Spiders spin multiple types of silks that are renowned for their superb mechanical properties. Flagelliform silk, used in the capture spiral of an orb‐web, is one of the few silks characterized by both cDNA and genomic DNA data. This fibroin is composed of repeating ensembles of three types of amino acid sequence motifs. The predominant subrepeat, GPGGX, likely forms a β‐turn, and tandem arrays of these turns are thought to create β‐spirals. These spring‐like helices may be critical for the (...) exceptional ability of capture silk to stretch and recoil. Each ensemble of motifs was found to correspond to a different exon within the flagelliform gene. The pattern of sequence similarity among exons indicates intragenic concerted evolution. Surprisingly, the introns between the iterated exons are also homogenized with each other. This unusual molecular architecture in the flagelliform silk gene has implications for the evolution and maintenance of spider silk proteins. BioEssays 23:750–756, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s). Three-dimensional structural data have shown that a TPR motif contains two antiparallel α-helices such that tandem arrays of TPR motifs generate a right-handed helical structure with an amphipathic channel that might accommodate the complementary region of a target protein. Most TPR-containing proteins are associated (...) with multiprotein complexes, and there is extensive evidence indicating that TPR motifs are important to the functioning of chaperone, cell-cycle, transcription, and protein transport complexes. The TPR motif may represent an ancient protein-protein interaction module that has been recruited by different proteins and adapted for specific functions. BioEssays 1999;21:932–939. © 1999 John Wiley & Sons, Inc. (shrink)

This article responds to two problems confronting social and human sciences: how to relate to digital data, inasmuch as it challenges established social science methods; and how to relate to life sciences, insofar as they produce knowledge that impinges on our own ways of knowing. In a case study of proteomics, we explore how digital devices grapple with large-scale multiples – of molecules, databases, machines and people. We analyse one particular visual device, a cluster-heatmap, produced by scientists by mining (...) data from a large number of experiments on human blood plasma proteins. These proteins make up a myriad multiple whose identity shifts in many ways. Rather than displaying data about proteins, the heatmap constructs a view of the differences and similarities between experiments. We find this attempt to construct a view on many things at once instructive in thinking about multiples more generally. Instead of flattening molecular ‘life itself’, this visual device superimposes layers of digital devices and techniques from a wide variety of disciplines. This layering suggests a different way of relating to the life sciences more generally: rather than what they know, how they know might be of use to social and human sciences when attending to multiplicities. (shrink)

How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain‐containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context‐ and cell‐specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC (...) class proteins, also evolutionary conserved HD‐containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox‐PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity. (shrink)

Biomedical Ontologies integrate diverse biomedical data and enable intelligent data-mining and help translate basic research into useful clinical knowledge. We present the RNA Ontology (RNAO), an o...

Membership in a protein domain database does not a domain make; a feature we realized when generating a consensus view of protein fold space with our consensus domain dictionary (CDD). This dictionary was used to select representative structures for characterization of the protein dynameome: the Dynameomics initiative. Through this endeavor we rejected a surprising 40% of the 1,695 folds in the CDD as being non‐autonomous folding units. Although some of this was due to the challenges of grouping (...) similar fold topologies, the dissonance between the cataloguing and structural qualification of protein domains remains surprising. Another potential factor is previously overlooked intrinsic disorder; predictions suggest that 40% of proteins have either local or global disorder. One thing is clear, filtering a structural database and ensuring a consistent definition for protein domains is crucial, and caution is prescribed when generalizations of globular domains are drawn from unfiltered protein domain datasets. (shrink)

Coronins constitute an evolutionarily conserved family of WD‐repeat actin‐binding proteins, which can be clearly classified into two distinct groups based on their structural features. All coronins possess a conserved basic N‐terminal motif and three to ten WD repeats clustered in one or two core domains. Dictyostelium and mammalian coronins are important regulators of the actin cytoskeleton, while the fly Dpod1 and the yeast coronin proteins crosslink both actin and microtubules. Apart from that, several coronins have been shown to (...) be involved in vesicular transport. C. elegans POD‐1 and Drosophila coro regulate the actin cytoskeleton, but also govern vesicular trafficking as indicated by mutant phenotypes. In both organisms, defects in cytoskeleton and trafficking lead to severe developmental defects ranging from abnormal cell division to aberrant formation of morphogen gradients. Finally, mammalian coronin 7 appears not to execute any cytoskeleton‐related functions, but rather participates in regulating Golgi trafficking. Here, we review recent data providing more insight into molecular mechanisms underlying the regulation of F‐actin structures, cytoskeletal rearrangements and intracellular membrane transport by coronin proteins and the way that they might link cytoskeleton with trafficking in development and disease. BioEssays 27:625–632, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Divergent evolution can explain how many proteins containing structurally similar domains, which perform a variety of related functions, have evolved from a relatively small number of modules or protein domains. However, it cannot explain how protein domains with similar, but distinguishable, functions and similar, but distinguishable, structures have evolved. Examples of this are the RNA‐binding proteins containing the RNA‐binding domain (RBD), and a newly established protein group, the cold‐shock domain (CSD) protein family. Both protein domains (...) contain conserved RNP motifs on similar single‐stranded nucleic acid‐binding surfaces. Apart from the RNP motifs, which have a similar function, the two families show little similarity in topology or amino acid sequence. This can be considered an interesting example of convergent evolution at the molecular level. Previously, a β‐sheet surface was found to interact with RNA in non‐homologous proteins from yeast, phage and man, revealing that this mode of RNA binding may be a widely recurring theme. (shrink)

