Miracle-dz/UniFAR-FTUs huggingface dataset:
The Structure‐function remodeling in rabbit hearts of myocardial infarction

Animal models are of importance to investigate basic mechanisms for ischemic heart failure (HF). The objective of the study was to create a rabbit model through multiple coronary artery ligations to investigate the postoperative structure‐function remodeling of the left ventricle (LV) and coronary arterial trees. Here, we hypothesize that the interplay of the degenerated coronary vasculature and increased ventricle wall stress relevant to cardiac fibrosis in vicinity of myocardial infarction (MI) precipitates the incidence and progression of ischemic HF. Echocardiographic measurements showed an approximately monotonic drop of fractional shortening and ejection fraction from 40% and 73% down to 28% and 58% as well as persistent enlargement of LV cavity and slight mitral regurgitation at postoperative 12 weeks. Micro‐CT and histological measurements showed that coronary vascular rarefaction and cardiac fibrosis relevant to inflammation occurred concurrently in vicinity of MI at postoperative 12 weeks albeit there was compensatory vascular growth at postoperative 6 weeks. These findings validate the proposed rabbit model and prove the hypothesis. The post‐MI rabbit model can serve as a reference to test various drugs for treatment of ischemic HF.
Cellular responses to human cytomegalovirus infection: Induction of a mesenchymal-to-epithelial transition (MET) phenotype

Significance Human cytomegalovirus (HCMV) causes birth defects and serious disease in immunocompromised patients. We do not fully understand the cellular processes that HCMV manipulates during infection. A holistic understanding of the cellular response to HCMV will help clarify mechanisms that underlie its replication and spread. This work uses systems virology to globally map the host response to HCMV infection. Our method identifies unappreciated pathways modulated by HCMV, including mesenchymal-to-epithelial transition (MET), an important developmental pathway involved in epithelial tissue formation, wound healing, and cancer metastasis. Our findings demonstrate that HCMV induces MET and raise the possibility that the transition influences not only viral pathogenesis but also the behavior of normal and diseased cells within an infected human host. Human cytomegalovirus (HCMV) is the prototypical human β-herpes virus. Here we perform a systems analysis of the HCMV host-cell transcriptome, using gene set enrichment analysis (GSEA) as an engine to globally map the host–pathogen interaction across two cell types. Our analysis identified several previously unknown signatures of infection, such as induction of potassium channels and amino acid transporters, derepression of genes marked with histone H3 lysine 27 trimethylation (H3K27me3), and inhibition of genes related to epithelial-to-mesenchymal transition (EMT). The repression of EMT genes was dependent on early viral gene expression and correlated with induction E-cadherin (CDH1) and mesenchymal-to-epithelial transition (MET) genes. Infection of transformed breast carcinoma and glioma stem cells similarly inhibited EMT and induced MET, arguing that HCMV induces an epithelium-like cellular environment during infection.
Flow Field Measurements to Characterize FlapSide-Edge Noise Generation

n this paper, the relation between noise generated at flap side-edges (FSE) and mean flow characteristics in the vicinity of the FSE solid surface is investigated. Of interest is (1) the identification of mean flow features near the flap tip which are important to FSE noise generation, (2) the extraction of quantitative parameters relating flap settings to the emitted noise levels and, finally, (3) the formulation of a prediction scheme based on these observations. The results of the investigation demonstrate that FSE noise can be properly represented by the summed contributions of two independent source mechanisms. Moreover, this new formulation necessitates only a limited knowledge of the mean flow parameters in the vicinity of the FSE to model the noise emission. It is assumed that unsteady vorticity fluctuations, originating from the unstable pressure side shear layer, sweeping over the forward half of the upper tip edge, lead to midto- high frequency noise production. Flow unsteadiness in the proximity of the suction side surface near the FSE aft half, are assumed to be the main contributor in the low-to-mid frequency range. A prediction scheme is formulated and validated for a wide range of experimental measurements at small scale wing configurations. This new formulation only necessitates knowledge of the flap chord length and lift coefficient to provide accurate estimates of the far field noise radiation.
No Improvement in Hemoglobin A1c Following Hepatitis C Viral Clearance in Patients With and Without HIV

