Alignment Search Research Articles

Faraday tomography of LoTSS-DR2 data. II. Multi-tracer analysis in the high-latitude outer Galaxy

We conducted a follow-up study on the analysis of the LOw Frequency ARray (LOFAR) Two-metre Sky Survey (LoTSS) mosaic in the high-latitude outer Galaxy presented in the first paper of this series. Here, we focus on the search for alignment between the magnetic field traced by dust, HI filaments, starlight optical linear polarisation, and linear depolarised structures (depolarisation canals) observed in low-frequency synchrotron polarisation. This alignment was previously found in several smaller fields observed with LOFAR, offering valuable insights into the nature of the interstellar medium and the 3D spatial distribution of the diffuse ionised medium. We aim to determine whether the alignment of the interstellar medium (ISM) phases observed through multiple tracers is a common occurrence or an exception. Additionally, in areas where depolarisation canals align with the magnetic field, we use starlight polarisation to constrain the distance to the structures associated with the observed canals. We employed the Rolling Hough Transform (RHT) and projected Rayleigh statistics (PRS) to identify and quantify the alignment between the different tracers. We used these tools to detect linear features in the data and quantify the significance of the orientation trends between pairs of tracers. On the scale of the whole mosaic, we did not find any evidence of a universal alignment among the three tracers. However, in one particular area, the western region (Dec between $29^ and $70^ and RA between $7 ^h ^m $ and $9 ^h ^m $), we do find a significant alignment between the magnetic field, depolarisation canals, and HI filaments. Based on this alignment, we used the starlight polarisation of stars with known parallax distances to estimate that the minimum distance to the structures observed by LOFAR in this region lies within the range of 200 to 240 pc. We associate these structures with the edge of the Local Bubble.

How did corporate responses to the Covid‐19 pandemic correspond with CSR?

AbstractThis editorial of the special issue addresses the question of whether/how responses to the Covid‐19 pandemic corresponded with authentic CSR. The literature on CSR has tended to endorse a business‐centric perspective and its inherent focus on the search for alignments between CSR activities and the economic/financial interests of the firm. The Covid‐19 pandemic has put this perspective to the test, pushing many companies to engage in distinctively more genuine and authentic CSR and/or demonstrating the importance of prior CSR engagement in facilitating crisis management. The papers included in the special issue appear to converge on the idea that firms combining evidence of both pre‐crisis engagement in CSR and strong CSR performance during the crisis (demonstrated through the deployment of various CSR assets and resources, including certified reporting, social marketing, individual engagement, resilience, legitimacy, trust) have coped better. This provides interested researchers with an opportunity to appreciate the value of CSR during a crisis.

CEOs’ search for alignment: the impact of strategic orientations on an extended adoption of Software-as-a-Service in SMEs

ABSTRACT As a recent technological innovation of great relevance to SMEs, this study focuses on the adoption of Software-as-a-Service (SaaS). We develop an extended SaaS adoption model that includes strategic orientations as antecedents of the key adoption drivers. Drawing on arguments from strategic IT alignment, we propose that CEOs’ extended SaaS adoption intention is determined by how much the perceived beliefs about SaaS fit the implemented strategic orientation. Our rationale is that CEOs play the dominant role in establishing alignment in SMEs as they make decisions about strategy and IT. We provide first evidence on the influence of CEOs’ strategic orientations on extended SaaS adoption.

Proposta para o alinhamento entre o plano estratégico institucional de um laboratório farmacêutico oficial e o departamento de ti

As organizações, quer sejam públicas ou privadas, necessitam de estratégias bem definidas para seus negócios, bem como um plano de gestão de seus recursos. Para o setor farmacêutico, não é diferente, haja vista que se trata de um setor que movimenta US$ 1,3 trilhões anualmente Quintiles and IMS Health, Inc. [IQVIA] (2019). Os Laboratórios Farmacêuticos Oficias (LFO) entram nesse contexto, com maior responsabilidade, pois gerenciam recursos públicos como devolutiva à Sociedade de medicamentos negligenciados pelas empresas farmacêuticas privadas. Contudo, a estratégia também deve estar alinhada com os demais setores da corporação, já que é sabido que falta de alinhamento estratégico em empresas acaba fazendo com que muitos recursos humanos e financeiros sejam empregados em projetos e iniciativas não tão relevantes para o negócio. Nesse sentido, a Tecnologia da Informação (TI) deve estar não só nas corporações, como também alinhada ao negócio de fato. Na busca pelo alinhamento entre a área de TI e o núcleo do negócio de um LFO, este trabalho pretende propor um modelo de alinhamento estratégico, tomando por base pontos dos modelos de Broadbeck e Hoppen (2003) e Kearns e Sabherwal (2006) estruturados sob a ideia trazida pelo modelo sistemático de Moreira (2002). Como resultado, uma sistemática para o alinhamento foi montada, assim como aplicada de maneira parcial no LFO em questão. O presente trabalho, portanto, além de contribuir diretamente para a estratégia organizacional do LFO, também contribui socialmente para todas as demais empresas ou setores públicos que desejarem aplicar o método para otimizar seus processos e práticas gerenciais e estratégicas.

