Department of Physics, Mathematics and Informatics

Developing a universal quality standard for thematic analysis (TA) is complicated by the existence of numerous iterations of TA that differ paradigmatically, philosophically and procedurally. This plurality in TA is often not recognised by editors, reviewers or authors, who promote ‘coding reliability measures’ as universal requirements of quality TA. Focusing particularly on our reflexive TA approach, we discuss quality in TA with reference to ten common problems we have identified in published TA research that cites or claims to follow our guidance. Many of the common problems are underpinned by an assumption of homogeneity in TA. We end by outlining guidelines for reviewers and editors – in the form of twenty critical questions – to support them in promoting high(er) standards in TA research, and more deliberative and reflexive engagement with TA as method and practice.

The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building large-scale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fields, including bioinformatics, communication theory, statistical physics, combinatorial optimization, signal and image processing, information retrieval and statistical machine learning. Many problems that arise in specific instances — including the key problems of computing marginals and modes of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing likelihoods, marginal probabilities and most probable configurations. We describe how a wide variety of algorithms — among them sum-product, cluster variational methods, expectation-propagation, mean field methods, max-product and linear programming relaxation, as well as conic programming relaxations — can all be understood in terms of exact or approximate forms of these variational representations. The variational approach provides a complementary alternative to Markov chain Monte Carlo as a general source of approximation methods for inference in large-scale statistical models.

There is growing evidence of the increasing participation in, and influence of, virtual communities in digital environments. To help explain this irresistible allure, the individual and social determinants of the member's intentions to participate are investigated. Conceptualizing virtual community participation as intentional social action, we explicate the concept of “we-intentions”, and use the Model of Goal-Directed Behavior to explain members’ we-intentions. Virtual community influences pertaining to compliance, internalization, and social identity are also elaborated on. An empirical study of regular virtual community participants ( N = 157) finds that we-intentions to participate are functions of both individual determinants (positive anticipated emotions and desires), and community influences (social identity). Implications for marketing and future research opportunities are discussed.

Summary The notion of a limit cycle, which can only exist in a non-linear system, plays the key role in the modelling of cyclical data. We have shown that the class of threshold autoregressive models is general enough to capture this notion, a definition of which in discrete time is proposed. The threshold value has an interesting interpretation. Simulation results are presented which demonstrate that this new class of models exhibits some well-known features of non-linear vibrations. Detailed analyses of several real data sets are discussed.

Abstract A general formulation for the curved, arbitrary shape of thick shell finite elements is presented in this paper along with a simplified form for axisymmetric situations. A number of examples ranging from thin to thick shell applications are given, which include a cooling tower, water tanks, an idealized arch dam and an actual arch dam with deformable foundation. A new process using curved, thick shell finite elements is developed overcoming the previous approximations to the geometry of the structure and the neglect of shear deformation. A general formulation for a curved, arbitrary shape of shell is developed as well as a simplified form suitable for axisymmetric situations. Several illustrated examples ranging from thin to thick shell applications are given to assess the accuracy of solution attainable. These examples include a cooling tower, tanks, and an idealized dam for which many alternative solutions were used. The usefulness of the development in the context of arch dams, where a ‘thick shell’ situation exists, leads in practice to a fuller discussion of problems of foundation deformation, etc., so that practical application becomes possible and economical.

Microplastic debris (<5 mm) is a prolific environmental pollutant, found worldwide in marine, freshwater and terrestrial ecosystems. This review assesses the numerous different methods used to identify microplastics ingested by marine organisms.

With these guidelines, we aim to unite the lignin-first biorefining research field around best practices for performing or reporting feedstock analysis, reactor design, catalyst performance, and product yields.