The Type VI secretion system is a multiprotein and mosaic apparatus that delivers protein effectors into prokaryotic or eukaryotic cells. Recent data on the enteroaggregative Escherichia coli T6SS have provided evidence that the TssA protein is a key component during T6SS biogenesis. The T6SS comprises a trans-envelope complex that docks the baseplate, a cytoplasmic complex that represents the assembly platform for the tail. The T6SS tail is structurally, evolutionarily and functionally similar to the contractile tails of bacteriophages. (...) We have shown that TssA docks to the membrane complex, recruits the baseplate complex and initiates and coordinates the polymerization of the inner tube with that of the sheath. Here, we review these recent findings, discuss the variations within TssA-like proteins, speculate on the role of EAEC TssA in T6SS biogenesis and propose future research perspectives. In the environment, bacteria have to cope with other microbial species and therefore have evolved anti-microbial mechanisms. The bacterial Type VI secretion system transports toxins into bacterial and/or eukaryotic cells using a contractile mechanism. At the architectural level, the T6SS could be viewed as a nano-speargun assembled in the bacterial cytoplasm and anchored to a trans-envelope complex. We describe and speculate on recent findings demonstrating that the TssA subunit is involved in the different stages of T6SS biogenesis. (shrink)

The topics approached in the 52 papers included in this book are: neutrosophic sets; neutrosophic logic; generalized neutrosophic set; neutrosophic rough set; multigranulation neutrosophic rough set (MNRS); neutrosophic cubic sets; triangular fuzzy neutrosophic sets (TFNSs); probabilistic single-valued (interval) neutrosophic hesitant fuzzy set; neutro-homomorphism; neutrosophic computation; quantum computation; neutrosophic association rule; data mining; big data; oracle Turing machines; recursive enumerability; oracle computation; interval number; dependent degree; possibility degree; power aggregation operators; multi-criteria group decision-making (MCGDM); expert set; soft sets; LA-semihypergroups; (...) single valued trapezoidal neutrosophic number; inclusion relation; Q-linguistic neutrosophic variable set; vector similarity measure; fundamental neutro-homomorphism theorem; neutro-isomorphism theorem; quasi neutrosophic triplet loop; quasi neutrosophic triplet group; BE-algebra; cloud model; Maclaurin symmetric mean; pseudo-BCI algebra; hesitant fuzzy set; photovoltaic plan; decision-making trial and evaluation laboratory (DEMATEL); Choquet integral; fuzzy measure; clustering algorithm; and many more. (shrink)

MutL family proteins contain an N‐terminal ATPase domain (NTD), an unstructured interdomain linker, and a C‐terminal domain (CTD), which mediates constitutive dimerization between subunits and often contains an endonuclease active site. Most MutL homologs direct strand‐specific DNA mismatch repair by cleaving the error‐containing daughter DNA strand. The strand cleavage reaction is poorly understood; however, the structure of the endonuclease active site is consistent with a two‐ or three‐metal ion cleavage mechanism. A motif required for this endonuclease activity is present (...) in the unstructured linker of Mlh1 and is conserved in all eukaryotic Mlh1 proteins, except those from metamonads, which also lack the almost absolutely conserved Mlh1 C‐terminal phenylalanine‐glutamate‐arginine‐cysteine (FERC) sequence. We hypothesize that the cysteine in the FERC sequence is autoinhibitory, as it sequesters the active site. We further hypothesize that the evolutionary co‐occurrence of the conserved linker motif with the FERC sequence indicates a functional interaction, possibly by linker motif‐mediated displacement of the inhibitory cysteine. This role is consistent with available data for interactions between the linker motif with DNA and the CTDs in the vicinity of the active site. (shrink)

