Hidden Structure Research Articles

Correlations reveal the hierarchical organization of biological networks with latent variables

Deciphering the functional organization of large biological networks is a major challenge for current mathematical methods. A common approach is to decompose networks into largely independent functional modules, but inferring these modules and their organization from network activity is difficult, given the uncertainties and incompleteness of measurements. Typically, some parts of the overall functional organization, such as intermediate processing steps, are latent. We show that the hidden structure can be determined from the statistical moments of observable network components alone, as long as the functional relevance of the network components lies in their mean values and the mean of each latent variable maps onto a scaled expectation of a binary variable. Whether the function of biological networks permits a hierarchical modularization can be falsified by a correlation-based statistical test that we derive. We apply the test to gene regulatory networks, dendrites of pyramidal neurons, and networks of spiking neurons.

Potential Problems with Having a Culture that is Too Strong in Modern Organizations

In each and every society today, culture is a very important concept for both individuals and organizations because it identifies the fundamental set of ideas, rituals, beliefs, meaning, values, norms and language, the way in which things are to be done in an organization and in the life of an individual. Therefore, organization’s culture encompasses what has been good and what has worked in the past. These practices can often be accepted within the organization by long serving members of an organization due to the fact that they have a collective interest towards building of a unified organization through shared system of beliefs, habits and traditions. In organizations there are deep-set beliefs about the way in which work should be organized, the way in which authority should be exercised and punished (Cole and Kelly, 2011). Organizational culture is not something that is written down or necessarily is easily stated. Rather, it is an intangible mixture of rules, relationships, values, custom which when taken together describe the distinctive feel of the organization. It is within this culture that individuals work and from which they learn the norms and values to which they are expected to subscribe. This is the arrangement and inter-relationship of the components parts position of an organization. Whereas culture is a hidden structure that can be seen and drawn in organization charts. Thus the organization Structure may reflect culture. This essay will describe three potential problems with having an organizational culture that is too strong.

A Bibliometric Analysis of English for Specific Purposes from 2011 to 2023 Using Citespace: Visualizing Status, Themes, Evolution, and Emerging Trends

Introduction. Research on English for Specific Purposes (ESP) emerged in the 1960s. A few researchers conducted reviews on ESP literature. However, there is currently a lack of up-to-date and comprehensive bibliometric analysis covering the last decade from an international perspective, particularly covering the last decade's developments in ESP research.
 Purpose. Combining bibliometric analysis and systematic review of the literature on English for Specific Purposes, this study serves to objectively maps the knowledge area, and aims to identify the current status, major research themes, evolution, and the emerging trends in this field.
 Method. To maintain the objectivity and transparency, the review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol. Based on literature retrieved from the Web of Science core collection, a total of 1657 bibliometric records published from 2011 to 2023 were visualized and analyzed via Citespace.
 Results. The current research status through publication distribution and co-country network shows that the research is undergoing a steady increase and international authorship. Clusters and systematic review of citing articles indicate four themes, i.e., “linguistic inquires”, “teaching pedagogy”, “student learning”, and “teacher development”. Through the timezone view of keyword co-occurrence network, four features, such as the predominance of genre, corpus and pedagogy, varied pedagogies, varied research methodologies, and technology-assisted teaching, were identified. The keyword and citation burst detection, as well as systematic review of citing articles, were conducted to identify the research trends. It is found that EAP, teacher development, needs analysis in under-researched settings, as well as EMI and Corpus-based teaching pedagogies are the new frontiers in this field.
 Conclusions. The field of English for Specific Purposes continues to experience exponential growth and development, indicating an ongoing expansion and advancement of research in this area. This paper provides references for researchers to understand the status, hidden structure, evolution, and emerging trends of research on English for Specific Purposes.

The why, the what and the so what of a qualitative empirical research article

The medical literature is dominated by clinical and laboratory sciences, and therefore, the social studies of medicine genre will be harder to decipher for health professional education researchers from a clinical background and other similar newcomers. In the medical literature, the typical format for articles follows a strict sequence known as Introduction, Methods, Results and Discussion, or simply the IMRaD format. In social studies of medicine, however, qualitative research articles are typically less clearly structured. Headings and subheadings are used to communicate the argument but do not necessarily carry titles that easily match the IMRaD elements. This is made more confusing when many qualitative researchers propagate a sense of “anything goes” (more or less) in terms of structure in order to give space for creativity. However, while it is true that there are not strict rules, the idea that there are no conventions at all can sometimes lead novice qualitative researchers astray, and they can become overly creative. Articles in the field of the social study of medicine (especially anthropology, sociology, science and technology studies (STS) and qualitative public health) do, in most cases, follow a particular logic and structure. This paper is about that hidden structure and the logic that justifies it. Its aim is to help newcomers to the field to build their arguments well and to assist people in other areas of medicine to better understand qualitative research articles.