Hepatitis C clearance with directly acting antivirals (DAAs) may be associated with acute decreases in hemoglobin A1c (HbA1c). We prospectively evaluated 251 chronic hepatitis C virus (HCV)-infected subjects (31% human immunodeficiency virus [HIV] positive) pre- and post-DAA therapy (median follow-up 28 months). Changes in HbA1c and glucose were minimal and did not differ by sustained virologic response (SVR), HIV, diabetes, or fibrosis. Following SVR, mean change in HbA1c was -0.022 ± 0.53%; however, total and low-density lipoprotein cholesterol increased significantly. Subjects with HIV had smaller transaminase reductions after SVR. Sustained benefits in glycemia were not identified following HCV clearance irrespective of HIV, diabetes, or fibrosis stage, whereas lipid alterations may warrant further investigation.
Corridor Use Predicted from Behaviors at Habitat Boundaries

Through empirical studies and simulation, I demonstrate how simple behaviors can be used in lieu of detailed dispersal studies to predict the effects of corridors on interpatch movements. Movement paths of three butterfly species were measured in large (1.64 ha) experimental patches of open habitat, some of which were connected by corridors. Butterflies that “reflected” off boundaries between open patches and the surrounding forest also emigrated from patches through corridors at rates higher than expected from random movement. This was observed for two open‐habitat species, Eurema nicippe and Phoebis sennae; however, edges and corridors had no effect on a habitat generalist, Papilio troilus. Behaviorally based simulation models, which departed from correlated random walks only at habitat boundaries, predicted that corridors increase interpatch movement rates of both open‐habitat species. Models also predicted that corridors have proportionately greater effects as corridor width increases, that movement rates increase before leveling off as corridor width increases, and that corridor effects decrease as patch size increases. This study suggests that corridors direct movements of habitat‐restricted species and that local behaviors may be used to predict the conservation potential of corridors in fragmented landscapes.
Mathematical modelling of gas and gas-liquid jets injected into a fluidized bed

This thesis presents the development of novel mathematical models of jet injection into fluidized beds. Two types of injections are considered: the first is gas-assisted liquid atomization including flow through a variable cross-section nozzle, followed by spray dispersion and interaction with fluidized bed particles (jet-bed interaction), and the second is a high speed injection of a gas jet with a purpose to break down solid particles (particle attrition). Both models are based on a multi-fluid Eulerian-Eulerian treatment and include the system of the ensemble-averaged Navier-Stokes equations together with the particle number density equation for each phase written independently of the local nature of the continuous phase. The models rely on a number of sub-models that form constitutive equations. Some of the sub-models, such as ones used for atomization, moisture and heat transport in a bed due to particle collisions, heat conduction through the particle core, multiphase wall functions, and breakage frequency, are developed during the course of this project. The jet-bed interaction model includes break-up and coalescence of bubbles and droplets due to interfacial (mean and turbulent) shear and collisions in order to account for spatial variations of the average diameters. Atomization is considered as a catastrophic phase inversion triggered by a critical local volume fraction. The jet-bed interaction model is applied to gas-liquid flow through a nozzle, spray dispersion in open air, and spray injection into the bed. Modelling results are compared with experimental data for pressure variation along the nozzle wall, radial profiles of the liquid flow rate and average droplet diameter, and cumulative liquid distribution in a fluidized bed. It is demonstrated that there is an overall satisfactory agreement. The particle attrition model connects the solid phase properties and the granular temperature with the breakage rate. Modelling results allow calculation of the grinding efficiency – a quantitative measure of the attrition performance. For validation purposes, the model is applied to a number of cases that have been previously investigated experimentally with a good agreement.
Monitoring Muscle Stem Cell Cultures with Impedance Spectroscopy

