Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigations into the mechanics of connective tissue

This thesis presents work on investigations into the mechanical properties of connective tissue. A model system of hydrogels was used to investigate how volume change through water flow is coupled to relaxation. This was done using digital image correlation (DIC) and a custom built setup. It was found, in hydrogels, that water loss is directly coupled to an increase in tension and water intake is directly coupled to tension relaxation. The experimental setup was tested by investigating the mechanical properties of the well known material polydimethylsiloxane (PDMS) and the novel materials of carbon nanotube (CNT) elastomers, cholesteric liquid crystal elastomers (CLCEs), and 3D polydomain liquid crystal elastomers (3DLCEs). The setup accurately demonstrated the incompressibility of PDMS, even at short time scales, and demonstrated how DIC can map the inhomogeneity of material by locating clusters of CNTs in CNT elastomers by how they deform. Novel results for 3DLCEs were also found, where it was discovered that there is a softening of the bulk modulus at small time scales resulting in a volume increase following deformation, the bulk modulus then recovers and there is over all no volume change. This is in stark contrast to the typical case, where it is the shear modulus that becomes comparable to the bulk modulus, resulting in increased volume. A theoretical investigation was carried out into critical damping in viscoelastic oscillators, where the aim was to apply to the findings to connective tissue. The fractional Maxwell model and zener model where both solved for, where it was found that damping decreases as the material becomes more solid and the peak of critical damping becomes broader. Finally, investigations into how strain relates to the viscoelastic properties of connective tissue were carried out on horse tendon and rat fascia. How relaxation changes was determined through the relaxation constant, where a large constant means it takes the sample longer to relax and it is more solid like. It was found, that in general, the relaxation constant increases quickly with an imposed strain and then either stabilises or increases more slowly. This growth of relaxation constant also occurs during the initial stages of tissue injury, where irreversible deformation occurs. Table of contents List of figures xv List of tables xxiii
Predictors of hospitalization after an emergency department visit for California youths with psychiatric disorders.

OBJECTIVE This study examined patient, hospital, and county characteristics associated with hospitalization after emergency department visits for pediatric mental health problems. METHODS Retrospective analysis of emergency department encounters (N=324,997) of youths age five years to 17 years with psychiatric diagnoses was conducted with 2005-2009 California Office of Statewide Health Planning and Development emergency department statewide data. RESULTS For youths with any psychiatric diagnosis, 23.4% of emergency department encounters resulted in hospitalization. In these cases, hospitalization largely was predicted by clinical need. Nonclinical factors that decreased the likelihood of hospitalization included demographic characteristics (such as younger age, lack of insurance, and rural residence) and resource characteristics (private hospital ownership, lack of psychiatric consultation in the emergency department, and lack of pediatric psychiatric beds). For youths with a significant psychiatric diagnosis plus a suicide attempt, 53.8% of emergency department encounters resulted in hospitalization. In these presumably more life-threatening cases, nonclinical factors that decreased the likelihood of hospitalization persisted: demographic characteristics (lack of insurance and rural residence) and resource characteristics (public hospital ownership, lack of psychiatric consultation, and lack of pediatric psychiatric beds). CONCLUSIONS Mental health service delivery can improve only by addressing nonclinical demographic and resource obstacles that independently decrease the likelihood of hospitalization after an emergency department visit for a mental health issue; this is true even for the most severely ill youths-those with a suicide attempt as well as a serious psychiatric diagnosis.
Clinically focused exome sequencing identifies an homozygous mutation that confers DOCK8 deficiency

Live (viral and mycobacterial) vaccines are generally contraindicated in immunocompromised individuals (10). However, as rotavirus vaccination is recommended to be started at the age of 2 months, many SCID patients have already received it at the time of diagnosis (7). TREC-based NBS for SCID has been found efficient for early diagnosis of the disease and could thus prevent the administration of live vaccines to those infants (2, 3). NBS for SCID has become nationally recommended in the USA in 2010 (2). It is not yet carried out in Europe, although trials for implementing population-wide NBS for SCID are currently ongoing in several European countries (3). Delfien Bogaert; Kristof Van Schil; Tom Taghon; Victoria Bordon; Carolien Bonroy; Melissa Dullaers; Elfride De Baere & Filomeen Haerynck Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Department of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium; Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium; Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium; Department of Pediatric Hematology and Oncology, Ghent University Hospital, Ghent, Belgium; Department of Clinical Chemistry, Microbiology and Immunology, Laboratory of Clinical Biology, Ghent University Hospital, Ghent, Belgium E-mail: filomeen.haerynck@uzgent.be DOI:10.1111/pai.12455
Venus - Bulk and Mantle Compositions: Are Venus and Earth Really Twins?

