Miracle-dz/UniFAR-FTUs huggingface dataset:
On Jirousek method and its generalizations

Professor Jirousek has been a very important driving force in the modern development of Trefftz method, contributing to its application in many different fields such as elasticity, shells and plates theory, Poisson equation and transient heat analysis. This article is dedicated to him. The focus of the paper is to incorporate Jirousek method into a very general framework of Trefftz method which has been introduced by Herrera. Usually finite element methods are developed using splines, but a more general point of view is obtained when they are formulated in spaces of fully discontinuous functions –i.e., spaces in which the functions together with their derivatives may have jump discontinuities–, and in the general context of boundary value problems with prescribed jumps. Two broad classes of Trefftz methods are obtained: direct (Trefftz–Jirousek) and indirect (Trefftz–Herrera) methods. In turn, each one of them can be divided into overlapping and non–overlapping.
A constructive algorithm for neural networks inspired on decision trees and evolutionary algorithms

Inspired on decision trees and evolutionary algorithms, this paper proposes a learning algorithm of constructive neural networks that relies on three principles: to layout the neurons in a tree-like structure; to train each neuron individually; and, to optimize all the weights using an evolutionary approach. This way, it is expected to advance in two main questions concerning multilayer perceptrons (MLPs): how to determine the network architecture and how to build models that are more comprehensible. Based on the normalized information gain of each attribute, the algorithm builds the network architecture. In the process, it automatically creates a set of training examples for each individual neuron and executes single-cell learning. Once the network is created and trained, particle swarm optimization is utilized to evolve the connections of the network. Five metrics were utilized to validate the method when compared to decision trees and MLPs: accuracy, sensitivity, specificity, precision and comprehensibility. The experiments were executed in thirteen different databases and the results suggest that the proposed algorithm can generate neural networks with good classification performance and more comprehensible.
Predictors of Resistance to Preoperative Trastuzumab and Vinorelbine for HER2-Positive Early Breast Cancer

Purpose: To assess pathologic complete response (pCR), clinical response, feasibility, safety, and potential predictors of response to preoperative trastuzumab plus vinorelbine in patients with operable, human epidermal growth factor receptor 2 (HER2)–positive breast cancer. Experimental Design: Forty-eight patients received preoperative trastuzumab and vinorelbine weekly for 12 weeks. Single and multigene biomarker studies were done in an attempt to identify predictors of response. Results: Eight of 40 (20%) patients achieved pCR (95% confidence interval, 9-36%). Of 9 additional patients recruited for protocol-defined toxicity analysis, 8 were evaluable; 42 of 48 (88%) patients had clinical response (16 patients, clinical complete response; 26 patients, clinical partial response). T1 tumors more frequently exhibited clinical complete response (P = 0.05) and showed a trend to exhibit pCR (P = 0.07). Five (13%) patients experienced grade 1 cardiac dysfunction during preoperative treatment. Neither HER2 nor estrogen receptor status changed significantly after exposure to trastuzumab and vinorelbine. RNA profiling identified three top-level clusters by unsupervised analysis. Tumors with extremes of response [pCR (n = 3) versus nonresponse (n = 3)] fell into separate groups by hierarchical clustering. No predictive genes were identified in pCR tumors. Nonresponding tumors were more likely to be T4 stage (P = 0.02) and express basal markers (P < 0.00001), growth factors, and growth factor receptors. Insulin-like growth factor-I receptor membrane expression was associated with a lower response rate (50% versus 97%; P = 0.001). Conclusions: Preoperative trastuzumab plus vinorelbine is active and well tolerated in patients with HER2-positive, operable, stage II/III breast cancer. HER2-overexpressing tumors with a basal-like phenotype, or with expression of insulin-like growth factor-I receptor and other proteins involved in growth factor pathways, are more likely to be resistant to this regimen.
Acculturation Profiles and Associations With Parenting Among Immigrant Latinos

Acculturation and accompanying acculturative stress affects the parenting practices of Latino immigrants. We (a) examine acculturation profiles based on heritage culture orientation, mainstream culture orientation, familismo, and acculturative stress; (b) describe how social support informs Latinos’ acculturation profiles; and (c) test how these acculturation profiles are associated with parenting behaviors (including parental involvement, monitoring, agency, and discipline self-efficacy) and family conflict. A three-step latent profile analysis revealed five profiles of acculturation: Cultural Individualism (n = 168, 15%), Cultural Engagement (n = 810, 71.3%), Cultural Assimilation (n = 47, 4.3%), Cultural Disengagement (n = 23, 2.1%), and Cultural Stress (n = 77, 7.3%). Social support predicted the Cultural Engagement profile, which was associated with positive parenting behaviors and family functioning. The Cultural Stress profile was associated with detrimental parenting behaviors and family conflict. Recommendations include family interventions that effectively support and strengthen culturally competent coping strategies in response to acculturative stress as a means to promote positive parenting practices.
Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations

Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous mutations that change the protein sequence; however, the selection of synonymous or ‘silent’ mutations in the HIV-1 genome with cART has been reported. These silent K65K and K66K mutations in the HIV-1 reverse transcriptase (RT) occur in over 35% of drug-experienced individuals and are highly associated with the thymidine analog mutations D67N and K70R, which confer decreased susceptibility to most nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the D67N/K70R substitutions in HIV-1 RT increase indel frequency by 100-fold at RT codons 65–67, consequently impairing viral fitness. Introduction of either K65K or K66K into HIV-1 containing D67N/K70R reversed the error-prone DNA synthesis at codons 65–67 in RT and improved viral replication fitness, but did not impact RT inhibitor drug susceptibility. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.
Mobilising a theory of kinetic politics

Abstract While mobilities research is cognisant of the need to theorise the politics of mobility, the extent to which a political theory of movement has been developed is debateable. In this paper, I develop a more substantive theorisation of movement as a constitutive political relation in light of the empirical advances generated by mobilities research. This account of kinetic politics is an important conceptual development that holds promise for the closer alignment of mobilities research with critical security studies, which in turn raises the possibility of a fuller understanding of movement in global politics.
Emission trading systems and the optimal technology mix

Cap and trade mechanisms enjoy increasing importance in environmental legislations worldwide. One of the important aspects of designing cap and trade mechanisms is the possibility of authorities to grant emission permits for free. Unlike analyzed in the seminal contributions on cap and trade systems, in reality free allocations are not made lump sum, but are updated contingent on firms’ actions, i.e., contingent on production decisions and contingent on facilities entering the market or retiring (see IEA, https://www.oecd-ilibrary.org/content/publication/b7d0842b-en , 2020). As it has already been shown in the literature, such updating yields distorted production decisions of firms (see e.g., Böhringer and Lange in Eur Econ Rev 49(8):2041–2055, 2005, Mackenzie et al. in Environ Resour Econ 39(3):265–282, 2008, or Damon et al. in Rev Environ Econ Policy 13(1):23–42, 2019). The impact of updating on firms’ investment and retiring decisions and the resulting technology mix has received much less attention up to now, however. It is the purpose of the present article to shed light on this aspect and to study the impact of a cap and trade mechanism not only on firms’ output decisions, but also on their investment incentives in different technologies and to analyze the optimal design of emission trading systems in such an environment.
As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile

The bacterium Clostridium difficile is a significant cause of nosocomial infections worldwide. The pathogenic success of this organism can be attributed to its flexible genome which is characterized by the exchange of mobile genetic elements, and by ongoing genome evolution. Despite its pathogenic status, C. difficile can also be carried asymptomatically, and has been isolated from natural environments such as water and sediments where multiple strain types (ribotypes) are found in close proximity. These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients. Little is known about the genomic content of strains in such reservoirs in the natural environment. In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types. To identify the genetic diversity within this strain collection, whole-genome comparisons were performed using the assemblies. The strains are highly genetically diverse with regards to the C. difficile “mobilome,” which includes transposons and prophage elements. We identified a novel transposon-like element in two R078 isolates. Multiple, related and unrelated, prophages were detected in isolates across ribotype groups, including two novel prophage elements and those related to the transducing phage φC2. The susceptibility of these isolates to lytic phage infection was tested using a panel of characterized phages found from the same locality. In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics.
Measurement and Analysis of Private Key Sharing in the HTTPS Ecosystem

The semantics of online authentication in the web are rather straightforward: if Alice has a certificate binding Bob's name to a public key, and if a remote entity can prove knowledge of Bob's private key, then (barring key compromise) that remote entity must be Bob. However, in reality, many websites' and the majority of the most popular ones-are hosted at least in part by third parties such as Content Delivery Networks (CDNs) or web hosting providers. Put simply: administrators of websites who deal with (extremely) sensitive user data are giving their private keys to third parties. Importantly, this sharing of keys is undetectable by most users, and widely unknown even among researchers. In this paper, we perform a large-scale measurement study of key sharing in today's web. We analyze the prevalence with which websites trust third-party hosting providers with their secret keys, as well as the impact that this trust has on responsible key management practices, such as revocation. Our results reveal that key sharing is extremely common, with a small handful of hosting providers having keys from the majority of the most popular websites. We also find that hosting providers often manage their customers' keys, and that they tend to react more slowly yet more thoroughly to compromised or potentially compromised keys.
Dissociating Controllable and Uncontrollable Effects of Affective Stimuli on Attitudes and Consumption

