Miracle-dz/UniFAR-FTUs huggingface dataset:
Flexible, Unified and Directable Methods for Simulating Deformable Objects

Deformable objects are omnipresent in our everyday life. In order to create believable virtual worlds in computer graphics that capture and creatively extend our familiar perception of reality, it is indispensable to reflect physical deformation behavior in a faithful, yet simple and efficient manner. In this thesis we revisit and extend FEM-based simulation techniques in each of its main components in order to achieve more flexible numerical handling, to unify the specialized geometry-dependent simulation codes, and to provide artists with better directabilty of simulation outcomes. The first part focuses on different discretization schemes in order to enable arbitrary polyhedral elements as simulation primitives for FEM, achieve convergent meshless simulations requiring just simple point sets as discretization structures, and enable feature preservation at sub-element scales. The novel methods result in considerably simpler handling of topological changes in the case of cutting or fracturing events, or when refining resolution in adaptive simulations. This discretization flexibility is achieved by employing recent advances in geometric interpolation schemes that enable the definition of suitable simulation subspaces. In the second part we focus on specialized simulation codes for different types of object geometries. Building up on the meshless approach of the first part, we follow the method of resultant-based formulation to its logical extreme and derive a higher-order integration rule, or elaston, measuring stretching, shearing, bending, and twisting along any axis. The theory and accompanying implementation do not distinguish between forms of different dimension (solids, shells, rods), nor between manifold regions and non-manifold junctions. Consequently, a single code accurately models a diverse range of elastoplastic behaviors, including buckling, writhing, cutting and merging. The third part of the thesis then concentrates on constitutive relation — how material responds to deformation — and proposes an example-based approach for simulating complex elastic material behavior. Supplied with a few poses that characterize a given object, the system starts by constructing a space of preferred deformations by means of interpolation. During simulation, this example manifold then acts as an additional elastic attractor that guides the object toward its space of preferred shapes. Added on top of existing solid simulation codes, this example potential
Java Obfuscation Approaches to Construct Tamper-Resistant Object-Oriented Programs

In Java programs, it is difficult to protect intellectual property rights and secret information in untrusted environments, since they are easy to decompile and reverse engineer. Consequently realization of software obfuscation becomes increasingly important. Unfortunately previous software obfuscation techniques share a major drawback that they do not have a theoretical basis and thus it is unclear how effective they are. Therefore we shall propose new software obfuscation techniques for Java in this paper. Our obfuscation techniques take advantage of features of object-oriented languages, and they drastically reduce the precision of points-to analysis of the programs. We show that determining precise points-to analysis in obfuscated programs is NP-hard and the fact provides a theoretical basis for our obfuscation techniques. Furthermore, in this paper we present some empirical experiments, whereby we demonstrate the effectiveness of our approaches.
Conserved properties of genetic architecture of renal and fat transcriptomes in rat models of insulin resistance

ABSTRACT To define renal molecular mechanisms that are affected by permanent hyperglycaemia and might promote phenotypes relevant to diabetic nephropathy, we carried out linkage analysis of genome-wide gene transcription in the kidneys of F2 offspring from the Goto-Kakizaki (GK) rat model of type 2 diabetes and normoglycaemic Brown Norway (BN) rats. We mapped 2526 statistically significant expression quantitative trait loci (eQTLs) in the cross. More than 40% of eQTLs mapped in the close vicinity of the linked transcripts, underlying possible cis-regulatory mechanisms of gene expression. We identified eQTL hotspots on chromosomes 5 and 9 regulating the expression of 80-165 genes, sex or cross direction effects, and enriched metabolic and immunological processes by segregating GK alleles. Comparative analysis with adipose tissue eQTLs in the same cross showed that 496 eQTLs, in addition to the top enriched biological pathways, are conserved in the two tissues. Extensive similarities in eQTLs mapped in the GK rat and in the spontaneously hypertensive rat (SHR) suggest a common aetiology of disease phenotypes common to the two strains, including insulin resistance, which is a prominent pathophysiological feature in both GK rats and SHRs. Our data shed light on shared and tissue-specific molecular mechanisms that might underlie aetiological aspects of insulin resistance in the context of spontaneously occurring hyperglycaemia and hypertension. Summary: Kidney and fat expression QTL mapping in rat models of spontaneously occurring insulin resistance associated with either diabetes or hypertension reveals conserved gene expression regulation, suggesting shared aetiology of disease phenotypes.
Metabolic Effect of Dietary Taurine Supplementation on Grouper (Epinephelus coioides): A 1H-NMR-Based Metabolomics Study