The aim of this work is to present a new circuit for the real-time monitoring the processes of cellular growth and differentiation of skeletal myoblast cell cultures. An impedance spectroscopy Oscillation-Based technique is proposed for the test circuit, converting the biological system into a voltage oscillator, and avoiding the use of very high performance circuitry or equipment. This technique proved to be successful in the monitoring of cell cultures growth levels and could be useful for determining the degree of differentiation achieved, of practical implications in tissue engineering.
Synthesis of spatio-temporal descriptors for dynamic hand gesture recognition using genetic programming

Automatic gesture recognition has received much attention due to its potential in various applications. In this paper, we successfully apply an evolutionary method-genetic programming (GP) to synthesize machine learned spatio-temporal descriptors for automatic gesture recognition instead of using hand-crafted descriptors. In our architecture, a set of primitive low-level 3D operators are first randomly assembled as tree-based combinations, which are further evolved generation-by-generation through the GP system, and finally a well performed combination will be selected as the best descriptor for high-level gesture recognition. To the best of our knowledge, this is the first report of using GP to evolve spatio-temporal descriptors for gesture recognition. We address this as a domain-independent optimization issue and evaluate our proposed method, respectively, on two public dynamic gesture datasets: Cambridge hand gesture dataset and Northwestern University hand gesture dataset to demonstrate its generalizability. The experimental results manifest that our GP-evolved descriptors can achieve better recognition accuracies than state-of-the-art hand-crafted techniques.
Multi-Approach Analysis for the Identification of Proteases within Birch Pollen

Birch pollen allergy is highly prevalent, with up to 100 million reported cases worldwide. Proteases in such allergen sources have been suggested to contribute to primary sensitisation and exacerbation of allergic disorders. Until now the protease content of Betula verrucosa, a birch species endemic to the northern hemisphere has not been studied in detail. Hence, we aim to identify and characterise pollen and bacteria-derived proteases found within birch pollen. The pollen transcriptome was constructed via de novo transcriptome sequencing and analysis of the proteome was achieved via mass spectrometry; a cross-comparison of the two databases was then performed. A total of 42 individual proteases were identified at the proteomic level. Further clustering of proteases into their distinct catalytic classes revealed serine, cysteine, aspartic, threonine, and metallo-proteases. Further to this, protease activity of the pollen was quantified using a fluorescently-labelled casein substrate protease assay, as 0.61 ng/mg of pollen. A large number of bacterial strains were isolated from freshly collected birch pollen and zymographic gels with gelatinase and casein, enabled visualisation of proteolytic activity of the pollen and the collected bacterial strains. We report the successful discovery of pollen and bacteria-derived proteases of Betula verrucosa.
Display advertising impact: search lift and social influence

We study the impact of display advertising on user search behavior using a field experiment. In such an experiment, the treatment group users are exposed to some display advertising campaign, while the control group users are not. During the campaign and the post-campaign period we monitor the user search queries and we label them as relevant or irrelevant to the campaign using techniques that leverage the bipartite query-URL click graph. Our results indicate that users who are exposed to the advertising campaign submit 5% to 25% more queries that are relevant to it compared to the unexposed users. Using the social graph of the experiment users, we also explore how users are affected by their friends who are exposed to ads. Our results indicate that a user with exposed friends is more likely to submit queries relevant to the campaign, as compared to a user without exposed friends. The result is surprising given that the display advertising campaign that we study does not include any incentive for social action, e.g., discount for recommending friends.
Electrodeposition and corrosion study of nanocrystalline cobalt and cobalt-iron alloy coatings

ii Preface . iv Table of Contents . vi List of Tables . xi List of Figures . xiv List of Symbols . xxiii List of Acronyms . xxv Acknowledgements . xxvii Dedication . xxviii 1 Introduction . 1 2 Literature Review . 4 2.1 Nanomaterials . 4 2.2 Synthesis of Nanomaterials . 8 2.3 Electrodeposited Nanocrystalline Co and CoFe Alloy . 13 2.3. 1 Phase Diagram of CoFe Alloy . 13 2.3. 2 Electrodeposition Mechanism . 17 2.3. 3 Electrodeposition Parameters . 20 2.3. 4 Applications . 24 2.4 Corrosion Behaviour of Nanocrystalline Materials . 25
Understanding the cellular mode of action of vernakalant using a computational model: answers and new questions