This research studies a fundamental and seemingly straightforward question: Can basic advertising elements, such as the presence of attractive imagery, have uncontrollable effects on consumers' attitudes and consumption decisions? Answering this question is methodologically challenging, because the presence of an uncontrollable process can be masked by a simultaneously operating controllable process. We argue first that existing methods conflate the contribution of both processes and are therefore unable to measure the presence of an uncontrollable process reliably. To solve the conundrum, we present a novel application of processing tree modeling. Evaluative conditioning is employed as a paradigm to study the influence of affective visual stimuli on attitudes and behavior. Across six experiments, we demonstrate the validity of the model parameters estimating controllable and uncontrollable processes. As predicted, the parameter estimate of the controllable process is susceptible to cognitive resources and levels of motivation to exert control. The parameter estimate of the uncontrollable process appears unaffected by these factors. We also demonstrate the external validity of our findings and their relevance to stimuli and instructions typical for consumer research. Finally, we find that controllable and uncontrollable processes are both predictive of product choice and consumption.We discuss implications for consumer protection.
How students perceive attending Church in Wales primary schools: A psychometric assessment of Section 50 inspection criteria

A sample of 4581 year 4, year 5 and year 6 students (8–11 years of age) attending Church in Wales primary schools completed six short scales designed to operationalise the Section 50 inspection criteria concerning aspects of the distinctiveness of Church school ethos and concerning school worship. The data demonstrated the internal consistency reliability of the six measures and showed more positive attitudes to be associated with being female, being younger, and attending Church. Overall, the students displayed positive attitudes toward school ethos, toward school experience, toward school teachers, toward relationships within school, and toward school and environment. Attitude toward school worship was less positive.
Prototyping and Experimental Comparison of IR-UWB Based High Precision Localization Technologies

Various localization technologies with diverse precision have been developed for location-based applications based on the Wireless sensor networks (WSN). With the distinct high temporal resolution, the Impulse Radio Ultra-Wide Band (IR-UWB) technology allows accurate determination of the time of arrival at the receiver, making it promising for high precision localization. In this paper, three types of IR-UWB-based real-time indoor localization systems (Deca Wave, Be Spoon, and OpenRTLS) are evaluated and compared by experiments using different ranging methods (TOA s. TDOA), and on different chipsets (Deca Wave vs. Be Spoon). Results from experiments show that 20cm level precision can be achieved by Deca Wave, Be Spoon prototypes without any post-processing, and the OpenRTLS prototype can even achieve 2cm level precision. Furthermore, the proposed systems also demonstrate the IR-UWB-based localization could provide high precision with fast and lightweight algorithms, which makes it promising for volume application in many industrial scenarios like building automation and factory automation.
Intramyocardial Hemorrhage: An Enigma for Cardiac MRI?

Cardiovascular magnetic resonance (CMR) is a useful noninvasive technique for determining the presence of microvascular obstruction (MVO) and intramyocardial hemorrhage (IMH), frequently occurring in patients after reperfused myocardial infarction (MI). MVO, or the so-called no-reflow phenomenon, is associated with adverse ventricular remodeling and a poor prognosis during follow-up. Similarly, IMH is considered a severe damage after revascularization by percutaneous primary coronary intervention (PPCI) or fibrinolysis, which represents a worse prognosis. However, the pathophysiology of IMH is not fully understood and imaging modalities might help to better understand that phenomenon. While, during the past decade, several studies examined the distribution patterns of late gadolinium enhancement with different CMR sequences, the standardized CMR protocol for assessment of IMH is not yet well established. The aim of this review is to evaluate the available literature on this issue, with particular regard to CMR sequences. New techniques, such as positron emission tomography/magnetic resonance imaging (PET/MRI), could be useful tools to explore molecular mechanisms of the myocardial infarction healing process.
Clarifying Intentions in Dialogue: A Corpus Study

As part of our ongoing work on grounding in dialogue, we present a corpus-based investigation of intention-level clarification requests. We propose to refine existing theories of grounding by considering two distinct types of intention-related conversational problems: intention recognition and intention adoption. This distinction is backed-up by an annotation experiment conducted on a corpus assembled with a novel method for automatically retrieving potential requests for clarification.
Modelling data access for a distributed network management system

This paper describes a model developed to assess data replication strategies employed in distributed operation support systems (OSSs) and network management systems (NMSs) for future public service networks. Maximum network throughput and optimum configuration is determined from network characteristics such as number of network and management nodes, connectivity, relative message processing rates and degree of replication. Practical illustration of the application of this model is demonstrated for a two-layer management network based on management functions for a 3G radio access network.
Managing ethical issues in patient care and the need for clinical ethics support.