Hidden structure in the medium-range order of amorphous zirconia-tantala films

Hidden structure in the medium-range order of amorphous zirconia-tantala films

Naturalism of consciousness: A dialogue between Colin McGinn and Owen Flanagan

Opinions are divided among naturalists on whether we can specify any property of the brain as the basis of consciousness. This is the question of naturalism of consciousness. While constructive naturalists hold that naturalism is possible, anti-constructive naturalists don’t think so. Owen Flanagan falls within the former camp, while McGinn is an anti-constructive naturalist. In this study, we assess the contributions of McGinn and Flanagan with respect to the possibility of naturalising consciousness. The research demonstrates that constructive naturalism is more plausible than anti-constructive naturalism. We do this through the following routes: 1) highlighting the weaknesses in McGinn’s postulation of the “hidden structure” of consciousness; 2) projecting the explanatory relevance of Flanagan’s use of brain scanner technology in consciousness studies; and 3) demonstrating, on the basis of science, how the immaterial can emerge from matter. The paper concludes that through the science of consciousness, we can achieve possible naturalism of consciousness.

The Sun Also Rises: A Pilgrimage Novel

While allusions to the Camino de Santiago are concealed in Ernest Hemingway’s The Sun Also Rises, Jake Barnes follows the Camino path in Paris, Burguete, Pamplona, San Sebastián and Madrid, and he visits the specific citygates, hostels, and hospitals used by Medieval pilgrims. The way Barnes uses language, perceives space and direction, depend largely upon his location in relation to the pilgrimage route. As his inner north, the Camino de Santiago provides a hidden structure in the novel: through a discussion of the social history of the Camino in Celtic and Catholic traditions, this article examines Hemingway’s first novel through the lens of the pilgrimage, an approach that sheds important light on how Hemingway’s conversion to Catholicism shaped his writing.

T-pattern detection in the scientific literature of this century: A systematic review.

Scientific literature contains mainly systematic reviews focused on substantial aspects, but there are also approaches that have combined both substantial and methodological aspects, which is our preferred option since it undeniably adds value. The aims of this study were: (1) to carry out a systematic review of the literatura on T-Pattern analysis (TPA), and (2) to explore the possible contribution of mixed methods research to the integration of qualitative and quantitative elements on a synthesis level. Based on PRISMA guidelines, searches were carried out in the Scopus, PsycINFO, and Web of Science databases. The general search syntax was: "THEME" AND ("T-Patterns" OR "T Patterns") carried out in title, keywords and abstract. In addition, we included empirical articles on THEME and T-Patterns collected in other sources based on citations in several empirical works and consultations with different authors. This selection process resulted in 125 primary documents making up this systematic review. The results showed that the detection of structures in behavior patterns forms a nexus between studies carried out in very diverse fields and contexts. Most studies are observational, whilst the applicability and power of T-Pattern detection are extraordinary. It allows the researcher to go deeper in a robust analysis that responds to the integration of qualitative and quantitative elements which constitutes the leit motive of mixed methods; and also to discover the deep, hidden structure that underlies the respective databases, regardless of the methodology used in each study. The possibilities in assigning parameters notably increase the options for obtaining results and their interpretation. It is relevant the extraordinary strength and applicability of T-pattern detection. There is a high presence of T-pattern detection and analysis in studies using observational methodology. It is necessary commit to consolidating the methodological analysis of selected works, as taking individual and collective responsibility for improving methodological quality of TPA studies, taking advantage of the resources provided by the THEME program.

A Clathrate Hydrate Structure Hidden in Plain Sight.

Clathrate hydrates have diverse crystal structures, and among them, the three (sI, sII, and sH) most prevalent ones cover nearly all known structures, while the norm is to consider other structures only when specific guest molecules are present. Here we report the observation of a hidden clathrate structure: the tetragonal structure (TS-I) in commonly formed gas hydrates, as evidenced from molecular dynamics simulations. We show that when two (or more) sI crystal grains with different growth directions come into contact or when the growth of a sI crystal encounters geometrical frustration, the TS-I results as a cocrystal. We give evidence that TS-I may also play an important role in the combination and/or transition between sI and sII. These results imply that this previously neglected structure may be commonly present whenever sI or sII is formed. This hidden structure must be identified, experimentally and in simulations; confining the possible structures may hinder an in-depth understanding of clathrate hydrates.