The topics approached in this collection of papers are: neutrosophic sets; neutrosophic logic; generalized neutrosophic set; neutrosophic rough set; multigranulation neutrosophic rough set (MNRS); neutrosophic cubic sets; triangular fuzzy neutrosophic sets (TFNSs); probabilistic single-valued (interval) neutrosophic hesitant fuzzy set; neutro-homomorphism; neutrosophic computation; quantum computation; neutrosophic association rule; data mining; big data; oracle Turing machines; recursive enumerability; oracle computation; interval number; dependent degree; possibility degree; power aggregation operators; multi-criteria group decision-making (MCGDM); expert set; soft sets; LA-semihypergroups; single valued trapezoidal (...) neutrosophic number; inclusion relation; Q-linguistic neutrosophic variable set; vector similarity measure; fundamental neutro-homomorphism theorem; neutro-isomorphism theorem; quasi neutrosophic triplet loop; quasi neutrosophic triplet group; BE-algebra; cloud model; fuzzy measure; clustering algorithm; and many more. (shrink)

The TRIM/RBCC proteins are defined by the presence of the tripartite motif composed of a RING domain, one or two B‐box motifs and a coiled‐coil region. These proteins are involved in a plethora of cellular processes such as apoptosis, cell cycle regulation and viral response. Consistently, their alteration results in many diverse pathological conditions. The highly conserved modular structure of these proteins suggests that a common biochemical function may underlie their assorted cellular roles. Here, we review recent data (...) indicating that some TRIM/RBCC proteins are implicated in ubiquitination and propose that this large protein family represents a novel class of ‘single protein RING finger’ ubiquitin E3 ligases. BioEssays 27:1147–1157, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

It has been widely theorized and empirically proven that self-regulated learning (SRL) is related to more desired learning outcomes, e.g., higher performance in transfer tests. Research has shifted to understanding the role of SRL during learning, such as the strategies and learning activities, learners employ and engage in the different SRL phases, which contribute to learning achievement. From a methodological perspective, measuring SRL using think-aloud data has been shown to be more insightful than self-report surveys as it helps better (...) in determining the link between SRL activities and learning achievements. Educational process mining on the basis of think-aloud data enables a deeper understanding and more fine-grained analyses of SRL processes. Although students’ SRL is highly contextualized, there are consistent findings of the link between SRL activities and learning outcomes pointing to some consistency of the processes that support learning. However, past studies have utilized differing approaches which make generalization of findings between studies investigating the unfolding of SRL processes during learning a challenge. In the present study with 29 university students, we measured SRLviaconcurrent think-aloud protocols in a pre-post design using a similar approach from a previous study in an online learning environment during a 45-min learning session, where students learned about three topics and wrote an essay. Results revealed significant learning gain and replication of links between SRL activities and transfer performance, similar to past research. Additionally, temporal structures of successful and less successful students indicated meaningful differences associated with both theoretical assumptions and past research findings. In conclusion, extending prior research by exploring SRL patterns in an online learning setting provides insights to the replicability of previous findings from online learning settings and new findings show that it is important not only to focus on the repertoire of SRL strategies but also on how and when they are used. (shrink)

Intermediate filament (IF) protein tetramers contain two DNA‐ and core‐histone‐binding motifs in rotational symmetry in one and the same structural entity. We propose that IF protein oligomers might displace histone octamers from nucleosomes in the process of transcription initiation and elongation, to deposit them transiently on their α‐helical coiled‐coil domains. We further propose that structurally related proteins of the karyoskeleton, constructed from an α‐helical domain capable of coiled‐coil formation and a basic DNA‐binding region adjacent to it, may (...) be similarly involved in nucleosome activation. These proteins would function as auxiliary factors that disrupt nucleosomal structure to permit transcription and other DNA‐dependent processes to proceed expiditiously. (shrink)

With decades of research seeking to generalize sterile alpha motif (SAM) biology, many outstanding questions remain regarding this multi‐tool protein module. Recent data from structural and molecular/cell biology has begun to reveal new SAM modes of action in cell signaling cascades and biomolecular condensation. SAM‐dependent mechanisms underlie blood‐related (hematologic) diseases, including myelodysplastic syndromes and leukemias, prompting our focus on hematopoiesis for this review. With the increasing coverage of SAM‐dependent interactomes, a hypothesis emerges that SAM interaction partners (...) and binding affinities work to fine tune cell signaling cascades in developmental and disease contexts, including hematopoiesis and hematologic disease. This review discusses what is known and remains unknown about the standard mechanisms and neoplastic properties of SAM domains and what the future might hold for developing SAM‐targeted therapies. (shrink)