Computation of alignments of business processes through relaxation labeling and local optimal search

A fundamental problem in conformance checking is aligning event data with process models. Unfortunately, existing techniques for this task are either complex, or can only be applicable to restricted classes of models. This in practice means that for large inputs, current techniques often fail to produce a result. In this paper we propose a method to compute alignments for unconstrained process models, which relies on the use of relaxation labeling techniques on top of a partial order representation of the process model. The technique proposed in this paper precomputes information used in the search for alignments, and is able to produce real alignments that may be close to optimal ones by combining the aforementioned techniques with a locally applied A∗ strategy. Remarkably, the implementation on the proposed technique achieves a speed-up of several orders of magnitude with respect to the approaches in the literature (either optimal, sup-optimal or approximate), often with a reasonable trade-off on the cost of the obtained alignment.

Molecular Autograph of Maturase-K Gene in Isodon rugosus (Lamiaceae)

AbstractMolecular autograph of trn/mat-K gene was used as one of the important candidate marker in addressing the questions of systematics and barcoding of medicinal plants. Features of trn/mat-K gene in Isodon rugosus (Lamiaceae) were assessed for the first time (NCBI GenBank Accession Number: MH939199.1). Sequence of 756 bp length was amplified by the universal matK primers (matK472F and matK1248R) in the cpDNA of the plant. It was reported to contain trnK gene (>1…..50; >746…..756), partial sequence; and matK gene (>51…..745), partial coding DNA sequence. Alignment search and analysis showed that only nine different Isodon species are currently available for matK sequences with repeated copy of submissions in GenBank. The matK sequences of I. rugosus was reported with 34.2 (G + C)% and 17 variable sites (VS), out of which seven were singleton (ST) and 10 sites were species-specific parsimoniously-informative (PI) that could be used to differentiate I. rugosus from other species as well as to authenticate the taxon. Phylogenetic analysis resulted into monophyletic clustering of I. rugosus near to the clade having I. coetsa by both maximum likelihood (ML) and maximum parsimony (MP) methods. Clades obtained in ML tree were more informative as compared to MP tree.

Non-target and suspected-target screening for potentially hazardous chemicals in food contact materials: investigation of paper straws

ABSTRACTA non-target screening strategy was developed for the safety evaluation of potentially hazardous chemicals in paper food contact materials (FCMs). A tentative list of suspect analytes was generated using publicly available FCM substance inventories, the presence of contaminants in paper straws was confirmed by high-resolution Orbitrap mass spectrometry. Data-independent and data-dependent MS and MS/MS results for candidate compounds were processed using a workflow including peak detection by deconvolution, blank subtraction, retention time alignment, formula assignment and fragmentation spectra search against spectral libraries followed by in silico generated spectra annotation. This workflow allowed for the identification of 74 suspect compounds, of which 40 were assigned a high confidence level of detection. A tentative in silico toxicity evaluation for mutagenic and carcinogenic activities was carried out. Using quantitative structure–activity relationship (QSAR) models it was found that two of the detected compounds tested positive for mutagenicity and three for carcinogenicity.

Fluctuating Saudi and Emirati Alignment Behaviours in the Horn of Africa

ABSTRACT The overthrow of Omar al-Bashir after three decades of rule has brought to light a dynamic that has been present for years: an interweaving of political, economic and security issues between the states of the Horn of Africa and the Gulf monarchies. Since 2011, the most active powers are the Kingdom of Saudi Arabia and the United Arab Emirates, which seek political support to counter both Iran’s influence and the growing Turkish presence. The two Gulf monarchies’ search for alignments with African counterparts has favoured the continuous reshuffling of alliances with direct effects on the local actors’ strategic choices. These dynamics need to be considered to understand the determinants behind the currently increasing instability in the Red Sea area.

