Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-conformal, non-overlapped IE-DDM for complicated multi-scale objects

To realize efficient solution of complicated multi-scale conducting objects, non-conformal, non-overlapped integral equation based domain decomposition method (IE-DDM) is developed. Based on Robin transmission condition, the normal continuity of surface currents on non-conformal touching faces is maintained. Different fast solvers like multilevel fast multipole algorithm, adaptive cross approximation can be used for different sub-domains. The flexibility of the present method enables us efficient analysis of electromagnetic scattering from 3D multi-scale objects. Some examples are shown in order to demonstrate the ability of the IE-DDM.
Proceedings of the Workshop on Constraint Satisfaction Techniques for Planning and Scheduling Problems

We study an unrelated parallel machines scheduling problem with sequence and machine dependent setup times. A logicbased Benders decomposition approach is proposed to minimize the makespan. The decomposition approach is a hybrid model that makes use of a mixed integer programming master problem and a travelling salesman problem subproblem. The master problem is a relaxation of the problem and is used to create assignments of jobs to machines, while the subproblem obtains optimal schedules based on the master problem assignments. Computational results comparing the Benders decomposition and mixed integer program formulation show that the Benders model is able to find optimal solutions to problems up to five orders of magnitude faster as well as solving problems four times the size possible previously.
Numerical simulations of 3D micro-resonators

Micro-resonators are critical optical components that have many exciting applications in fields such as telecommunications, quantum cryptography and optical signal processing. Fabrication techniques allow many different designs of micro-resonator to be realised, but at present their optimisation and simulation remain firmly entrenched in 2D. The geometrical complexity of many micro-resonators mitigates against analytic study. Thus there is a strong demand for comprehensive 3D numerical simulations. We discuss some of the difficulties and challenges when modelling micro-resonators and recent progress towards their 3D modelling using time-domain codes.
Cell death and proliferation characteristics of the retina after optic nerve section in chickens

I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. Abstract Optic nerve section (ONS) is an experimental model for damage of the optic nerve associated with diseases such as glaucoma and optic neuritis. Damage to the optic nerve causes loss of retinal ganglion cells that are attached, once the cells are damaged, they are not typically replaced. Recently, Fischer and Reh (2003) found that Müller glia have the potential to adopt phenotypes and functional capabilities similar to those of retinal progenitors, a potential source of retinal regeneration. In the chick, when the specific retinal cells are targeted for damage by chemotoxins, there is widespread apoptosis but also mitotically active cells that label with retinal progenitor markers. Fischer and Reh (2002) also discovered that the combination of growth factors FGF2 and insulin is capable of stimulating the regenerative response of the Müller glia to retinal progenitor cells in chick eyes. This study was conducted to analyse damage to the ganglion cells by optic nerve section in chicks to determine the effect of age on the cell death timeline, the proliferative qualities of the retina and to see if injections of growth factors had the ability to increase the proliferation. Histological methods were used to analyse cellular changes and ultrasound to monitor eye growth. Apoptotic activity preceded retinal thinning and ganglion cell loss, indicating that ONS-related cell death is mediated at least in part by apoptotic mechanisms and age did not affect the time course, although, age did affect the eye growth changes, which may be attributed to the plasticity of the younger eyes. ONS damage elicited proliferative activity in the retina as did growth factor injections alone. The combination of ONS damage and growth factor injections increased the proliferative activity and the overall total number of cells in the ganglion cell layer. These findings can potentially lead to the development of therapeutic strategies for the preservation or restoration of retinal cells in diseased eyes. iv Acknowledgements
Uncovering precision phenotype-biomarker associations in traumatic brain injury using topological data analysis

Background Traumatic brain injury (TBI) is a complex disorder that is traditionally stratified based on clinical signs and symptoms. Recent imaging and molecular biomarker innovations provide unprecedented opportunities for improved TBI precision medicine, incorporating patho-anatomical and molecular mechanisms. Complete integration of these diverse data for TBI diagnosis and patient stratification remains an unmet challenge. Methods and findings The Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot multicenter study enrolled 586 acute TBI patients and collected diverse common data elements (TBI-CDEs) across the study population, including imaging, genetics, and clinical outcomes. We then applied topology-based data-driven discovery to identify natural subgroups of patients, based on the TBI-CDEs collected. Our hypothesis was two-fold: 1) A machine learning tool known as topological data analysis (TDA) would reveal data-driven patterns in patient outcomes to identify candidate biomarkers of recovery, and 2) TDA-identified biomarkers would significantly predict patient outcome recovery after TBI using more traditional methods of univariate statistical tests. TDA algorithms organized and mapped the data of TBI patients in multidimensional space, identifying a subset of mild TBI patients with a specific multivariate phenotype associated with unfavorable outcome at 3 and 6 months after injury. Further analyses revealed that this patient subset had high rates of post-traumatic stress disorder (PTSD), and enrichment in several distinct genetic polymorphisms associated with cellular responses to stress and DNA damage (PARP1), and in striatal dopamine processing (ANKK1, COMT, DRD2). Conclusions TDA identified a unique diagnostic subgroup of patients with unfavorable outcome after mild TBI that were significantly predicted by the presence of specific genetic polymorphisms. Machine learning methods such as TDA may provide a robust method for patient stratification and treatment planning targeting identified biomarkers in future clinical trials in TBI patients. Trial Registration ClinicalTrials.gov Identifier NCT01565551
TNFAIP3 Maintains Intestinal Barrier Function and Supports Epithelial Cell Tight Junctions