In this paper, I investigate the phonological similarity of different elements of the phonological pole of multi-word units. I discuss two case studies on slightly different levels of abstractness. The first case study investigates lexically fully-specified V-NPDirObj idioms such as kick the bucket and lose one's cool; the idioms investigated are taken from the Collins Cobuild Dictionary of Idioms (Harper Collins, 2002). The second case study investigates the lexically less specified way-construction, which is exemplified by He fought his way through (...) the crowd (cf. Goldberg, Constructions: A Construction Grammar approach to argument structure, The University of Chicago Press, 1995: Ch. 9), on the basis of data from the British National Corpus 1.0. I show that both patterns exhibit a strong phonological within-pole relation, namely a strong preference for having their slots filled with phonologically similar elements, where phonological similarity is manifested in alliteration patterns. These preferences are statistically significant when compared to chance-level expectations derived both from the corpora and from the CELEX database (Baayen et al., The CELEX Lexical Database (CD-ROM), University of Pennsylvania, 1995) and are explained on the basis of Langacker's concept of syntactic and phonological constituents as well as current exemplar-/usage-based approaches. (shrink)

R‐spondins (RSPOs) are a family of secreted proteins and stem cell growth factors that are potent co‐activators of Wnt signaling. Recently, RSPO2 and RSPO3 were shown to be multifunctional, not only amplifying Wnt‐ but also binding BMP‐ and FGF receptors to downregulate signaling. The common mechanism underlying these diverse functions is that RSPO2 and RSPO3 act as “endocytosers” that link transmembrane proteins to ZNRF3/RNF43 E3 ligases and trigger target internalization. Thus, RSPOs are natural protein targeting chimeras for cell surface (...) proteins. Conducting data mining and cell surface binding assays we report additional candidate RSPO targets, including SMO, PTC1,2, LGI1, ROBO4, and PTPR(F/S). We propose that there is an “R‐spondin code” that imparts combinatorial signaling ON‐OFF states of multiple growth factors. This code involves the modular RSPO domains, notably distinct motifs in the divergent RSPO‐TSP1 domains to mediate target interaction and internalization. The RSPO code offers a novel framework for the understanding how diverse signaling pathways may be coordinately regulated in development and disease. (shrink)

This paper introduces coupled clustering—a novel computational framework for detecting corresponding themes in unstructured data. Gaining its inspiration from the structure mapping theory, our framework utilizes unsupervised statistical learning tools for automatic construction of aligned representations reflecting the context of the particular mapping being made. The coupled clustering algorithm is demonstrated and evaluated through detecting conceptual correspondences in textual corpora. In its current phase, the method is primarily oriented towards context-dependent feature-based similarity. However, it is preliminary demonstrated how it (...) could be utilized for identification of relational commonalities, as well. (shrink)

Members of the CAR group of Ig‐like type I transmembrane proteins mediate homotypic cell adhesion, share a common overall extracellular domain structure and are closely related at the amino acid sequence level. CAR proteins are often found at tight junctions and interact with intracellular scaffolding proteins, suggesting that they might modulate tight junction assembly or function. However, impairment of tight junction integrity has not been reported in mouse knockout models or zebrafish mutants of CAR members. In contrast, in the same (...) knockout models deficits in gap junction communication were detected in several organ systems, including the atrioventricular node of the heart, smooth muscle cells of the intestine and the ureter and in Sertoli cells of the testes. Possible interactions between BT‐IgSF and connexin41.8 on the disturbed pattern of pigment stripes found in zebrafish mutants and between ESAM and connexin43 during hematopoiesis in the mouse are also discussed. On the basis of the combined data and phenotypic similarities between CAR member mutants and connexin mutants I hypothesize that they primarily play a role in the organization of gap junction communication. Also see the video abstract here: https://youtu.be/i0yq2KhuDAE. (shrink)

Web mining refers to the whole of data miningand related techniques that are used toautomatically discover and extract informationfrom web documents and services. When used in abusiness context and applied to some type ofpersonal data, it helps companies to builddetailed customer profiles, and gain marketingintelligence. Web mining does, however, pose athreat to some important ethical values likeprivacy and individuality. Web mining makes itdifficult for an individual to autonomouslycontrol the unveiling and dissemination of dataabout his/her private life. To study (...) thesethreats, we distinguish between `content andstructure mining' and `usage mining.' Webcontent and structure mining is a cause forconcern when data published on the web in acertain context is mined and combined withother data for use in a totally differentcontext. Web usage mining raises privacyconcerns when web users are traced, and theiractions are analysed without their knowledge.Furthermore, both types of web mining are oftenused to create customer files with a strongtendency of judging and treating people on thebasis of group characteristics instead of ontheir own individual characteristics and merits(referred to as de-individualisation). Althoughthere are a variety of solutions toprivacy-problems, none of these solutionsoffers sufficient protection. Only a combinedsolution package consisting of solutions at anindividual as well as a collective level cancontribute to release some of the tensionbetween the advantages and the disadvantages ofweb mining. The values of privacy andindividuality should be respected and protectedto make sure that people are judged and treatedfairly. People should be aware of theseriousness of the dangers and continuouslydiscuss these ethical issues. This should be ajoint responsibility shared by web miners (bothadopters and developers), web users, andgovernments. (shrink)