Sustainable Development Goals and University Social Responsibility

The organizations seek strategic positioning directing the socioeconomic behavior, in the search for alignment with the stakeholders, considering the high degrees of competitiveness of the market. The demands of business in the demands, especially regarding the social and sustainable development of Brazil at the municipal, state, or federal level, form a scenario in which sustainable practices started to be implemented in the projects of an increasing number of companies. This study aimed to describe the Sustainable Development Objectives (ODS) that attends a Higher Education Institution that has been awarded Stamps of the Social Seal Program in the municipality of Itajaí/Brazil/SC. The research was descriptive, based on the report issued by the Secretariat for Institutional and Thematic Relations (SERIT) of the companies participating in the Social Program based on the UN model (2015), which highlights the ten sustainable development objectives. For the processing of the collected data, descriptive statistical techniques were applied. The results showed that the most present objectives in the institution analyzed were Partnership and Means of Implementation (ODS 17), Education and Quality (ODS 4), and Health and Welfare (ODS 3).

COMPETITIVE PRIORITIES AND STRATEGIC ALIGNMENT AS MEDIATORS IN THE RELATIONSHIP BETWEEN COMPANIES IN THE BRAZILIAN AUTOMOTIVE SUPPLY CHAIN

This study aimed to assess how the search for strategic alignment and competitive priorities influences the relationship between companies in the Brazilian automotive supply chain. To achieve this, qualitative research was conducted using an integrated case study in the automotive segment of companies that had business relationships with each other. The following elements were studied: an automaker, three automotive systems suppliers, and three second-tier suppliers. The results show that there is a strategic alignment in the chain, mainly driven by the automaker and the systems suppliers, and that competitive priorities shape the forms of the relationships between companies in the automotive supply chain.

At the Interface between Personal Motives, Organizational Purpose and Societal Development

The search for sustainable alignments between economic, environmental and social goals at the personal, organizational and societal level has been a key task of scholars from different disciplines....

Sequence Alignment and Homology Search.

Bioinformatics was brought into the spotlight in the late 1990s through the Human Genome Project. With the rapid accumulation of completed genomes, it was soon realized that for the vast majority of the newly identified genes and other functional regions of the genomes there were no other biological data. One way of inferring biological function is through homology: Because homologous genes have a common evolutionary descent, they are likely to have the same biological function. A large number of bioinformatics tools have been designed for rapidly and accurately comparing sequences of genes or proteins, comparing gene sequences with genomes, and comparing genomes. Two widely used tools for sequence alignment and homology searches, BLAST and ClustalW, are introduced here.

Entrepreneurial Philanthropy Meet with Non-Profits - In Search for Alignment

Entrepreneurial philanthropy is becoming more significant in the domain of social change, yet an understanding of how non-profit organisations respond to the phenomenon, and vice versa, has received minimal academic research outside the United States. However, charitable giving with a venture bent may be an uncomfortable realm and can impose a culture shock for non-profits. Also the organisational processes of non-profits can be equally as uncomfortable for entrepreneurs, which may cause potential frictions. The paper seeks theoretical considerations to determine a framework that describes the alignment paradigm, in the situation entrepreneurial philanthropy will meet up with non-profit organisations. The primary focus is to select valid domains where compelling choices for both are foreseen, along with the qualifying variables to guide the meeting process effectively. The paper proposes a conceptual approach of alignment that may offer observations for enhancing the concept of entrepreneurial philanthropy.

Noncoding RNA alignment and homology search using extended RNA secondary structure

Noncoding RNA alignment and homology search using extended RNA secondary structure

ApicoAlign: an alignment and sequence search tool for apicomplexan proteins

BackgroundOver the recent years, a number of genomes have been successfully sequenced and this was followed by genome annotation projects to help understand the biological capabilities of newly sequenced genomes. To improve the annotation of Plasmodium falciparum proteins, we earlier developed parasite specific matrices (PfSSM) and demonstrated their (Smat80 and PfFSmat60) better performance over standard matrices (BLOSUM and PAM). Here we extend that study to nine apicomplexan species other than P. falciparum and develop a web application ApicoAlign for improving the annotation of apicomplexan proteins.ResultsThe SMAT80 and PfFSmat60 matrices perform better for apicomplexan proteins compared to BLOSUM in detecting the orthologs and improving the alignment of these proteins with their potential orthologs respectively. Database searches against non-redundant (nr) database have shown that SMAT80 gives superior performance compared to BLOSUM series in terms of E-values, bit scores, percent identity, alignment length and mismatches for most of the apicomplexan proteins studied here. Using these matrices, we were able to find orthologs for rhomboid proteases of P. berghei, P. falciparum &P. vivax and large subunit of U2 snRNP auxiliary factor of Cryptosporidium parvum in Arabidopsis thaliana. We also show improved pairwise alignments of proteins from Apicomplexa viz. Cryptosporidium parvum and P. falciparum with their orthologs from other species using the PfFSmat60 matrix.ConclusionsThe SMAT80 and PfFSmat60 substitution matrices perform better for apicomplexan proteins compared to BLOSUM series. Since they can be helpful in improving the annotation of apicomplexan genomes and their functional characterization, we have developed a web server ApicoAlign for finding orthologs and aligning apicomplexan proteins.