Tight junctions between intestinal epithelial cells mediate the permeability of the intestinal barrier, and loss of intestinal barrier function mediated by TNF signaling is associated with the inflammatory pathophysiology observed in Crohn's disease and celiac disease. Thus, factors that modulate intestinal epithelial cell response to TNF may be critical for the maintenance of barrier function. TNF alpha-induced protein 3 (TNFAIP3) is a cytosolic protein that acts in a negative feedback loop to regulate cell signaling induced by Toll-like receptor ligands and TNF, suggesting that TNFAIP3 may play a role in regulating the intestinal barrier. To investigate the specific role of TNFAIP3 in intestinal barrier function we assessed barrier permeability in TNFAIP3−/− mice and LPS-treated villin-TNFAIP3 transgenic mice. TNFAIP3−/− mice had greater intestinal permeability compared to wild-type littermates, while villin-TNFAIP3 transgenic mice were protected from increases in permeability seen within LPS-treated wild-type littermates, indicating that barrier permeability is controlled by TNFAIP3. In cultured human intestinal epithelial cell lines, TNFAIP3 expression regulated both TNF-induced and myosin light chain kinase-regulated tight junction dynamics but did not affect myosin light chain kinase activity. Immunohistochemistry of mouse intestine revealed that TNFAIP3 expression inhibits LPS-induced loss of the tight junction protein occludin from the apical border of the intestinal epithelium. We also found that TNFAIP3 deubiquitinates polyubiquitinated occludin. These in vivo and in vitro studies support the role of TNFAIP3 in promoting intestinal epithelial barrier integrity and demonstrate its novel ability to maintain intestinal homeostasis through tight junction protein regulation.
Selaginella and the Satyr: Euptychia westwoodi (Lepidoptera: Nymphalidae) Oviposition Preference and Larval Performance

Members of the plant genus Selaginella (de Beauvois 1805) have few known insect herbivores even though they are considered by some to be ‘living fossils’, with extant taxa virtually indistinguishable from 300 Mya fossils. Butterflies are well-known herbivores, and the satyrs are among the most speciose of them despite having radiated ∼35 Mya ago. Nearly all satyrs feed on grass or sedges, but members of the Neotropical genus Euptychia Hübner 1818 feed on Selaginella; little is known about the degree to which this butterfly favors this ancient plant over those that its close relatives utilize. To advance our knowledge of Euptychia natural history, we conducted a series of experiments to examine oviposition preference and growth rates across a series of potential host plants on a Euptychia westwoodi population in Costa Rica. We found that Euptychia westwoodi Butler 1867 exhibit a strong preference to oviposit on Selaginella eurynota over the sympatric Selaginella arthritica, though they perform equally well as larvae on both plants. We did not observe oviposition on a sympatric grass that is commonly consumed by close relatives of E. westwoodi, and when larvae were offered the grass they refused to eat. These results suggest that E. westwoodi in Costa Rica exhibit a strong preference for Selaginella and may have lost the ability to feed on a locally abundant grass commonly used by other Satyrinae.
FPGA Based Sensor Integration and Communication Protocols for Automated Robot Control in Linear Welding

Electric arc welding is a complex task that is mainly hand-operated in shop floors nowadays. A high degree of process control is necessary to meet the international standards for fusion welding. Focused on this application case, we designed a camera interface that integrates a Terasic TRDB-D5M CMOS camera and an Altera DE0-Nano FPGA board which are used for image acquisition on a Vision-Based Measurement (VBM) system that executes on a computer. Given the board limitations in terms of memory, clock, and connectivity many features and protocols were developed from scratch. We present a system level modeling and synthesis and the integration to the whole digital linear welding system, using only 28% of the FPGA's slices. Results show the approach is a viable option to automate the process that is currently widely adopted in industry.
Harmful Effects of Recreational Ecstasy Use on Memory Functioning