The statistics-based method ignores the semantic constraints in the English grammar area branch training model and is unable to identify the orientation information effectively. This paper systematically discusses the close relationship between English grammar area branch training model filtering, English grammar area branch training model retrieval, and machine learning. By analyzing the role of the situation in the understanding of the English grammar area branch training model, the relationship between the English grammar area branch training model and situation model and (...) the correlation between the features of the English grammar area branch training model and situation model are determined, and then, a set of filtering methods for the English grammar area branch training model are proposed. At present, there are few research studies on bias filtering, and the method of thematic filtering is generally used, which has poor effect. This paper makes full use of the domain knowledge and adopts the semantic pattern analysis technology to establish a wealth of semantic analysis resources, including various dictionaries, rules, and weight representation, so as to effectively filter the inclined English grammar area branch training model. The introduction of semantic data sources solves the problem of data sparsity and cold start in the traditional collaborative filtering system. In addition, in order to improve the scalability and real-time performance of the recommendation system, the data mining method is used to perform fuzzy clustering for users and projects in the offline data preprocessing stage. This paper proposes a search and filter scheme based on the orientation of the training model in English grammar area, elaborates on the details, constructs a whole set of function structure from representation to weight, and gives the experimental results, which prove that the system has a good filtering effect and is fast. Compared with the traditional statistical methods, the results are satisfactory. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

International large-scale assessments, such as PISA, provide structured and static data. However, due to its extensive databases, several researchers place it as a reference in Big Data in Education. With the goal of exploring which factors at country, school and student level have a higher relevance in predicting student performance, this paper proposes an Educational Data Mining approach to detect and analyze factors linked to academic performance. To this end, we conducted a secondary data analysis and (...) built decision trees (C4.5 algorithm) to obtain a predictive model of school performance. Specifically, we selected as predictor variables a set of socioeconomic, process and outcome variables from PISA 2018 and other sources (World Bank, 2020). Since the unit of analysis were schools from all the countries included in PISA 2018 (n= 21,903), student and teacher predictor variables were imputed to the school database. Based on the available student performance scores in Reading, Math, and Science, we applied k-means clustering to obtain a categorized (three categories) target variable of global school performance. Results show the existence of two main branches in the decision tree, split according to the schools’ mean socioeconomic status (SES). While performance in high-SES schools is influenced by educational factors such as metacognitive strategies or achievement motivation, performance in low-SES schools is affected in greater measure by country-level socioeconomic indicators such as GDP, and individual educational indicators are relegated to a secondary level. Since these evidences are in line and delve into previous research, this work concludes by analyzing its potential contribution to support the decision making processes regarding educational policies. (shrink)

In vertebrates, members of the cysteine‐rich protein (CRP) family are characterized by the presence of two LIM domains linked to short glycine‐rich repeats. These proteins mediate protein–protein interactions and are of fundamental importance for cell differentiation, cytoskeletal remodeling, and transcriptional regulation. To date, a vast amount of information about vertebrate CRPs has become available, including their biological functions, interacting partners, and three‐dimensional structures. Compatible with a molecular adapter role, structural data reveal that the LIM domains (...) within these proteins represent completely independent folded units bridged by flexible linker regions. The physiological roles for individual CRPs was determined by targeted gene disruption analysis and by identification of common and specific binding partners by means of yeast and mammalian two‐hybrid screens. Several CRP‐like LIM domain proteins with close structural and sequence similarity were identified in arthropods, protozoas and plants, supporting the notion that this subset of LIM domain proteins has been highly conserved over the span of evolution thereby emphasizing the importance of their function. BioEssays 25:152–162, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Digital humanities research has developed haphazardly, with substantive contributions in some disciplines and only superficial uses in others. It has made almost no inroads in philosophy; for example, of the nearly two million articles, chapters, and books housed at philpapers.org, only sixteen pop up when one searches for ‘digital humanities’. In order to make progress in this field, we demonstrate that a hypothesis-driven method, applied by experts in data-collection, -aggregation, -analysis, and -visualization, yields philosophical fruits. “Call no one happy (...) until they are dead.” “De mortuis nil nisi bonum.” These ancient norms still inform how we speak of the dead. From their beginnings in the nineteenth century, modern obituaries have been both practical and honorary. They are written with two aims: to pay respect to the deceased and to inspire the living to follow in their footsteps. The obituary of William Custis of Virginia exemplifies these aims, say that “it is due to his memory publicly to record his virtues,” and that “There is in the life a noble, independent and honest man, something so worthy of imitation, something that so strongly commends itself to the approbation of the virtuous mind, that his name should not be left to oblivion” (Daily National Intelligencer, 18 November 1838). Likewise, philosophers have emphasized that we can determine what counts as a virtue for a given type of person in a given community by analyzing what people say about the dead (Zagzebski, L. Virtues of the Mind. Cambridge University Press, 1996, p. 135). By adhering to norms of praise, admiration, and respect, obituaries reveal what counts as a virtue, value, or constituent of wellbeing (VVC) for a particular type of person in a particular community. -/- One way to explore this insight would be to close-read a small number of obituaries of people from intersecting demographics, crossing dimensions such as gender, age, race, class, educational attainment, veteran status, religion, and location. Another, which we demonstrate in this chapter, is to harness digital humanities resources to distance-read a much larger number of obituaries, extracting both demographic meta-data and first-order content expressive of VVC. We then analyze and visualize this information to establish the structures of VVC associated with different types of people in different communities, arguing that data-science measures such as eigenvector centrality can be used to identify cardinal virtues. We also explain the rudiments of our text- and meta-data mining, our method of aggregating and comparing texts, and our visualization techniques. In so doing, we pave the way for researchers in philosophy and related fields to generate similar analyses and visualizations. (shrink)