Abstract Vernakalant is a new antiarrhythmic agent for the treatment of atrial fibrillation. While it has proven to be effective in a large share of patients in clinical studies, its underlying mode of action is not fully understood. In this work, we aim to link experimental data from the subcellular, tissue, and system level using an in-silico approach. A Hill’s equation-based drug model was extended to cover the frequency dependence of sodium channel block. Two model variants were investigated: M1 based on subcellular data and M2 based on tissue level data. 6 action potential (AP) markers were evaluated regarding their dose, frequency and substrate dependence. M1 comprising potassium, sodium, and calcium channel block reproduced the reported prolongation of the refractory period. M2 not including the effects on potassium channels reproduced reported AP morphology changes on the other hand. The experimentally observed increase of ERP accompanied by a shortening of APD90 was not reproduced. Thus, explanations for the drug-induced changes are provided while none of the models can explain the effects in their entirety. These results foster the understanding of vernakalant’s cellular mode of action and point out relevant gaps in our current knowledge to be addressed in future in-silico and experimental research on this aspiring antiarrhythmic agent.
Cortical responses before 6 months of life associate with later autism

Autism spectrum disorder (ASD) is a common, highly heritable, developmental disorder and later‐born siblings of diagnosed children are at higher risk of developing ASD than the general population. Although the emergence of behavioural symptoms of ASD in toddlerhood is well characterized, far less is known about development during the first months of life of infants at familial risk. In a prospective longitudinal study of infants at familial risk followed to 36 months, we measured functional near‐infrared spectroscopy (fNIRS) brain responses to social videos of people (i.e. peek‐a‐boo) compared to non‐social images (vehicles) and human vocalizations compared to non‐vocal sounds. At 4–6 months, infants who went on to develop ASD at 3 years (N = 5) evidenced‐reduced activation to visual social stimuli relative to low‐risk infants (N = 16) across inferior frontal (IFG) and posterior temporal (pSTS‐TPJ) regions of the cortex. Furthermore, these infants also showed reduced activation to vocal sounds and enhanced activation to non‐vocal sounds within left lateralized temporal (aMTG‐STG/pSTS‐TPJ) regions compared with low‐risk infants and high‐risk infants who did not develop ASD (N = 15). The degree of activation to both the visual and auditory stimuli correlated with parent‐reported ASD symptomology in toddlerhood. These preliminary findings are consistent with later atypical social brain responses seen in children and adults with ASD, and highlight the need for further work interrogating atypical processing in early infancy and how it may relate to later social interaction and communication difficulties characteristic of ASD.
Capturing the Shifting Shapes

With the increasing availability of LCD displays and phone cameras in today's environment, screen-camera communication using dynamic barcode has emerged as a convenient infrastructure-free form to establish impromptu communication channel among mobile devices. Due to the short wavelengths and narrow beams of visible light, screen-camera communication is highly directional, low-interference and secure, which envisions a wide range of application scenarios. Conventional screen-camera communication systems encode data bits with color in dynamic barcodes, which suffers from the frame mixture problem caused by the rolling shutter effect of CMOS camera in high capturing rate. In this paper, we propose a novel design of dynamic barcode called ShiftCode that encodes data bits with shifting shape patterns, which provide a new way to expand the barcode capacity for screen-camera communications. ShiftCode adopts a pattern-based layout design to embed multiple data bits in a symbol representation. With such layout, it exploits a decoding mechanism to solve the frame mixture problem and achieves high frame capturing rate. It further intruduces a two-level reliability technique for intra-frame error correction and inter-frame redundancy, which reduces the overhead and delay of retransmission. The proposed ShiftCode is implemented on the Android platform, and extensive experiments show that it achieves at least two-fold improvement on goodput compared with the conventional screen-camera communication systems.
Optimization of alginate purification using polyvinylidene difluoride membrane filtration: Effects on immunogenicity and biocompatibility of three-dimensional alginate scaffolds