A method for aligning RNA secondary structures and its application to RNA motif detection

BackgroundAlignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases.ResultsWe present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for single-stranded regions and the other for double-stranded regions. The time complexity of RSmatch is O(mn) where m is the size of the query structure and n that of the subject structure. When applied to searching a structure database, RSmatch can find similar RNA substructures, and is capable of conducting multiple structure alignment and iterative database search. Therefore it can be used to identify functional RNA motifs. The accuracy of RSmatch is tested by experiments using a number of known RNA structures, including simple stem-loops and complex structures containing junctions.ConclusionWith respect to computing efficiency and accuracy, RSmatch compares favorably with other tools for RNA structure alignment and motif detection. This tool shall be useful to researchers interested in comparing RNA structures obtained from wet lab experiments or RNA folding programs, particularly when the size of the structure dataset is large.

Theory and practice of parallel direct optimization.

Our ability to collect and distribute genomic and other biological data is growing at a staggering rate (Pagel, 1999). However, the synthesis of these data into knowledge of evolution is incomplete. Phylogenetic systematics provides a unifying intellectual approach to understanding evolution but presents formidable computational challenges. A fundamental goal of systematics, the generation of evolutionary trees, is typically approached as two distinct NP-complete problems: multiple sequence alignment and phylogenetic tree search. The number of cells in a multiple alignment matrix are exponentially related to sequence length. In addition, the number of evolutionary trees expands combinatorially with respect to the number of organisms or sequences to be examined. Biologically interesting datasets are currently comprised of hundreds of taxa and thousands of nucleotides and morphological characters. This standard will continue to grow with the advent of highly automated sequencing and development of character databases. Three areas of innovation are changing how evolutionary computation can be addressed: (1) novel concepts for determination of sequence homology, (2) heuristics and shortcuts in tree-search algorithms, and (3) parallel computing. In this paper and the online software documentation we describe the basic usage of parallel direct optimization as implemented in the software POY (ftp://ftp.amnh.org/pub/molecular/poy).

Intelligent control of fibre optic components assembly

This paper presents an ‘intelligent’ automatic alignment system for use in the assembly of optical fibre components. The system optimizes the light output from a fibre by applying a gradient-based algorithm enhanced with momentum information. The algorithm parameters are adjusted on-line by a fuzzy controller according to the progress of the alignment process. Using past experience, a neuron-like element directs the starting point of the search for the optimum alignment towards the most favourable position. The automatic alignment system yielded 100 per cent success in a test involving 100 different samples of components. The system achieved significant reductions in alignment times compared with manual or conventional automatic methods. The system was also almost twice as fast as an alternative based on simulated annealing. Moreover, the use of fuzzy logic facilitated the design of the controller and provided noise rejection capabilities.

Markovian Structures in Biological Sequence Alignments

The alignment of multiple homologous biopolymer sequences is crucial in research on protein modeling and engineering, molecular evolution, and prediction in terms of both gene function and gene product structure. In this article we provide a coherent view of the two recent models used for multiple sequence alignment—the hidden Markov model (HMM) and the block-based motif model—to develop a set of new algorithms that have both the sensitivity of the block-based model and the flexibility of the HMM. In particular, we decompose the standard HMM into two components: the insertion component, which is captured by the so-called “propagation model,” and the deletion component, which is described by a deletion vector. Such a decomposition serves as a basis for rational compromise between biological specificity and model flexibility. Furthermore, we introduce a Bayesian model selection criterion that—in combination with the propagation model, genetic algorithm, and other computational aspects—forms the core of PROBE, a multiple alignment and database search methodology. The application of our method to a GTPase family of protein sequences yields an alignment that is confirmed by comparison with known tertiary structures.

Ligature modeling for online cursive script recognition

Online recognition of cursive words is a difficult task owing to variable shape and ambiguous letter boundaries. The approach proposed is based on hidden Markov modeling of letters and inter-letter patterns called ligatures occurring in cursive script. For each of the letters and the ligatures we create one HMM that models temporal and spatial variability of handwriting. By networking the two kinds of HMMs, we can design a network model for all words or composite characters. The network incorporates the knowledge sources of grammatical and structural constraints so that it can better capture the characteristics of handwriting. Given the network, the problem of recognition is formulated into that of finding the most likely path from the start node to the end node. A dynamic programming-based search for the optimal input-network alignment performs character recognition and letter segmentation simultaneously and efficiently. Experiments on Korean character showed correct recognition of up to 93.3% on unconstrained samples. It has also been compared with several other schemes of HMM-based recognition to characterize the proposed approach.