With the continuous progress and penetration of automated data collection technology, enterprises and organizations are facing the problem of information overload. The demand for expertise in data mining and analysis is increasing. Self-efficacy is a pivotal construct that is significantly related to willingness and ability to perform a particular task. Thus, the objective of this study is to develop an instrument for assessing self-efficacy in data mining and analysis. An initial measurement list was developed based on the (...) skills and abilities about executing data mining and analysis, and expert recommendations. A useful sample of 103 university students completed the online survey questionnaire. A 19-item four-factor model was extracted by exploratory factor analysis. Using the partial least squares-structural equation modeling technique, the model was cross-examined. The instrument showed satisfactory reliability and validity. The proposed instrument will be of value to researchers and practitioners in evaluating an individual’s abilities and readiness in executing data mining and analysis. (shrink)

With the development of the digital economy, the emerging marketing strategy of the e-commerce flash sales has been changing the traditional purchasing habits of customers. This imposes new decision-making challenges for companies involved in flash sales. It is important for companies to build the accurate product demand forecast analysis focusing on the characteristics of the flash sales and customer behaviors. In this paper, VIPS is taken as a case study with the key focus on how sentiment factors in customer reviews (...) affect product demand in flash sale platforms. The paper adopts two sentiment analysis methods based on emotional dictionaries. The method with a higher evaluation index is adopted to integrate the emotional factors into the autoregressive model for product demand and assessment. The experiments prove that the autoregressive model for integrating the sentiment factors demonstrates better forecasting performances than the models without sentiment factors. The experiments further confirm that when product demand for the previous two weeks and customer review sentiment factors in the previous week are taken into consideration, demand forecast effects are most accurate. (shrink)

The Philippines is one of the fast-growing economies in the South-East Asian and the Pacific region. This study considered eight factors: HEI PRC rate, crime rate, education, employment, health, poverty, income, and basic family amenities of the 17 regions of the country, all taken from the year 2012 databases of the Philippine Statistics Authority (PSA), the Philippine Institute for Development Studies (PIDS) and Open Data Philippines. Principal Component Analysis (PCA) generated the indices of the six factors and Cluster Analysis (...) (CA) to group regional similarities. Clustering revealed that ARMM and MIMAROPA Regions have clustered independently, in two individual clusters, while the rest of the 15 regions have clustered in two groups of five and 10. The study revealed that crime, poverty and health mortality rates have generally inverse relationships with HEI PRC percentage performance, employment, education, income and basic housing amenities. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the (...) purposes of making computers understand medical natural language. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation (...) class='Hi'>data set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

The necessity, method and content of childhood religious education are discussed from various perspectives in our country and around the world. The ‘Gift to the Child’ education method, which is applied in England where different religions live together, is a secular religious education approach with psychological, pedagogical and theological foundations. According to this method, which was developed with different methods from adult religious education and considering educational-scientific inferences, children can learn many information and skills based on religions and can transform (...) this into positive gains in their lives. The ‘Gift to the Child’ method processes concepts such as Allah, prophet, revelation and prayer with values such as responsibility, empathy, tolerance and love. It is distinguished from other religious education practices by aiming to highlight the child’s sense of holiness.This study examines the effect of the ‘Call to Prayer’ section, which is included in the ‘Gift to the Child’ method, one of the childhood religious education approaches, on children’s religious development in the Religious Culture and Moral Knowledge course. The applicability of the ‘Gift to the Child’ method, which aims to obtain educational-scientific inferences by comparing children with religious content, is discussed in terms of the educational process, teacher-student-material dimension and religious education.In examining the applicability of this approach, which evaluates religious development theory and development theories together and can be evaluated in terms of its achievements; After conducting a literature review from relevant sources, the data of the study were collected with the semi-structured interview technique, which is one of the qualitative research methods. The data of the study were collected through teacher interviews conducted with the cross-sectional research method. Semi-structured interviews were conducted with 10 teachers working in secondary schools of official educational institutions affiliated to the Ministry of National Education. During the course, the teachers allowed the students to express their opinions on the subject and did not intervene in their questions and answers. As a result of the findings obtained from the data, it was observed that the use of achievements and materials prepared according to the ‘Gift to the Child’ method in religious education positively affected the religious development of the students. (shrink)