BACKGROUND: Resistance to triazoles was recently reported in Aspergillus fumigatus isolates cultured from patients with invasive aspergillosis. The prevalence of azole resistance in A. fumigatus is unknown. We investigated the prevalence and spread of azole resistance using our culture collection that contained A. fumigatus isolates collected between 1994 and 2007. METHODS AND FINDINGS: We investigated the prevalence of itraconazole (ITZ) resistance in 1,912 clinical A. fumigatus isolates collected from 1,219 patients in our University Medical Centre over a 14-y period. The spread of resistance was investigated by analyzing 147 A. fumigatus isolates from 101 patients, from 28 other medical centres in The Netherlands and 317 isolates from six other countries. The isolates were characterized using phenotypic and molecular methods. The electronic patient files were used to determine the underlying conditions of the patients and the presence of invasive aspergillosis. ITZ-resistant isolates were found in 32 of 1,219 patients. All cases were observed after 1999 with an annual prevalence of 1.7% to 6%. The ITZ-resistant isolates also showed elevated minimum inhibitory concentrations of voriconazole, ravuconazole, and posaconazole. A substitution of leucine 98 for histidine in the cyp51A gene, together with two copies of a 34-bp sequence in tandem in the gene promoter (TR/L98H), was found to be the dominant resistance mechanism. Microsatellite analysis indicated that the ITZ-resistant isolates were genetically distinct but clustered. The ITZ-sensitive isolates were not more likely to be responsible for invasive aspergillosis than the ITZ-resistant isolates. ITZ resistance was found in isolates from 13 patients (12.8%) from nine other medical centres in The Netherlands, of which 69% harboured the TR/L98H substitution, and in six isolates originating from four other countries. CONCLUSIONS: Azole resistance has emerged in A. fumigatus and might be more prevalent than currently acknowledged. The presence of a dominant resistance mechanism in clinical isolates suggests that isolates with this mechanism are spreading in our environment.

This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.

Preclinical studies indicate autophagy inhibition with hydroxychloroquine (HCQ) can augment the efficacy of DNA-damaging therapy. The primary objective of this trial was to determine the maximum tolerated dose (MTD) and efficacy of HCQ in combination with radiation therapy (RT) and temozolomide (TMZ) for newly diagnosed glioblastoma (GB). A 3 + 3 phase I trial design followed by a noncomparative phase II study was conducted in GB patients after initial resection. Patients received HCQ (200 to 800 mg oral daily) with RT and concurrent and adjuvant TMZ. Quantitative electron microscopy and immunoblotting were used to assess changes in autophagic vacuoles (AVs) in peripheral blood mononuclear cells (PBMC). Population pharmacokinetic (PK) modeling enabled PK-pharmacodynamic correlations. Sixteen phase I subjects were evaluable for dose-limiting toxicities. At 800 mg HCQ/d, 3/3 subjects experienced Grade 3 and 4 neutropenia and thrombocytopenia, 1 with sepsis. HCQ 600 mg/d was found to be the MTD in this combination. The phase II cohort (n = 76) had a median survival of 15.6 mos with survival rates at 12, 18, and 24 mo of 70%, 36%, and 25%. PK analysis indicated dose-proportional exposure for HCQ. Significant therapy-associated increases in AV and LC3-II were observed in PBMC and correlated with higher HCQ exposure. These data establish that autophagy inhibition is achievable with HCQ, but dose-limiting toxicity prevented escalation to higher doses of HCQ. At HCQ 600 mg/d, autophagy inhibition was not consistently achieved in patients treated with this regimen, and no significant improvement in overall survival was observed. Therefore, a definitive test of the role of autophagy inhibition in the adjuvant setting for glioma patients awaits the development of lower-toxicity compounds that can achieve more consistent inhibition of autophagy than HCQ.

Deterministic neural nets have been shown to learn effective predictors on a wide range of machine learning problems. However, as the standard approach is to train the network to minimize a prediction loss, the resultant model remains ignorant to its prediction confidence. Orthogonally to Bayesian neural nets that indirectly infer prediction uncertainty through weight uncertainties, we propose explicit modeling of the same using the theory of subjective logic. By placing a Dirichlet distribution on the class probabilities, we treat predictions of a neural net as subjective opinions and learn the function that collects the evidence leading to these opinions by a deterministic neural net from data. The resultant predictor for a multi-class classification problem is another Dirichlet distribution whose parameters are set by the continuous output of a neural net. We provide a preliminary analysis on how the peculiarities of our new loss function drive improved uncertainty estimation. We observe that our method achieves unprecedented success on detection of out-of-distribution queries and endurance against adversarial perturbations.