Taurine is an indispensable amino acid for many fish species and taurine supplementation is needed when plant-based diets are used as the primary protein source for these species. However, there is limited information available to understand the physiological or metabolic effects of taurine on fish. In this study, 1H nuclear magnetic resonance (NMR)-based metabolomic analysis was conducted to identify the metabolic profile change in the fish intestine with the aim to assess the effect of dietary taurine supplementation on the physiological and metabolomic variation of fish, and reveal the possible mechanism of taurine’s metabolic effect. Grouper (Epinephelus coioides) were divided into four groups and fed diets containing 0.0%, 0.5%, 1.0%, and 1.5% taurine supplementation for 84 days. After extraction using aqueous and organic solvents, 25 significant taurine-induced metabolic changes were identified. These metabolic changes in grouper intestine were characterized by differences in carbohydrate, amino acid, lipid and nucleotide. The results reflected both the physiological state and growth of the fish, and indicated that taurine supplementation significantly affects the metabolome of fish, improves energy utilization and amino acid uptake, promotes protein, lipid and purine synthesis, and accelerates fish growth.
Implementation of an Interdisciplinary Approach to Promote Workers Global Health Status in the Oil Industry, Brazil (2006–2015)

This study intends to analyse the behaviour of epidemiological variables of workers in an oil industry of Bahia, Brazil, before and after implementation of interdisciplinary practices in occupational health assessments between 2006 and 2015. This is a retrospective longitudinal study carried out in two time periods. Data were collected from the workers electronic medical record and time trends were analysed before (2006–2010) and after (2011–2015) the implementation of the interdisciplinary practices focusing on health promotion. The data were complementarily compared to a control group from the same industry. A statistically significant reduction for data on the number of smokers, periodontal disease and of days away from work was obtained. A significant increase in the number of physically active subjects was also observed. While not statistically significant, a reduction in the number of workers with obesity and overweight, with caries and altered glycemia, was identified. Coronary risk and high blood pressure indicators have shown aggravation. It can be concluded that an interdisciplinary health approach during the annual occupational assessments, with action directed to the population needs, can be associated with the improvement of the health indicators assessed, contributing to increased worker productivity in the oil industry.
Liquefaction of Biomass and Upgrading of Bio-Oil: A Review

The liquefaction of biomass is an important technology to converse the biomass into valuable biofuel. The common technologies for liquefaction of biomass are indirect liquefaction and direct liquefaction. The indirect liquefaction refers to the Fischer–Tropsch (F–T) process using the syngas of biomass as the raw material to produce the liquid fuel, including methyl alcohol, ethyl alcohol, and dimethyl ether. The direct liquefaction of biomass refers to the conversion biomass into bio-oil, and the main technologies are hydrolysis fermentation and thermodynamic liquefaction. For thermodynamic liquefaction, it could be divided into fast pyrolysis and hydrothermal liquefaction. In addition, this review provides an overview of the physicochemical properties and common upgrading methods of bio-oil.
Utility of stereo-electroencephalography recording guided by magnetoencephalography in the surgical treatment of epilepsy patients with negative magnetic resonance imaging results