We now know the structures of over 200 proteins to atomic resolution. Despite the impressive extent and quality of the results, crystal‐structure analysis has often been thought of as limited in scope, not only in its restriction to samples that can be crystallized, but in the more important respect that taking ‘snapshots’ of proteins does not directly address the complex spatio‐temporal organization of the processes in which proteins participate. It is suggested here that, as the field has matured, this second (...) limitation is gradually being overcome. As we gain increased access to structures of proteins in different conformational states – for example, in conformations produced by different states of ligation – and to families of homologous proteins, we can proceed from the statics of protein structure to the dynamics of conformational change, function, and evolution.A new scientific speciality has grown up around the solved structures: it has as its goal the elucidation of general principles of protein structure and function, to provide a theoretical framework for understanding the properties of proteins revealed by experiment. In this article we shall discuss some of the activity in this field. It will emerge clearly, I believe, that the increasing number and variety of solved structures is exerting a cumulative force. General principles are emerging from comparisons of related proteins and contrasts of dissimilar ones: the whole corpus of data is greater than the sum of the parts. (shrink)

Similarity profiled association mining from time stamped transaction databases is an important topic of research relatively less addressed in the field of temporal data mining. Mining temporal patterns from these time series databases requires choosing and applying similarity measure for similarity computations and subsequently pruning temporal patterns. This research proposes a novel z-space based interest measure named as Krishna Sudarsana for time-stamped transaction databases by extending interest measure Srihass proposed in previous research. Krishna Sudarsana is designed by using the (...) product based fuzzy Gaussian membership function and performs similarity computations in z-space to determine the similarity degree between any two temporal patterns. The interest measure is designed by considering z-values between z = 0 and z = 3.09. Applying the Krishna Sudarsana requires moving the threshold value given by user to a different transformation space which is a defined as a function of standard deviation. In addition to proposing interest measure, new expressions for standard deviation and equivalent z-space threshold are derived for similarity computations. For experimental evaluation, we considered Naïve, Sequential and Spamine algorithms that applies Euclidean distance function and compared performance of these three approaches to Z-Spamine algorithm that uses Krishna Sudarsana by choosing various test cases. Experiment results proved the performance of the proposed approach is better to Sequential approach that uses snapshot database scan strategy and Spamine approach that uses lattice based database scan strategy. (shrink)

Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure (...) are often closely related to local protein flexibility and disorder, large‐scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution. (shrink)

RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence‐specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross‐linking immuno‐precipitation (CLIP) and other recently developed high‐throughput methods provide comprehensive, genome‐wide maps of protein‐RNA interactions in the cell. Structural biology gives detailed (...) insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high‐throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein‐RNA recognition in gene regulation, as we review in this article. (shrink)

We propose a new hybrid data mining method for predicting protein-protein interactions combining Likelihood-Ratio with rule induction algorithms. In essence, the new method consists of using a rule induction algorithm to discover rules representing partitions of the data, and then the discovered rules are interpreted as “bins” which are used to compute likelihood ratios. This new method is applied to the prediction of protein-protein interactions in the Saccharomyces Cerevisiae genome, using predictive genomic features in (...) an integrated scheme. The results show that the new hybrid method outperforms a pure likelihood ratio based approach. (shrink)

The very expertise with which psychologists wield their tools for achieving laboratory control may have had the unwelcome effect of blinding psychologists to the possibilities of discovering principles of behavior without conducting experiments. When creatively interrogated, a diverse range of large, real-world data sets provides powerful diagnostic tools for revealing principles of human judgment, perception, categorization, decision-making, language use, inference, problem solving, and representation. Examples of these data sets include patterns of website links, dictionaries, logs of group interactions, (...) collections of images and image tags, text corpora, history of financial transactions, trends in twitter tag usage and propagation, patents, consumer product sales, performance in high-stakes sporting events, dialect maps, and scientific citations. The goal of this issue is to present some exemplary case studies of mining naturally existing data sets to reveal important principles and phenomena in cognitive science, and to discuss some of the underlying issues involved with conducting traditional experiments, analyses of naturally occurring data, computational modeling, and the synthesis of all three methods. (shrink)

