Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods

Previous studies have indicated that the conventional tests used for the identification of mycobacteria may (i) frequently result in erroneous identification and (ii) underestimate the diversity within the genus Mycobacterium. To address this issue in a more systematic fashion, a study comparing phenotypic and molecular methods for the identification of mycobacteria was initiated. Focus was given to isolates which were difficult to identify to species level and which yielded inconclusive results by conventional tests performed under day-to-day routine laboratory conditions. Traditional methods included growth rate, colonial morphology, pigmentation, biochemical profiles, and gas-liquid chromatography of short-chain fatty acids. Molecular identification was done by PCR-mediated partial sequence analysis of the gene encoding the 16S rRNA. A total of 34 isolates was included in this study; 13 of the isolates corresponded to established species, and 21 isolates corresponded to previously uncharacterized taxa. For five isolates, phenotypic and molecular analyses gave identical results. For five isolates, minor discrepancies were present; four isolates remained unidentified after biochemical testing. For 20 isolates, major discrepancies between traditional and molecular typing methods were observed. Retrospective analysis of the data revealed that the discrepant results were without exception due to erroneous biochemical test results or interpretations. In particular, phenotypic identification schemes were compromised with regard to the recognition of previously undescribed taxa. We conclude that molecular typing by 16S rRNA sequence determination is not only more rapid (12 to 36 h versus 4 to 8 weeks) but also more accurate than traditional typing.     

Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family

Bovine acyl-coenzyme A binding protein is a four-helix bundle protein belonging to a group of homologous eukaryote proteins that binds medium and long-chain acyl-coenzyme A esters with a very high affinity. The three-dimensional structure of both the free and the ligated protein together with the folding kinetics have been described in detail for the bovine protein and with four new sequences reported here, a total of 16 closely related sequences ranging from yeasts and plants to human are known. The kinetics of folding and unfolding in different concentrations of guanidine hydrochloride together with equilibrium unfolding have been measured for bovine, rat and yeast acyl-coenzyme A binding protein. The bovine and rat sequences are closely related whereas the yeast is more distantly related to these. In addition to the three natural variants, kinetics of a bovine mutant protein, Tyr31 --> Asn, have been studied. Both the folding and unfolding rates in water of the yeast protein are 15 times faster than those of bovine. The folding rates in water of the two mammalian forms, rat and bovine, are similar, though still significantly different. A faster unfolding rate both for rat and the bovine mutant protein results from a lower stability of the native states of these. These hydrophobic regions, mini cores, have been identified in the three-dimensional structure of the bovine protein and found to be formed primarily by residues that have been conserved throughout the entire eukaryote evolution from yeasts to both plants and mammals as seen in the sample of 16 sequences. The conserved residues are found to stabilize helix-helix interactions and serve specific functional purposes for ligand binding. The fast one-step folding mechanism of ACBP has been shown to be a feature that seems to be maintained throughout evolution despite numerous differences in sequence and even dramatic differences in folding kinetics and protein stability. The protein study raises the question to what extent does the conserved hydrophobic residues provide a scaffold for an efficient one-step folding mechanism.     

基于矩阵分解双线性池化的多模态融合虚假新闻检测

现有的大多数虚假新闻检测方法将视觉和文本特征串联拼接,导致模态信息冗余并且忽略了不同模态信息之间的相关性。为了解决上述问题,提出一种基于矩阵分解双线性池化的多模态融合虚假新闻检测算法。首先,该算法将多模态特征提取器捕捉的文本和视觉特征利用矩阵分解双线性池化方法进行有效融合,然后与虚假新闻检测器合作鉴别虚假新闻;此外,在训练阶段加入了事件分类器来预测事件标签并去除事件相关的依赖。在Twitter和微博两个多模态谣言数据集上进行了对比实验,证明了该算法的有效性。实验结果表明提出的模型能够有效地融合多模态数据,缩小模态间的异质性差异,从而提高虚假新闻检测的准确性。     

An evaluation of web-based voting usability and accessibility

Several countries are considering web-based voting as an alternative to, or a replacement of, traditional voting methods. It is argued that electronic voting could increase voter participation and help strengthen democracy, as e-voting would increase accessibility for large sections of the population, particularly with regard to groups that previously have experienced difficulties with the traditional voting setup. With a focus on usability and accessibility, this paper reports on a study evaluating several electronic voting prototypes in Norway, involving technical aspects as well as expert evaluation and user testing in the field, with users from a wide range of disabled user groups participating in the study. Technical testing regarding accessibility standard compliance, testing with the personas method and user testing revealed that many rather basic universal design principles were either not fully understood or not prioritized for implementation by the solution providers. However, despite various accessibility difficulties, the participants generally showed a positive attitude towards web-based elections. Through the findings of this study, the authors highlight factors that are important to consider in the development and testing of web-based voting systems.     

A propositional probabilistic logic with discrete linear time for reasoning about evidence

The aim of the paper is to present a sound, strongly complete and decidable probabilistic temporal logic that can model reasoning about evidence. The formal system developed here is actually a solution of a problem proposed by Halpern and Pucella (J Artif Intell Res 26:1–34, 2006).     

Using column generation to solve parallel machine scheduling problems with minmax objective functions

In this paper we consider the parallel machine scheduling problem of minimizing an objective function of the minmax type, like maximum lateness, subject to release dates, deadlines, and/or generalized precedence constraints. We use a destructive strategy to compute a lower bound. Here we test the feasibility of a decision problem by applying column generation to compute a bound on the number of machines that we need to feasibly accommodate all jobs. After having derived the lower bound, we try to find a matching upper bound by identifying a feasible schedule with objective function value equal to this lower bound. Our computational results show that our lower bound is so strong that this is almost always possible. We are able to solve problems with up to 160 jobs and 10 machines in 10 minutes on average.     

A dynamic-programming-based exact algorithm for general single-machine scheduling with machine idle time

This paper proposes an efficient exact algorithm for the general single-machine scheduling problem where machine idle time is permitted. The algorithm is an extension of the authors’ previous algorithm for the problem without machine idle time, which is based on the SSDP (Successive Sublimation Dynamic Programming) method. We first extend our previous algorithm to the problem with machine idle time and next propose several improvements. Then, the proposed algorithm is applied to four types of single-machine scheduling problems: the total weighted earliness-tardiness problem with equal (zero) release dates, that with distinct release dates, the total weighted completion time problem with distinct release dates, and the total weighted tardiness problem with distinct release dates. Computational experiments demonstrate that our algorithm outperforms existing exact algorithms and can solve instances of the first three problems with up to 200 jobs and those of the last problem with up to 80 jobs.