Abstract Objective: It is challenging for neurosurgeons to perform surgeries on patients without detectable structural lesions. Therefore, this retrospective study aimed to explore the outcome of stereo-electroencephalography (SEEG) in suspicious areas guided by magnetoencephalography (MEG)-magnetic resonance imaging (MRI) reconstruction in MRI-negative epilepsy patients. Methods: This study included 47 patients with negative-MRI epilepsy. Seizure outcome at 24 months was assessed using a modified Engel’s classification. Accordingly, class I and II were considered favorable outcomes, whereas classes III and IV were unfavorable. Furthermore, patients were classified into a consistent group if the results of MEG and SEEG indicated the same area of the brain. The relationship between surgical outcome and the concordance of MEG and SEEG was analyzed. Results: A complete seizure-free condition was achieved in 22 (47%) patients. Sex, handedness, age and duration of illness were not significantly associated with seizure-free outcome (p = .187 [Pearson chi-squared test]). The number of patients with favorable outcome (Engle I and II) was as high as 68% at the time of follow-up. Furthermore, more seizure-free patients were found in the SEEG and MEG consistent group. Conclusions: SEEG is a valuable tool in the pre-evaluation for resective epilepsy surgery, particularly in negative-MRI epilepsy patients; MEG greatly facilitates localization for SEEG electrode implantation. However, none of these tools are absolutely sensitive and reliable; therefore, collecting as much information as possible is necessary to achieve satisfactory results in epilepsy surgery.
Foreword by the Secretariat of the WHO Framework Convention on Tobacco Control

The WHO Framework Convention on Tobacco Control (WHO FCTC) is one of the biggest public health achievements of the 21st century. It is the world’s first public health treaty negotiated under the WHO constitutional framework and is today legally binding in 181 Parties (180 countries and the European Union). The Convention aims to protect present and future generations from the devastating health, economic, social and environmental impact of tobacco and requires implementation of a comprehensive set of supply and demand reduction measures to this effect. It is a strong public health instrument to the effect that it entails the involvement of a number of different sectors for its implementation and a combination of cross-cutting provisions, such as Article 5.3 on protection of public health policies from tobacco industry interference and Article 19 on liability as a public health measure. The Conference of the Parties is the governing body of the WHO FCTC, the world’s only intergovernmental body fully responsible for shaping global directions in tobacco control. Through its decisions, the Conference of the Parties guides the Parties to the Convention in their implementation work and facilitates engagement with other stakeholders at regional and global levels to mobilise support for the implementation of the Convention. Its decisions and the guidelines on various WHO FCTC articles that it adopted provide guidance to Parties on how to implement strong policies and legislation in line with the requirements of the Convention, thus addressing an epidemic that claims globally 7 million deaths each year, due to either tobacco use or exposure to secondhand smoke. The WHO FCTC had been in force for almost 10 years, when the Conference of the Parties, in late 2014 at its sixth session held in Moscow, Russian Federation, decided to assess its impact. The WHO FCTC impact assessment was carried out …
Current and future expectations of mifepristone treatment in early pregnancy failure: a survey among Dutch gynaecologists

Abstract To investigate the current and future addition of mifepristone to misoprostol treatment in case of early pregnancy failure (EPF), a digital questionnaire was distributed to a representative sample of all Dutch hospitals (25/79). In non-teaching centres, the presence of a local protocol was significantly lower compared to academic and teaching hospitals (p=.012). If a local protocol was present, the first choice of treatment was medical in 54.5%. Four respondents (16%) always prescribed mifepristone in case of EPF. The most common reason not prescribing mifepristone was the lack of sufficient scientific evidence. An average increase in success rate of 21.7% was desired to prescribe mifepristone in the future for EPF. Completeness of evacuation of products of conception from the uterus was usually assessed after 1 week by ultrasonography combined with clinical signs. If a complete evacuation was not achieved by the initial medical treatment, expectant management was proposed just as often as surgical intervention. Impact Statement What is already known on this subject? In case of early pregnancy failure (EPF), women can choose from both expectant medical (misoprostol, whether or not combined with mifepristone) and surgical (D and C) treatment. In The Netherlands, a national guideline concerning the treatment of EPF is still lacking. A questionnaire performed by Verschoor et al. (2014) showed there was a large practice variety between Dutch clinics. What the results of this study add? In this study, a representative sample of all Dutch clinics received a questionnaire about the treatment of EPF. The results confirm a large practice variation regarding treatment of EPF. The first choice of treatment, the medical treatment regimen, and the assessment of whether or not the treatment have been variations of successful between clinics. With regards to the addition of mifepristone to the medical treatment regime with misoprostol, gynaecologists are willing to consider mifepristone if an improvement of efficacy of approximately 20% is scientifically proven. What the implications are of these findings for clinical practice and/or further research? In our opinion, these results emphasise the need for a national guideline concerning the treatment of EPF. Our results also demonstrate that, if the addition of mifepristone to medical treatment with misoprostol proves to be more efficient than misoprostol alone, gynaecologists are willing to prescribe mifepristone in the future. Whether the addition is indeed more effective than misoprostol alone, will be the subject of a multicentre, double-blind, placebo-controlled randomised controlled trial, planned to begin in the first half of 2018.
Environmental Hotspots for Azole Resistance Selection of Aspergillus fumigatus, the Netherlands