Sodium alginate is an effective biomaterial for tissue engineering applications. Non-purified alginate is contaminated with protein, lipopolysaccharide, DNA, and RNA, which could elicit adverse immunological reactions. We developed a purification protocol to generate biocompatible alginate based on (a) activated charcoal treatment, (b) use of hydrophobic membrane filtration (we used hydrophobic polyvinylidene difluoride membranes to remove organic contaminants), (c) dialysis, and finally (d) ethanol precipitation. Using this approach, we could omit pre-treatment with chloroform and significantly reduce the quantities of reagents used. Purification resulted in reduction of residual protein by 70% down to 0.315 mg/g, DNA by 62% down to 1.28 µg/g, and RNA by 61% down to less than 10 µg/g, respectively. Lipopolysaccharide levels were reduced by >90% to less than 125 EU/g. Purified alginate did not induce splenocyte proliferation in vitro. Three-dimensional scaffolds generated from purified alginate did not elicit a significant foreign body reaction, fibrotic overgrowth, or macrophage infiltration 4 weeks after implantation. This study describes a simplified and economical alginate purification method that results in alginate purity, which meets clinically useful criteria.
HOx budgets during HOxComp: A case study of HOx chemistry under NOx‐limited conditions

[1] Recent studies have shown that measured OH under NOx-limited, high-isoprene conditions are many times higher than modeled OH. In this study, a detailed analysis of the HOx radical budgets under low-NOx, rural conditions was performed employing a box model based on the Master Chemical Mechanism (MCMv3.2). The model results were compared with HOx radical measurements performed during the international HOxComp campaign carried out in Julich, Germany, during summer 2005. Two different air masses influenced the measurement site denoted as high-NOx (NO, 1–3 ppbv) and low-NOx (NO, < 1 ppbv) periods. Both modeled OH and HO2 diurnal profiles lay within the measurement range of all HOx measurement techniques, with correlation slopes between measured and modeled OH and HO2 around unity. Recently discovered interference in HO2 measurements caused by RO2 cross sensitivity was found to cause a 30% increase in measured HO2 during daytime on average. After correction of the measured HO2 data, the model HO2 is still in good agreement with the observations at high NOx but overpredicts HO2 by a factor of 1.3 to 1.8 at low NOx. In addition, for two different set of measurements, a missing OH source of 3.6 ± 1.6 and 4.9 ± 2.2 ppb h−1 was estimated from the experimental OH budget during the low-NOx period using the corrected HO2 data. The measured diurnal profile of the HO2/OH ratio, calculated using the corrected HO2, is well reproduced by the MCM at high NOx but is significantly overestimated at low NOx. Thus, the cycling between OH and HO2 is better described by the model at high NOx than at low NOx. Therefore, similar comprehensive field measurements accompanied by model studies are urgently needed to investigate HOx recycling under low-NOx conditions.
Computational Investigation on the Biomechanical Responses of the Osteocytes to the Compressive Stimulus: A Poroelastic Model

Osteocytes, the major type of bone cells embedded in the bone matrix and surrounded by the lacunar and canalicular system, can serve as biomechanosensors and biomechanotranducers of the bone. Theoretical analytical methods have been employed to investigate the biomechanical responses of osteocytes in vivo; the poroelastic properties have not been taken into consideration in the three-dimensional (3D) finite element model. In this study, a 3D poroelastic idealized finite element model was developed and was used to predict biomechanical behaviours (maximal principal strain, pore pressure, and fluid velocity) of the osteocyte-lacunar-canalicular system under 150-, 1000-, 3000-, and 5000-microstrain compressive loads, respectively, representing disuse, physiological, overuse, and pathological overload loading stimuli. The highest local strain, pore pressure, and fluid velocity were found to be highest at the proximal region of cell processes. These data suggest that the strain, pore pressure, and fluid velocity of the osteocyte-lacunar-canalicular system increase with the global loading and that the poroelastic material property affects the biomechanical responses to the compressive stimulus. This new model can be used to predict the mechanobiological behaviours of osteocytes under the four different compressive loadings and may provide an insight into the mechanisms of mechanosensation and mechanotransduction of the bone.