Introduction: Venus is Earth’s twin in size and bulk density [1], but obviously has a very different climate and climate history. Direct comparison of their histories [2] assumes implicitly that they have similar chemical compositions and internal structures; parts of these assumptions are testable with Venera and VEGA chemical analyses of Venus’ surface. From available chemical analyses, it is reasonable that the Earth and Venus are indeed twins, with similar bulk compositions (at least for non-atmophile elements), mantle compositions, and core sizes [3,4]. Such similarity between Earth and Venus is not necessarily consistent with current models of planetary accretion. Principles: Solar system planetary bodies apparently all accreted with cosmochemically refractory elements (e.g., U, Th, Ca, Ti, Al, Mg) in nearly the
Regulation of Epithelial Cell Tight Junctions by Protease-Activated Receptor 2

ABSTRACT A layer of epithelial cells prevents the invasion of bacteria and the entry of foreign substances into the underlying tissue. The disruption of epithelial tight junctions initiates and exacerbates inflammation. However, the precise mechanism underlying the disruption of the epithelial tight junction remains unclear. The activation of protease-activated receptor 2 (PAR2) by serine proteases produced by some bacteria and mast cells contributes to inflammation in many tissues. In the present study, we tested the hypothesis that PAR2 activation affects the structure and function of tight junctions in Madin-Darby canine kidney (MDCK) cells. Although the application of a PAR2-activating peptide, PAR2-AP, from the apical side of MDCK cells failed to modify the transepithelial resistance (TER), its application from the basal side markedly suppressed the TER. In 3-dimensional cultures of MDCK cells expressing the mCherry-tagged PAR2, a lateral localization of PAR2 was observed. The application of PAR2-AP from the basal side changed the localization of the tight junctional protein, zonula occludin-1. Furthermore, PAR2-AP induced the phosphorylation of p38 MAP kinase. A p38 MAP kinase inhibitor, SB202190, inhibited PAR2-AP-induced changes in TER. Our results suggest that the activation of PAR2 leads to the disruption of tight junctions and increases the barrier permeability through the activation of p38 MAPK, which may cause the initiation and exacerbation of inflammation.
Effect of compatibilizers on the crystallization kinetics of cellulose-filled high density polyethylene

High density polyethylene (HDPE) is a ubiquitous material with versatile properties. It is produced and used in greater volume than any other thermoplastic. HDPE is often filled with a variety of materials for various applications. Glass fiber and wood flour are two common fillers for HDPE. This study investigated microcrystalline cellulose (MCC) as a filler in HDPE. The use of compatibilizers, or coupling agents, was investigated as a means of improving the dispersion of the cellulose filler in the HDPE matrix and the mechanical properties of the resulting composites. One compatibilizer was shown to improve the strength of the resulting composite. The stiffness was unaffected, as expected. Thermal properties were measured by means of differential scanning calorimetry. Analysis of the crystallization kinetics indicated that the Avrami coefficient was altered by the filler and was also modified by the presence of the compatibilizer. The presence of cellulose and/or compatibilizer increased the matrix degree of crystallinity. The two compatibilizers studied did not behave similarly and may have different mechanisms of compatibilization.
Compensation and Community Corrosion: Perceived Inequalities, Social Comparisons, and Competition Following the Deepwater Horizon Oil Spill.

After disasters, victim compensation programs are typically associated with individual healing and community rebuilding. But post-disaster compensation systems also have the potential to introduce confusion and competition, further fraying the social fabric of communities affected by trauma. To assess the perceived effects of disaster compensation processes on community social relations, as well as the mechanisms that underlie such effects, we turn to the case of the Deepwater Horizon oil spill, after which BP implemented one of the largest compensation systems in U.S. HISTORY Using data from interviews of residents of four Gulf Coast communities, we examine the extent to which this claims process hindered efforts to recover from this disaster. Our data suggest that while BP money helped some residents in the Gulf during a difficult economic time, many interviewees perceived uncertainty, randomness, and unevenness in the compensation process, which led to negative social comparisons and competition among community members. Because of this animosity, we argue that BP's compensation system was a disruptive mechanism that contributed to community corrosion and introduced another source of psychological stress into already traumatized areas.
Obtaining the parameters required to model labile phosphorus for South African soils

Abstract Modelling phosphorus (P) in the environment can increase our understanding of potential transfer pathways into receiving water bodies as well as the plant availability of this nutrient in soil. Many current models make use of algorithms originally developed for the EPIC model over two decades ago. These algorithms were developed primarily using continental USA soils. Obtaining the required input parameters can therefore be challenging when applying this approach to soils not classified according to the USA system, and for soils for which similar parameters are not available. In this paper, new equations for the estimation of labile P from Ambic P, Bray 2 P and the modified ISFEI method are proposed. Guidelines for the classification of South African soils as calcareous, slightly weathered and highly weathered are further suggested, and we propose that only topsoil properties be used for this purpose. Depending on the amount of soil information available, this classification can be achieved using the clay fraction SiO2:Al2O3 molecular ratio, the sum of exchangeable Ca, Mg, K and Na, or a newly proposed categorization system for South African soil forms. It is clear that the above approaches should be thoroughly tested and relevant local research carried out to improve our ability to model P in South African soils.
Transmission of multidrug-resistant tuberculosis