Metrics and mechanisms: Measuring the unmeasurable in the science of science

What science does, what science could do, and how to make science work? If we want to know the answers to these questions, we need to be able to uncover the mechanisms of science, going beyond metrics that are easily collectible and quantifiable. In this perspective piece, we link metrics to mechanisms by demonstrating how emerging metrics of science not only offer complementaries to existing ones, but also shed light on the hidden structure and mechanisms of science. Based on fundamental properties of science, we classify existing theories and findings into: hot and cold science referring to attention shift between scientific fields, fast and slow science reflecting productivity of scientists and teams, soft and hard science revealing reproducibility of scientific research. We suggest that interest about mechanisms of science since Derek J. de Solla Price, Robert K. Merton, Eugene Garfield, and many others complement the zeitgeist in pursuing new, complex metrics without understanding the underlying processes. We propose that understanding and modeling the mechanisms of science condition effective development and application of metrics.

Certification of quantum states with hidden structure of their bitstrings

The rapid development of quantum computing technologies already made it possible to manipulate a collective state of several dozens of qubits, which poses a strong demand on efficient methods for characterization and verification of large-scale quantum states. Here, we propose a numerically cheap procedure to distinguish quantum states which is based on a limited number of projective measurements in at least two different bases and computing inter-scale dissimilarities of the resulting bit-string patterns via coarse-graining. The information one obtains through this procedure can be viewed as a ‘hash function’ of quantum state—a simple set of numbers which is specific for a concrete wave function and can be used for certification. We show that it is enough to characterize quantum states with different structure of entanglement, including the chaotic quantum states. Our approach can also be employed to detect phase transitions in quantum magnetic systems.

Inferential statistical sampling of hyper-heterogeneous lots with hidden structure: the importance of proper Decision Unit definition

Sampling is nothing more than the practical application of statistics. If statistics were not available, then one would have to sample every portion of an entire population to determine one or more parameters of interest. There are many potential statistical tests that could be employed in sampling, but many statistical tests are useful only if certain assumptions about the population are valid. Prior to any sampling event, the operative Decision Unit (DU) must be established. The Decision Unit is the material object that an analytical result makes inference to. In many cases, there is more than one Decision Unit in a population. A lot is a collection (population) of individual Decision Units that will be treated as a whole (accepted or rejected), depending on the analytical results for individual Decision Units. The application of the Theory of Sampling (TOS) is critical for sampling the material within a Decision Unit. However, knowledge of the analytical concentration of interest within a Decision Unit may not provide information on unsampled Decision Units; especially for a hyper-heterogenous lot where a Decision Unit can be of a completely different characteristic than an adjacent Decision Unit. In cases where every Decision Unit cannot be sampled, application of non-parametric statistics can be used to make inference from sampled Decision Units to Decision Units that are not sampled. The combination of the TOS for sampling of individual Decision Units along with non-parametric statistics offers the best possible inference for situations where there are more Decision Units than can practically be sampled.

Sequential Clustering and Classification Approach to Analyze Sales Performance of Retail Stores Based on Point-of-Sale Data

Point-of-Sale (POS) data analysis is usually used to explore sales performance in business commence. This manuscript aims to combine unsupervised clustering and supervised classification methods in an integrated data analysis framework to analyze the real-world POS data. Clustering method, which is performed on sales dataset, is used to cluster the stores into several groups. The clustering results, data labels, are then combined with other information in store features dataset as the inputs of the classification model which classifies the clustering labels by using store features dataset. Non-dominated sorting generic algorithm-II (NSGA-II) is applied in the framework to employ the multi-objective of clustering and classification. The experimental case study shows clustering results can reveal the hidden structure of sales performance of retail stores while classification can reveal the major factors that effect to the sales performance under different group of retail stores. The correlations between sales clusters and the store information can be obtained sequentially under a series of data analysis with the proposed framework.

Automated meta-analysis of the event-related potential (ERP) literature

Event-related potentials (ERPs) are a common approach for investigating the neural basis of cognition and disease. There exists a vast and growing literature of ERP-related articles, the scale of which motivates the need for efficient and systematic meta-analytic approaches for characterizing this research. Here we present an automated text-mining approach as a form of meta-analysis to examine the relationships between ERP terms, cognitive domains and clinical disorders. We curated dictionaries of terms, collected articles of interest, and measured co-occurrence probabilities in published articles between ERP components and cognitive and disorder terms. Collectively, this literature dataset allows for creating data-driven profiles for each ERP, examining key associations of each component, and comparing the similarity across components, ultimately allowing for characterizing patterns and associations between topics and components. Additionally, by examining large literature collections, novel analyses can be done, such as examining how ERPs of different latencies relate to different cognitive associations. This openly available dataset and project can be used both as a pedagogical tool, and as a method of inquiry into the previously hidden structure of the existing literature. This project also motivates the need for consistency in naming, and for developing a clear ontology of electrophysiological components.

