method can be used for analyzing this general queue system including establishing its stability criterion and for obtaining the explicit stationary probability and the waiting time distributions. This also settles the unwritten myth that Matrix–geometric method is limited to cases with at least one Markov based characterizing parameter, i.e. either interarrival or service times, in the case of queueing systems.     

Universally Optimal Designs Balanced for Neighbor Effects

The performance of a treatment is affected by the treatments applied to its adjacent plots, especially in the experiments of agriculture, horticulture, forestry, serology and industry. Neighbor designs ensure that treatment comparisons are least affected by neighbor effects, therefore, this is a rich field of investigation. In this paper, criterion for construction of universally optimal neighbor balanced designs is discussed.     

劳动契约的历史追溯与概念界定

对劳动契约的历史追溯表明,劳动契约的产生既确立了劳动者从＂身份到契约＂转变的主体地位,又确立了政府对劳动者的＂从契约到身份＂倾斜保护的义务。因而劳动契约是一个包括劳动基准契约与劳动约定契约的契约体系,其主体涉及劳方、资方及政府三方主体,其内容包括在劳动契约的缔结、履行和终止过程中而发生的劳方与资方、劳方与政府、资方与政府的各种权利义务关系。     

论林则徐《玉环同知杨君丹山墓表》的价值及不足

林则徐撰《玉环同知杨君丹山墓表》一文内容详实,舛误不多,且非颂谀文字。不仅可以补史志之阙,订史志之误,更为重要的是对研究杨国翰生平事迹、杨国翰与林则徐的交往等问题,具有重要的历史价值。     

Valid Resampling of Higher-Order Statistics Using the Linear Process Bootstrap and Autoregressive Sieve Bootstrap

We show that the linear process bootstrap (LPB) and the autoregressive sieve bootstrap (AR sieve) are, in general, not valid for statistics whose large-sample distribution depends on moments of order higher than two, irrespective of whether the data come from a linear time series or not. Inspired by the block-of-blocks bootstrap, we circumvent this non-validity by applying the LPB and AR sieve to suitably blocked data and not to the original data itself. In a simulation study, we compare the LPB, AR sieve, and moving block bootstrap applied directly and to blocked data.     

Non binary partially neighbor balanced designs for circular blocks

ABSTRACT

Neighbor designs are recommended for the cases where the performance of treatment is affected by the neighboring treatments as in biometrics and agriculture. In this paper we have constructed two new series of non binary partially neighbor balanced designs for v = 2n and v = 2n+1 number of treatments, respectively. The blocks in the design are non binary and circular but no treatment is ever a neighbor to itself. The designs proposed here are partially balanced in terms of nearest neighbors. No such series are known in the literature.