Aim. To compare the Mycobacterium tuberculosis isolates of adult index cases with multidrug-resistant (MDR) tuberculosis to the isolates obtained from their child contacts. Patients and methods. A 4-year prospective study in the Western Cape Province of South Africa. We evaluated 149 child contacts of 80 adult MDR pulmonary tuberculosis cases. This report includes those cases where a culture for M. tuberculosis was obtained from both the adult source case and the child contact. Isolates were compared by drug susceptibility pattern and restriction fragment length polymorphism analysis. Results. Six adult-child pairs with cultures for M. tuberculosis were identified. Two children had contact with more than one adult tuberculosis case. One child received previous isoniazid prophylaxis. Drug susceptibility pattern and restriction fragment length polymorphism analysis were identical for five adult-child pairs. One child, with no other known source case, had a strain different from that of the identified source case, but the MDR M. tuberculosis strain with which he was infected was prevalent in the community in which he resided. All children responded well to treatment. Conclusion. This study confirms that most of the childhood contacts of adults with MDR tuberculosis are likely to be infected by these MDR source cases despite their exposure to other drug-susceptible adults with tuberculosis in some instances. Child contacts of adults with MDR tuberculosis should be treated according to the drug susceptibility patterns of the likely source cases’M. tuberculosis strains unless their own strain’s susceptibility testing indicates otherwise. Contact tracing remains of fundamental importance in identifying children at risk.
Role of the Axonal Initial Segment in Psychiatric Disorders: Function, Dysfunction, and Intervention

The progress of developing effective interventions against psychiatric disorders has been limited due to a lack of understanding of the underlying cellular and functional mechanisms. Recent research findings focused on exploring novel causes of psychiatric disorders have highlighted the importance of the axonal initial segment (AIS), a highly specialized neuronal structure critical for spike initiation of the action potential. In particular, the role of voltage-gated sodium channels, and their interactions with other protein partners in a tightly regulated macromolecular complex has been emphasized as a key component in the regulation of neuronal excitability. Deficits and excesses of excitability have been linked to the pathogenesis of brain disorders. Identification of the factors and regulatory pathways involved in proper AIS function, or its disruption, can lead to the development of novel interventions that target these mechanistic interactions, increasing treatment efficacy while reducing deleterious off-target effects for psychiatric disorders.
On the Respective Contributions of Awareness of Unconditioned Stimulus Valence and Unconditioned Stimulus Identity in Attitude Formation through Evaluative Conditioning a Memory-based Criterion of Awareness Examining the Role of Awareness in Ec at the Level of Cs-us Contingencies Contingency Awarene

Evaluative conditioning (EC) is a central mechanism for both classic and current theories of attitude formation. In contrast to Pavlovian conditioning, it is often conceptualized as a form of evaluative learning that occurs without awareness of the conditioned stimulus– unconditioned stimulus (CS-US) contingencies. In the present research, the authors directly address this point by assessing the respective roles of US valence awareness and US identity awareness in attitude formation through EC. Across 4 experiments, EC was assessed with evaluative ratings as well as evaluative priming measures, and the impact of valence and identity awareness on EC was evaluated. EC effects on priming and rating measures occurred only for CSs for which participants could report the associated US valence, and US identity awareness did not further contribute to EC. This finding was obtained both for semantically meaningless (i.e., nonword letter sequences) and meaningful (i.e., consumer products) CSs. These results provide further support for the critical role of contingency awareness in EC, albeit valence awareness, not identity awareness. Social psychological research has long been concerned with how attitudes can be measured, with how attitudes can be changed, and with the conditions that moderate the attitude-behavior link. In comparison, there is a relative lack of empirical research concerned with the basic learning processes through which new attitudes are acquired. One current view in social psychology, mainly in dual-process models of attitude formation, is that attitudes can be learned through purely associative processes. These processes are generally conceptualized as a low-level, automatic type of learning. The best case for this associative form of attitude learning is evaluative conditioning (EC), which has classically been thought to be independent of awareness, goals, and resources. The present research brings together new findings from the social psychological and learning literatures to elucidate the conditions under which attitudes can be learned through EC. EC refers to the change in valence of initially neutral stimuli (conditioned stimuli [CSs]) after their pairing with evaluatively positive or negative stimuli (unconditioned stimuli [USs]). For example, if an unfamiliar face is encountered repeatedly in spatial and temporal proximity to a friendly face, EC predicts that the unfamiliar face will eventually be evaluated more positively. Since its initial discovery (Levey & Martin, 1975), EC has received considerable attention, and the amount of research on EC is ever increasing (for recent reviews, Theoretically , EC is conceptualized as one of the simplest evaluative learning mechanisms, and …
An Efficient Genetic Algorithm for the Design of Hub-and-Spoke Networks