Azole resistance is a major concern for treatment of infections with Aspergillus fumigatus. Environmental resistance selection is a main route for Aspergillus spp. to acquire azole resistance. We investigated the presence of environmental hotspots for resistance selection in the Netherlands on the basis of the ability of A. fumigatus to grow and reproduce in the presence of azole fungicide residues. We identified 3 hotspots: flower bulb waste, green waste material, and wood chippings. We recovered azole-resistant A. fumigatus from these sites; all fungi contained cyp51A tandem repeat–mediated resistance mechanisms identical to those found in clinical isolates. Tebuconazole, epoxiconazole, and prothioconazole were the most frequently found fungicide residues. Stockpiles of plant waste contained the highest levels of azole-resistant A. fumigatus, and active aerobic composting reduced Aspergillus colony counts. Preventing plant waste stockpiling or creating unfavorable conditions for A. fumigatus to grow in stockpiles might reduce environmental resistance burden.
Effect of micro-osteoperforation on the rate of orthodontic tooth movement-a systematic review and a meta-analysis.

BACKGROUND The micro-osteoperforation can be used to increase the rate of tooth movement, simplify complex orthodontic movements, and also help adjust the anchorage but there are conflicting reports on the effectiveness and adverse effects of this intervention. OBJECTIVES The aim of our systematic review and meta-analysis was to evaluate the effects of micro-osteoperforation on the rate of tooth movement in patients undergoing orthodontic treatment. SEARCH METHODS A comprehensive search of MEDLINE, ISI web of science, EMBASE, Scopus, and CENTRAL online databases for studies measuring the effects of micro-osteoperforation on the rate of orthodontic tooth movement from inception to February 2019 was performed. SELECTION CRITERIA Based on the PICO model, human studies which evaluated the effects of MOP on the rate of tooth movement in patients undergoing orthodontic treatment were selected for this review. DATA COLLECTION AND ANALYSIS The relevant data from the eligible studies were extracted using piloted custom extraction forms. The data were combined and analysed using inverse-variance random-effect meta-analysis and the mean difference was used for comparing the outcome measures. RESULTS Six randomized clinical trials were finally included in this meta-analysis. The rate of canine retraction per month was significantly higher in the MOP group [mean difference (MD) = 0.45 mm, 95% CI = 0.17-0.74]. These results were similar with regard to different malocclusions, the jaw on which it was performed, and MOP methods. The patients did not report any significant differences in terms of pain severity levels after MOP. With regard to the adverse effects, one study reported higher amounts of root resorption among patients undergoing MOP. CONCLUSIONS The rate of tooth movement was increased after performing MOP but in at least one study higher root resorption was observed. Therefore, the use of MOP can be recommended after weighing the benefits and disadvantages this intervention can bring for each patient. REGISTRATION The protocol for this review was registered via crd.york. ac.uk/prospero with the ID CRD42019115499.
Emerging gene therapies for cystic fibrosis