Abstract The two‐dimensional scattering and diffraction of plane SH waves by a semi‐cylindrical canyon is analysed for a general angle of wave incidence. The closed‐form solution of the problem shows that the surface topography can have prominent effects on incident waves only when the wavelengths of incident motion are short compared to the radius of a canyon. The surface amplification of displacement amplitudes around and in the canyon changes rapidly from one point to another, but the amplification is always less than 2. The over‐all trends of amplification pattern are determined by two principal parameters: (1) γ, the angle of incidence of plane SH waves, and (2) η, the ratio of radius of the canyon to one‐half wave length of incident waves. The higher η leads to greater complexity of the pattern of surface displacement amplitudes characterized by more abrupt changes of amplification from one point to another, while γ mainly determines the over‐all trends of displacement amplitudes. For grazing and nearly grazing incidences, for example, a strong shadow zone is developed behind the canyon. The qualitative analysis of the topographic effects on the Pacoima Dam accelerogram, 1 based on the semi‐cylindrical canyon, suggests that this strong‐motion record was not seriously affected by surface topography of the recording site.

This review covers the literature published in 2014 for marine natural products (MNPs), with 1116 citations (753 for the period January to December 2014) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1378 in 456 papers for 2014), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

Heterogeneous photocatalytic systems have the potential to provide green organic synthesis routes for a number of industrially important chemicals. This review presents the latest achievements in this research field and compares them with traditional catalytic systems employed in organic synthesis.

Abstract Data obtained in Mayo's Older Americans Normative Studies (MOANS) provide age-specific norms for the Wechsler Adult Intelligence Scale-Revised (WAIS-R) on a sample of 512 cognitively normal persons age 56 to 97. IQ scores derived from these norms are termed “MAYO Verbal, Performance and Full Scale IQs” to differentiate them from traditional WAIS-R IQs. MAYO IQs are, by design, estimates of WAIS-R IQs. A normative procedure that adjusts both for age and also for differences between the WAIS-R's national normative sample and this project's sample is described. The tables needed to convert WAIS-R raw scores to MAYO IQs are presented for ages 56 through 97. The assumptions that underlie the development of MAYO IQs are discussed. Concordance rates are presented which suggest that MAYO IQs are very similar to traditional WAIS-R IQs at ages where both can be validly calculated. The availability of MAYO IQs should enhance the use of the WAIS-R beyond age 74 and should also assist future research designed to distinguish “normal” from “abnormal” intellectual change at life's oldest ages.

We present a method to control the interfacial tension of a liquid alloy of gallium via electrochemical deposition (or removal) of the oxide layer on its surface. In sharp contrast with conventional surfactants, this method provides unprecedented lowering of surface tension (∼ 500 mJ/m(2) to near zero) using very low voltage, and the change is completely reversible. This dramatic change in the interfacial tension enables a variety of electrohydrodynamic phenomena. The ability to manipulate the interfacial properties of the metal promises rich opportunities in shape-reconfigurable metallic components in electronic, electromagnetic, and microfluidic devices without the use of toxic mercury. This work suggests that the wetting properties of surface oxides--which are ubiquitous on most metals and semiconductors--are intrinsic "surfactants." The inherent asymmetric nature of the surface coupled with the ability to actively manipulate its energetics is expected to have important applications in electrohydrodynamics, composites, and melt processing of oxide-forming materials.

Supramolecular cancer nanotheranostics have shown promising potentials in early-stage diagnosis and personal therapy. Herein, we summarize the progress of supramolecular cancer nanotheranostics and provide guidance for designing new targeted supramolecular theranostic agents.

Abstract In recent years, the tendency of the number of financial institutions to include cryptocurrencies in their portfolios has accelerated. Cryptocurrencies are the first pure digital assets to be included by asset managers. Although they have some commonalities with more traditional assets, they have their own separate nature and their behaviour as an asset is still in the process of being understood. It is therefore important to summarise existing research papers and results on cryptocurrency trading, including available trading platforms, trading signals, trading strategy research and risk management. This paper provides a comprehensive survey of cryptocurrency trading research, by covering 146 research papers on various aspects of cryptocurrency trading ( e . g ., cryptocurrency trading systems, bubble and extreme condition, prediction of volatility and return, crypto-assets portfolio construction and crypto-assets, technical trading and others). This paper also analyses datasets, research trends and distribution among research objects (contents/properties) and technologies, concluding with some promising opportunities that remain open in cryptocurrency trading.