MDMA (3,4-methylenedioxymethamphetamine), often referred to as ‘ecstasy’, has been shown to selectively and persistently impair central serotonergic neurotransmission in laboratory animals. As of recent, evidence in human studies has suggested a link between recreational ecstasy use and a disruption of the brain’s serotonergic system. However, human neurocognitive and neuroimaging studies have yielded inconsistent findings regarding the functional impact of these neuro-adaptations, possibly due to methodological difficulties. Although the literature on the effects of recreational ecstasy use on neurocognitive function remains inconclusive, studies have most consistently shown negative effects on memory. Here, we provide a review of accumulating evidence supporting a link between recreational ecstasy use and impaired memory.
Estimation of Japanese DRT intelligibility using Articulation Index Band Correlations

We proposed and evaluated an estimation method for the forced selection Japanese Diagnostic Rhyme Test (DRT). The proposed measure takes into account the forced selection manner of the DRT from a pair of rhyming words. The objective distance measure used here was based on the Articulation index Band Correlation (ABC), which showed favorable results for the English Modified Rhyme Test (MRT). The correlation of time-frequency patterns between the test word and the template word speech of the two words in the candidate word pair was calculated. The word with the higher correlation was decided to be the likely candidate word. The time-frequency (T-F) pattern was calculated in the Articulation Index (AI) bands, and the correlation was calculated between the corresponding bands of the test and candidate word sample. The candidate word with more AI bands showing higher correlation values was finally chosen. The ratio of bands with higher correlation with the candidate word vs. the total number of bands is calculated to quantify how well the test word matches the candidate word in the word pair. We estimated a logistic mapping function from this ratio to intelligibility scores using speech mixed with known noise. The mapping functions were then used to estimate the intelligibility of speech mixed with unknown noise. This estimation was compared to another measure that we previously have evaluated, the frequency-weighed segmental SNR, and was proven to be more accurate, with the correlation between estimated and estimated intelligibility over 0.93, and the root mean square below 0.15. Thus, it should be possible to "screen" the intelligibility in many of the noise conditions to be tested, and cut down on the scale of the subjective test needed.
Crosslinked chitosan-dextran sulfate nanoparticle for improved topical ocular drug delivery

Purpose To examine the benefits of chitosan-dextran sulfate nanoparticles (CDNs) as a topical ocular delivery system with lutein as a model drug. Methods CDNs were developed by polyelectrolyte complexation of positively charged chitosan (CS) and negatively charged dextran sulfate (DS). 1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) and polyethylene glycol 400 (PEG400) were used as co-crosslinking and stabilizing agents, respectively. The influence of these on the properties of CDNs, including drug release and mucoadhesiveness, was examined. The chemical stability of lutein in CDNs (LCDNs) was also examined. Results Typically, LCDNs showed a spherical shape, possessing a mean size of ~400 nm with a narrow size distribution. The entrapment efficiency of lutein was in the range of 60%–76%. LCDNs possessing a positive surface charge (+46 mV) were found to be mucoadhesive. The release profile of LCDNs followed Higuchi’s square root model, suggesting drug release by diffusion from the polymer matrix. Lutein in LCDNs showed increased chemical stability during storage compared to its solution form. Conclusions These characteristics of CDNs make them suitable for drug delivery to the ocular surface.
The impact of plant associations on Macrosteles quadrilineatus management in carrots

Habitat diversification can influence the interactions of insects with plants and this can be used in agroecosystems for the management of pest populations. Plant diversification can be achieved through planting crops, such as trap crops, or by adjusting weed management. Aster leafhopper, Macrosteles quadrilineatus Forbes (Hemiptera: Cicadellidae), is a polyphagous species that uses cereals, vegetables, and weeds as host plants. The influence of weeds on M. quadrilineatus abundance was investigated experimentally in carrot [Daucus carota L. cv. Canada (Apiaceae)] field plots by adjusting the level of management of two groups of weeds (broadleaf and grass) and by comparing it to weed‐free plots. The preference of M. quadrilineatus for different cereal and weed species relative to carrots was tested in choice test assays. Habitat context influenced the abundance of M. quadrilineatus in the field experiments. The presence of border crops such as oat, rye, barley, wheat, and triticale did not significantly attract or repel this insect to carrot plots compared to the no‐border treatment. However, spelt‐bordered plots had 42% fewer M. quadrilineatus than three treatments, triticale, wheat, and barley, that had the highest insect abundance. The type of weed management affected M. quadrilineatus abundance in carrot plots, but not the frequency of herbicide application. Plots that had carrot growing with broadleaf‐weeds had about 59% fewer M. quadrilineatus compared with those growing with crabgrass or carrot alone. In the greenhouse choice tests, grasses (e.g., cereals) attracted and broadleaf‐weeds repelled M. quadrilineatus relative to carrots. In summary, carrot growers may be able to manage this pest by reducing the interaction of cereal cover crops with carrots and eliminating grassy weeds in commercial production fields.
Prison voices: Lessons on youth recidivism