Hidden structure in disordered proteins is adaptive to changes in the cellular environment

Intrinsically disordered protein regions (IDRs) play key roles in cellular pathways and are vital to cellular function. Unlike folded proteins, an IDR exists in an “ensemble” of conformations that can change rapidly in response to the physical-chemical characteristics of its surroundings, and the relationship of the structural preferences of this ensemble to sequence and function remains poorly understood. Here we attempt to quantify the structural dynamics that occur in IDR ensembles and trace the molecular underpinnings that govern them.

Research on Classification of Primary Liver Cancer Syndrome Based on Data Mining Technology.

This study is based on the analysis of the status quo of the research on liver cancer syndromes, starting with the clinical objective and true four-diagnosis information of TCM inpatients with primary liver cancer, using computer data mining technology to analyze and summarize the syndrome rules from the bottom to the top. Let the data itself show the essence of liver cancer syndrome. First, with the help of hierarchical cluster analysis, we can understand the general characteristics through the rough preliminary classification of the four-diagnosis information of liver cancer patients. Then, with the help of the emerging and mature hidden structure model analysis in recent years, through data modeling, the classification of common syndromes of liver cancer and the corresponding relationship with the four-diagnosis information are comprehensively analyzed. Finally, considering the inherent shortcomings of implicit structure and hierarchical clustering based on the assumption that there is a unique one-to-one correspondence between the four diagnostic information factors and the class (or hidden class) when classifying, we plan to use factor analysis and joint cluster analysis, as supplementary means to further explore the classification of liver cancer syndromes and the corresponding relationship with the four-diagnosis information.

Hidden Structure in Disordered Proteins is Adaptive to Intracellular Changes

Hidden Structure in Disordered Proteins is Adaptive to Intracellular Changes

The Application of Architectural Language in Ceramic Art

In the creation of ceramic art, there has always been a hidden structure and mystery of architecture. Different forms of high and low scattered or single element repeated stacking have the same geometric distribution as architecture, giving people visual aesthetic enjoyment. By analyzing the individuality and commonality of architectural language and ceramic language, combing and summarizing the relationship between the two, and studying how to apply the transformation of architectural language to the creation of ceramic art, it can not only broaden the expression form of ceramic art, but also enrich the connotation of ceramic art.

Anomalies as obstructions: from dimensional lifts to swampland

We revisit the relation between the anomalies in four and six dimensions and the Chern-Simons couplings one dimension below. While the dimensional reduction of chiral theories is well-understood, the question which three and five-dimensional theories can come from a general circle reduction, and are hence liftable, is more subtle. We argue that existence of an anomaly cancellation mechanism is a necessary condition for liftability. In addition, the anomaly cancellation and the CS couplings in six and five dimensions respectively determine the central charges of string-like BPS objects that cannot be consistently decoupled from gravity, a.k.a. supergravity strings. Following the completeness conjecture and requiring that their worldsheet theory is unitary imposes bounds on the admissible theories. We argue that for the anomaly-free six-dimensional theories it is more advantageous to study the unitarity constraints obtained after reduction to five dimensions. In general these are slightly more stringent and can be cast in a more geometric form, highly reminiscent of the Kodaira positivity condition (KPC). Indeed, for the F-theoretic models which have an underlying Calabi-Yau threefold these can be directly compared. The unitarity constraints (UC) are in general weaker than KPC, and maybe useful in understanding the consistent models without F-theoretic realisation. We catalogue the cases when UC is more restrictive than KPC, hinting at more refined hidden structure in elliptic Calabi-Yau threefolds with certain singularity structure.

Functional Inequalities: Nonlinear Flows and Entropy Methods as a Tool for Obtaining Sharp and Constructive Results

Interpolation inequalities play an essential role in analysis with fundamental consequences in mathematical physics, nonlinear partial differential equations (PDEs), Markov processes, etc., and have a wide range of applications in various other areas of Science. Research interests have evolved over the years: while mathematicians were originally focussed on abstract properties (for instance appropriate notions of functional spaces for the existence of weak solutions in PDEs), more qualitative questions (for instance, bifurcation diagrams, multiplicity of the solutions in PDEs and their qualitative behaviour) progressively emerged. The use of entropy methods in nonlinear PDEs is a typical example: in some cases, the optimal constant in the inequality can be interpreted as an optimal rate of decay of an entropy for an associated evolution equation. Much more has been learned by adopting this point of view. This paper aims at illustrating some of these recent aspect of entropy-entropy production inequalities, with applications to stability in Gagliardo–Nirenberg–Sobolev inequalities and symmetry results in Caffarelli–Kohn–Nirenberg inequalities. Entropy methods provide a framework which relates nonlinear regimes with their linearized counterparts. This framework allows to prove optimality results, symmetry results and stability estimates. Some emphasis will be put on the hidden structure which explain such properties. Related open problems will be listed.