Broad‐complex, Tramtrack, and Bric‐à‐brac/poxvirus and zinc finger (BTB/POZ) is a conserved domain found in many eukaryotic proteins with diverse cellular functions. Recent studies revealed its importance in multiple developmental processes as well as in the onset and progression of oncological diseases. Most BTB domains can form multimers and selectively interact with non‐BTB proteins. Structural studies of BTB domains delineated the presence of different interfaces involved in various interactions mediated by BTBs and provided a basis for the specific inhibition of (...) distinct protein‐interaction interfaces. BTB domains originated early in eukaryotic evolution and progressively adapted their structural elements to perform distinct functions. In this review, we summarize and discuss the structural principles of protein‐protein interactions mediated by BTB domains based on the recently published structural data and advances in protein modeling. We propose an update to the structure‐based classification of BTB domain families and discuss their evolutionary interconnections. (shrink)

The solution structures of several small proteins have recently been determined from high‐resolution nuclear magnetic resonance data. The principal features of the methods available to do this are outlined here, together with the advantages, limitations and future prospects of the technique.

Bacteria use trans‐translation to rescue stalled ribosomes and target incomplete proteins for proteolysis. Despite similarities between tRNAs and transfer‐messenger RNA (tmRNA), the key molecule for trans‐translation, new structural and biochemical data show important differences between translation and trans‐translation at most steps of the pathways. tmRNA and its binding partner, SmpB, bind in the A site of the ribosome but do not trigger the same movements of nucleotides in the rRNA that are required for codon recognition by tRNA. tmRNA‐SmpB (...) moves from the A site to the P site of the ribosome without subunit rotation to generate hybrid states, and moves from the P site to a site outside the ribosome instead of to the E site. During catalysis, transpeptidation to tmRNA appears to require the ribosomal protein bL27, which is dispensable for translation, suggesting that this protein may be conserved in bacteria due to trans‐translation. These differences provide insights into the fundamental nature of trans‐translation, and provide targets for new antibiotics that may have decrease cross‐reactivity with eukaryotic ribosomes. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (...) (GO). PRO relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Our current age offers us dramatic new possibilities in terms of the exchange and development of textual research resources, as we can now gather and transmit information with an ease and rapidity which was inconceivable through earlier media. Although most people will no doubt always prefer to have a hard copy of a book or lengthy article to sit down and read, lexicographical and encyclopedic style reference materials, which have relatively brief and compartmentalized data formats, are extremely well-suited for (...) the digital domain, as they can be furnished with search and retrieval capabilities which are impossible in paper form. The twin CJK lexicographical models presented here stand as an early model of the possibilities such digital reference materials. They have special relevance in the fact that they are not created by a professional software company, or as the fruit of a large, endowed research team. Rather, they have been developed to their current state almost exclusively by a lone humanities scholar possessed of only the most minimal of programming skills with simple HTML techniques. (shrink)

The protein Po has long been proposed to be responsible for the compact nature of peripheral myelin through interactions of both its extracellular and cytoplasmic domains. Recent studies support such a role for Po's extracellular region while more precise mapping of its adhesive domains are ongoing. As Po is a member of the immunoglobulin gene superfamily and perhaps bears the closest similarity to the ancestral molecule of this whole family, these studies may also have more general implications for adhesive (...) interactions. In addition, although long believed to be purely an inert, structural molecule, Po has been reported to promote neurite outgrowth, which suggests a more dynamic role for this interesting molecule. (shrink)

It has long been assumed that the architectural proteins of chromatin (the histones, for example) are unrelated to their functional proteins (transcription factors, polymerases, etc). New studies(1,2)drastically change this perspective. It appears that a portion of the general transcription initiation complex TFIID is made up of proteins that not only carry marked sequence and structural resemblances to the core histones of the nucleosome, but also form an octameric complex similar to the histone octamer. This can now be seen as (...) part of a general pattern of continuity among structural and functional chromatin proteins. (shrink)

At present, a series of economic structural changes created by the network economy have brought challenges to the entire economy and society. Traditional social commerce has also suffered severe tests under the background of network economy and global integration, and the rise and development of network commercial activities lack legal constraints. Based on the Big Data technology, in view of the characteristics of data mining services, this paper expands and changes the traditional model and proposes the Big (...) Data alliance data mining service process model. Moreover, this paper uses intelligent decision-making theory and knowledge reasoning methods to construct a fast-responding, service-reusable, and intelligent service model to realize the scalability of data mining services. In addition, this paper constructs system function modules according to the requirements of Internet commercial judicial data mining and verifies the performance of the system constructed in this paper through experimental analysis. The research results show that the system constructed in this paper has certain practical effects. (shrink)