We propose an efficient genetic algorithm (GA) for the design of hub-and-spoke networks with single allocation. The creation of the initial population is based on the greedy randomized search procedure, which provides high quality individuals. Furthermore, new crossover and mutation operators were implemented in order to improve the solution over the evolutionary process. Additionally, a local search procedure is applied in the best individuals. The adapted GA is tested in the Australian Post (AP) and Civil Aeronautics Board (CAB) data sets and clearly outperforms four other evolutionary algorithms of the literature, both in solution quality and CPU time.
Equipping IDEs with XML-Path Reasoning Capabilities

One of the challenges in Web development is to achieve a good level of quality in terms of code size and runtime performance for popular domain-specific languages such as XQuery, XSLT, and XML Schema. We present the first IDE augmented with static detection of inconsistent XPath expressions that assists the programmer with simplifying development and debugging of any application involving XPath expressions. The tool is based on newly developed formal verification techniques based on expressive modal logics, which are now mature enough to be introduced in the process of software development. We further develop this idea in the context of XQuery for which we introduce an analysis for identifying and eliminating dead code automatically. This proof of concept aims at illustrating the benefits of equipping modern IDEs with reasoning capabilities.
The lexical properties of the gene ontology

The Gene Ontology (GO) is a construct developed for the purpose of annotating molecular information about genes and their products. The ontology is a shared resource developed by the GO Consortium, a group of scientists who work on a variety of model organisms. In this paper we investigate the nature of the strings found in the Gene Ontology and evaluate them for their usefulness in natural language processing (NLP). We extend previous work that identified a set of properties that reliably identifies natural language phrases in the Unified Medical Language System (UMLS). The results indicate that a large percentage (79%) of GO terms are potentially useful for NLP applications. Some 35% of the GO terms were found in a corpus derived from the MEDLINE bibliographic database, and 27% of the terms were found in the current edition of the UMLS.
Foundations of a rapid denoising technique in real time image processing applications

A noise is an inherent entity of the imaging technologies that tend to deteriorate the quality of processed images at all levels. At the hardware level they appear as the dark current, shot noise etc. however at the imaging side they may involve artefacts arising from interference patterns, undesired shadows, flickering etc. Eliminating such signals are challenging. Though suggesting a hardware changes and improving the imaging technologies is one way, the problem still remains. An ideal de-noising technique should know apriori various estimates of the noisy data both spatially and temporally. In the context of devising an ideal de-noisy method, I chose to estimate the limits of the intensities levels for the raw data and the edges determined by abs-Laplacian, Robert, Sobel, Prewitt and Canny’s method during day time, with incandescent lightning compared with darkness. Results show that the conventional wavelet based de-nosing can only deteriorate the edge profiles and are not useful in real time applications. abs-Laplacian still stands out as the better edge detection technique in comparison but with large bandgap. There is a negligible change in temporal distributions. A change of 12 units was observed during prolonged imaging of a static background that comprises about 4.7% of the maximum intensity. It appears that prolonged imaging has an effect of sharpening the edges or in other words a set of subsequent images would be useful in enhancing edge profiles. Keeping in view the timing constraints for real time applications, the only choice left in formulating rapid de-noising technique would be in learning the ways the noise manifest itself.
Developing Large-Scale Bayesian Networks by Composition: Fault Diagnosis of Electrical Power Systems in Aircraft and Spacecraft

In this paper, we investigate the use of Bayesian networks to construct large-scale diagnostic systems. In particular, we consider the development of large-scale Bayesian networks by composition. This compositional approach reflects how (often redundant) subsystems are architected to form systems such as electrical power systems. We develop high-level specifications, Bayesian networks, clique trees, and arithmetic circuits representing 24 different electrical power systems. The largest among these 24 Bayesian networks contains over 1,000 random variables. Another BN represents the real-world electrical power system ADAPT, which is representative of electrical power systems deployed in aerospace vehicles. In addition to demonstrating the scalability of the compositional approach, we briefly report on experimental results from the diagnostic competition DXC, where the ProADAPT team, using techniques discussed here, obtained the highest scores in both Tier 1 (among 9 international competitors) and Tier 2 (among 6 international competitors) of the industrial track. While we consider diagnosis of power systems specifically, we believe this work is relevant to other system health management problems, in particular in dependable systems such as aircraft and spacecraft. (See CASI ID 20100021910 for supplemental data disk.)