ABSTRACT Introduction: Cystic fibrosis (CF) remains a life-threatening genetic disease, with few clinically effective treatment options. Gene therapy and gene editing strategies offer the potential for a one-time CF cure, irrespective of the CFTR mutation class. Areas covered: We review emerging gene therapies and gene delivery strategies for the treatment of CF particularly viral and non-viral approaches with potential to treat CF. Expert opinion: It was initially anticipated that the challenge of developing a gene therapy for CF lung disease would be met relatively easily. Following early proof-of-concept clinical studies, CF gene therapy has entered a new era with innovative vector designs, approaches to subvert the humoral immune system and increase gene delivery and gene correction efficiencies. Developments include integrating adenoviral vectors, rapamycin-loaded nanoparticles, and lung-tropic lentiviral vectors. The characterization of novel cell types in the lung epithelium, including pulmonary ionocytes, may also encourage cell type-specific targeting for CF correction. We anticipate preclinical studies to further validate these strategies, which should pave the way for clinical trials. We also expect gene editing efficiencies to improve to clinically translatable levels, given advancements in viral and non-viral vectors. Overall, gene delivery technologies look more convincing in producing an effective CF gene therapy. Trial registration: ClinicalTrials.gov identifier: NCT01621867. Trial registration: ClinicalTrials.gov identifier: NCT02564354. Trial registration: ClinicalTrials.gov identifier: NCT02532764. Trial registration: ClinicalTrials.gov identifier: NCT03375047. Trial registration: ClinicalTrials.gov identifier: NCT03288493. Trial registration: ClinicalTrials.gov identifier: NCT03140969. Trial registration: ClinicalTrials.gov identifier: NCT03605069. Trial registration: ClinicalTrials.gov identifier: NCT03780257. Trial registration: ClinicalTrials.gov identifier: NCT02939820. Trial registration: ClinicalTrials.gov identifier: NCT03399448.
Perceived barriers and enablers for implementing water protocols in acute stroke care: A qualitative study using the Theoretical Domains Framework

Abstract Purpose: To identify perceived enablers and barriers that may influence the implementation of water protocols (WPs) as an intervention for dysphagia in acute stroke settings. Method: Semi-structured interviews were conducted with nine nurses, eight speech-language pathologists (SLPs), five doctors and four dietitians working in acute stroke units in a major city in Australia. Data were thematically analysed and themes were mapped to the Theoretical Domains Framework. Result: Ten barriers and nine enablers were identified. Key barriers were: nurses lack oral care skills and agency nurses lack stroke-specific skills; only SLPs are perceived to be involved with WPs; WP rules will not get followed and may lead to adverse patient outcomes; WPs increase nursing workload; transient workforce impacts efficiency of implementation; and established culture of using thickened fluids. Key enablers were: patients would benefit from WPs; communication and education systems are already in place; acute hospital brings unique benefits; and peer support and modelling support implementation. Conclusion: The perceptions of barriers and enablers to implementation of WPs can be used to inform future studies designed to evaluate the safety and efficacy of WPs and subsequently facilitate their uptake in acute stroke as an alternate dysphagia management strategy.
Biology and Role of Extracellular Vesicles (EVs) in the Pathogenesis of Thrombosis

Extracellular vesicles (EVs) are well-established mediators of cell-to-cell communication. EVs can be released by every cell type and they can be classified into three major groups according to their biogenesis, dimension, density, and predominant protein markers: exosomes, microvesicles, and apoptotic bodies. During their formation, EVs associate with specific cargo from their parental cell that can include RNAs, free fatty acids, surface receptors, and proteins. The biological function of EVs is to maintain cellular and tissue homeostasis by transferring critical biological cargos to distal or neighboring recipient cells. On the other hand, their role in intercellular communication may also contribute to the pathogenesis of several diseases, including thrombosis. More recently, their physiological and biochemical properties have suggested their use as a therapeutic tool in tissue regeneration as well as a novel option for drug delivery. In this review, we will summarize the impact of EVs released from blood and vascular cells in arterial and venous thrombosis, describing the mechanisms by which EVs affect thrombosis and their potential clinical applications.