OBJECTIVE To investigate the range, frequency and management of ethical issues encountered by clinicians working in hospitals in New South Wales (NSW), Australia. METHODS A cross-sectional survey was conducted of a convenience sample of 104 medical, nursing and allied health professionals in two NSW hospitals. RESULTS Some respondents did not provide data for some questions, therefore the denominator is less than 105 for some items. Sixty-two (62/104; 60%) respondents reported occasionally to often having ethical concerns. Forty-six (46/105; 44%) reported often to occasionally having legal concerns. The three most common responses to concerns were: talking to colleagues (96/105; 91%); raising the issue in a group forum (68/105; 65%); and consulting a relevant guideline (64/105; 61%). Most respondents were highly (65/99; 66%) or moderately (33/99; 33%) satisfied with the ethical environment of the hospital. Twenty-two (22/98; 22%) were highly satisfied with the ethical environment of their department and 74 (74/98; 76%) were moderately satisfied. Most (72/105; 69%) respondents indicated that additional support in dealing with ethical issues would be helpful. CONCLUSION Clinicians reported frequently experiencing ethical and legal uncertainty and concern. They usually managed this by talking with colleagues. Although this approach was considered adequate, and the ethics of their hospital was reported to be satisfactory, most respondents indicated that additional assistance with ethical and legal concerns would be helpful. Clinical ethics support should be a priority of public hospitals in NSW and elsewhere in Australia.
Gray Matter Features of Reading Disability: A Combined Meta-Analytic and Direct Analysis Approach1234

Abstract Meta-analysis of voxel-based morphometry dyslexia studies and direct analysis of 293 reading disability and control cases from six different research sites were performed to characterize defining gray matter features of reading disability. These analyses demonstrated consistently lower gray matter volume in left posterior superior temporal sulcus/middle temporal gyrus regions and left orbitofrontal gyrus/pars orbitalis regions. Gray matter volume within both of these regions significantly predicted individual variation in reading comprehension after correcting for multiple comparisons. These regional gray matter differences were observed across published studies and in the multisite dataset after controlling for potential age and gender effects, and despite increased anatomical variance in the reading disability group, but were not significant after controlling for total gray matter volume. Thus, the orbitofrontal and posterior superior temporal sulcus gray matter findings are relatively reliable effects that appear to be dependent on cases with low total gray matter volume. The results are considered in the context of genetics studies linking orbitofrontal and superior temporal sulcus regions to alleles that confer risk for reading disability.
The Association Among Gene Expression Responses to Nine Abiotic Stress Treatments in Arabidopsis thaliana

The identification and analysis of genes exhibiting large expression responses to several different types of stress may provide insights into the functional basis of multiple stress tolerance in plant species. This study considered whole-genome transcriptional profiles from Arabidopsis thaliana root and shoot organs under nine abiotic stress conditions (cold, osmotic stress, salt, drought, genotoxic stress, ultraviolet light, oxidative stress, wounding, and high temperature) and at six different time points of stress exposure (0.5, 1, 3, 6, 12, and 24 hr). In roots, genomewide correlations between transcriptional responses to different stress treatments peaked following 1 hr of stress exposure, while in shoots, correlations tended to increase following 6 hr of stress exposure. The generality of stress responses at the transcriptional level was therefore time and organ dependent. A total of 67 genes were identified as exhibiting a statistically significant pattern of gene expression characterized by large transcriptional responses to all nine stress treatments. Most genes were identified from early to middle (1–6 hr) time points of stress exposure. Analysis of this gene set indicated that cell rescue/defense/virulence, energy, and metabolism functional classes were overrepresented, providing novel insight into the functional basis of multiple stress tolerance in Arabidopsis.
High-order 3D Voronoi tessellation for identifying isolated galaxies, pairs and triplets

A geometric method based on the high-order 3D Voronoi tessellation is proposed for identifying single galaxies, pairs and triplets. This approach allows us to select small galaxy groups and isolated galaxies in different environments and to find the isolated systems. The volumelimited sample of galaxies from the Sloan Digital Sky Survey Data Release 5 spectroscopic survey was used. We conclude that in such small groups as pairs and triplets, segregation by luminosity is clearly observed: galaxies in isolated pairs and triplets are on average two times more luminous than isolated galaxies. We consider the dark matter content in differ