Bailey, Shad E. Ph.D., Ed.D. , May 2004 Educational Leadership Prison Voices: Lessons on Youth Recidivism Director: Roberta D. Evans, Ed.D. This qualitative study examined the experiences of home, school, and community by incarcerated males at Montana State Prison, a maximum-security prison in Deer Lodge, Montana. These perceptions were examined using qualitative data techniques to gain new insight regarding how the experiences of inmates can influence the approaches taken with children today. A purposefully selected sample of 30 volunteers was subjected to a taped interview at the prison. An interview protocol inquiring about experiences in school, home, and community were used to refine extant grounded theories. The data were transcribed and submitted to analysis following the prescription of Strauss and Corbin (1998). The processes of open, axial and selective coding resulted in eight distinct categories of data, including: (a) Early Trauma, (b) Skipping School, (c) Number of Schools Attended, (d) Teacher Attributes, and (e) Suggestions for Teachers. The following conclusions were delineated: 1. Prisoners reveal early trauma to have a profound impact on the future successes of children. The ability to complete schoolwork, establish positive fi*iendships, and feel a sense of self-worth is associated in part on either the absence of early trauma or the ability of caregivers to provide necessary counseling to assure the impact of early trauma is negated. 2. Prisoners believe the prevention of the use of drugs and alcohol is critical to the health and well being of young people, as well as criminality deterrence. 3. Prisoners feel adolescents who have not yet been incarcerated but who exhibit such patterns need intervention and whole-family counseling. 4. Prisoners recognize that many first-time mothers need parenting information and help. Indeed, instructional “welcoming” visits to new mothers would be highly beneficial. 5. Prisoners believe educators’ ability to recognize family neglect and abuse in children, then to work aggressively to address diverse needs would go a long way toward ameliorating youth recidivism in the juvenile justice system. ii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission.
Ivy League Bound: A Case Study of a Brilliant African American Male Mathematics Major

ABSTRACT: The educational outcomes of African American male students have been examined by several researchers, and there is a growing body of research reporting on African American male students’ academic talents and gifts. This qualitative case study examines the racial and academic experiences of Malik, an African American male mathematics major. His case is reported and analyzed across three developmental stages: 1) early childhood and adolescence, 2) secondary schooling years, and 3) college years. In this article, critical race theory (CRT) is used to document and analyze his experiences. Finally, implications for research and practice are shared to advance research in this area and promote the brilliance of African American male students.
Calibration of human cardiac ion current models to patch clamp measurement data

Generally, models of cardiac electrophysiology describe physiologic conditions in detail. However, other conditions, such as drug interactions or mutations of ion channels are of interest for research. Therefore, the simulated ion currents have to be fitted to measured voltage or patch clamp data. In this work, three different methods for the model parametrization were compared: one based on Powell's algorithm implemented in a modular C++ framework and two optimization techniques realized in Matlab. The latter two approaches differed in solving the ordinary differential equations describing the channel gating. They can either be approximated numerically or solved analytically, since the transmembrane voltage is a piecewise constant function during the applied clamp protocol. All three methods were compared regarding computing time and quality of the fit using least squares. The modular C++ framework was slower than the numerical Matlab method, which took longer than the analytical one. The quality of the fit was similar for almost all analyzed methods. Therefore, the analytical method grants a fast and reliable solution for the calibration of ion current models for applications with constant membrane voltage, as e.g. in case of voltage or patch clamp data.
State and parameter estimation of the heat shock response system using Kalman and particle filters

MOTIVATION Traditional models of systems biology describe dynamic biological phenomena as solutions to ordinary differential equations, which, when parameters in them are set to correct values, faithfully mimic observations. Often parameter values are tweaked by hand until desired results are achieved, or computed from biochemical experiments carried out in vitro. Of interest in this article, is the use of probabilistic modelling tools with which parameters and unobserved variables, modelled as hidden states, can be estimated from limited noisy observations of parts of a dynamical system. RESULTS Here we focus on sequential filtering methods and take a detailed look at the capabilities of three members of this family: (i) extended Kalman filter (EKF), (ii) unscented Kalman filter (UKF) and (iii) the particle filter, in estimating parameters and unobserved states of cellular response to sudden temperature elevation of the bacterium Escherichia coli. While previous literature has studied this system with the EKF, we show that parameter estimation is only possible with this method when the initial guesses are sufficiently close to the true values. The same turns out to be true for the UKF. In this thorough empirical exploration, we show that the non-parametric method of particle filtering is able to reliably estimate parameters and states, converging from initial distributions relatively far away from the underlying true values. AVAILABILITY AND IMPLEMENTATION Software implementation of the three filters on this problem can be freely downloaded from http://users.ecs. soton.ac. uk/mn/HeatShock