Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial Constraint Satisfaction of Disjunctive Temporal Problems

We present a method for finding optimal partial solutions to overconstrained instances of the Disjunctive Temporal Problems (DTP). The solutions are optimal in that they satisfy a maximal number of constraints. While partial constraint satisfaction (PCS) has been commonly applied to finite-domain CSPs, its application in this setting is of particular interest, as temporal problems are traditionally solved using a meta-CSP approach, in which the constraints of the original problem become the variables of the meta-level problem. We show how to adopt nearly all previous pruning techniques in DTP solving for use with PCS, and provide results demonstrating their effectiveness. We also introduce an incremental technique that leads to substantially improved performance.
Managing Problems of Postmodernity: Some Heuristics for Evaluation of Systems Approaches

According to social scientists the contemporary western societies manifest an unparalleled scientific, technological and economic development, and, at the same time, a normative, ethical and spiritual crisis. This imbalance makes the management of societal problems very difficult. In this research, the question of investigation is: what help does the contemporary scientific problem-management approaches provide to our postmodern societies? Hence in order to manage its problems, the contemporary western societies - that is us - have designed an amount of intellectual problem-solving instruments - called here systems approaches - such as Operations Research & Management Sciences, Systems Analysis, Systems Engineering, Decision Sciences, Cybernetics, Soft Systems Thinking, etc. This self-referentiality asks for investigation, that is, what is the relation between the characteristics of the contemporary western societies and the problem-solving instruments that these societies have conceived? By means of meta-modeling, a set of evaluation heuristics have been constructed and employed to some of the main contemporary problem-solving systems approaches. Two types of results have been obtained. First, evaluation heuristics have provided some new intelligibility that previous findings have not been able to do; therefore they seem to be a valuable addition to support an understanding of scientific problem-solving approaches. Second, the diversity of systems approaches promises to become a powerful support in managing societal problems when combined in the form of a toolbox, but, at the same time, an impotence of systems thinking has been identified with regard to its various religious ground-motives. The latter makes any prospects of human advancement pessimistic.
Spatial Patterns of Water Age: Using Young Water Fractions to Improve the Characterization of Transit Times in Contrasting Catchments

Transit time distributions (TTDs) are crucial descriptors of flow and transport processes in catchments, which can be determined from stable water isotope data. Recently, the young water fraction (Fyw) has been introduced as an additional metric derivable from seasonal isotope cycles. In this study, we calculated Fyw and TTDs using monthly isotope data from 24 contrasting subcatchments in a mesoscale catchment (3,300 km2) in Germany. Fyw ranged from 0.01 to 0.27 (mean = 0.11) and was smallest in mountainous catchments. Assuming gamma‐shaped TTDs, we determined stationary TTDs with the convolution integral method for each subcatchment. The convolution integral was first calibrated against the isotope data only (i.e., traditional calibration) and, second, using a multiobjective calibration with the Fyw estimates as an additional constraint. This yielded largely differing TTD parameters even for neighboring catchments, with Fyw values below 0.1 generally involving a delayed peak in TTDs (i.e., gamma‐distribution shape parameter > 1). While the traditional calibration resulted in large uncertainties in TTD parameters, these uncertainties were reduced with the multiobjective calibration, thereby improving the assessment of mean transit times (2 years on average, ranging between 9.6 months and 5.6 years). This highlights the need for uncertainty assessment when using simple isotope models and shows that the traditional calibration might not yield an optimum solution in that it may give a TTD nonconsistent with Fyw. Given the robustness of Fyw estimates, isotope models should thus aim at accurately describing both Fyw and measured isotope data in order to improve the description of flow and transport in catchments.
Segmentation of Bone with Region Based Active Contour Model in PD Weighted MR Images of Shoulder

Proton density (PD) weighted MR images present inhomogeneity problem, low signal to noise ratio (SNR) and cannot define bone borders clearly. Segmentation of PD weighted images is hampered with these properties of PD weighted images which even limit the visual inspection. The purpose of this study is to determine the effectiveness of segmentation of humeral head from axial PD MR images with active contour without edge (ACWE) model. We included 219 images from our original data set. We extended the use of speckle reducing anisotropic diffusion (SRAD) in PD MR images by estimation of standard deviation of noise (SDN) from ROI. To overcome the problem of initialization of the initial contour of these region based methods, the location of the initial contour was automatically determined with use of circular Hough transform. For comparison, signed pressure force (SPF), fuzzy C-means, and Gaussian mixture models were applied and segmentation results of all four methods were also compared with the manual segmentation results of an expert. Experimental results on our own database show promising results. This is the first study in the literature to segment normal and pathological humeral heads from PD weighted MR images.
On the tradeoff between economic efficiency and strategy proofness in randomized social choice

Two fundamental notions in microeconomic theory are efficiency---no agent can be made better off without making another one worse off---and strategyproofness---no agent can obtain a more preferred outcome by misrepresenting his preferences. When social outcomes are probability distributions (or lotteries) over alternatives, there are varying degrees of these notions depending on how preferences over alternatives are extended to preference over lotteries. We show that efficiency and strategyproofness are incompatible to some extent when preferences are defined using stochastic dominance (SD) and therefore introduce a natural weakening of SD based on Savage's sure-thing principle (ST). While random serial dictatorship is SD-strategyproof, it only satisfies ST-efficiency. Our main result is that strict maximal lotteries---an appealing class of social decision schemes due to Kreweras and Fishburn---satisfy SD-efficiency and ST-strategyproofness.
High Diversity Detection Using Semidefinite Relaxation

Receiver diversity is an important measure of a receivers robustness towards fading in wireless communications. For the detection of binary symbols transmitted over a general MIMO channel, the semidefinite relaxation (SDR) detector is a computationally attractive alternative to exact ML detection. In the SDR detector, the hard combinatorial optimization problem arising in the ML detector is relaxed into a simple convex optimization problem followed by component wise threshold decisions. In this work, we argue that the SDR detector will provide an increase in diversity over simpler decoder structures such as the ZF and MMSE detectors. Specifically, for the case of uncoded V-BLAST transmission over a MIMO channel with real valued i.i. d. Gaussian channel coefficients we present an analytic result stating that the SDR detector achieves the maximum possible receiver diversity.
Bayesian Model Assessment and Comparison Using Cross-Validation Predictive Densities

In this work, we discuss practical methods for the assessment, comparison, and selection of complex hierarchical Bayesian models. A natural way to assess the goodness of the model is to estimate its future predictive capability by estimating expected utilities. Instead of just making a point estimate, it is important to obtain the distribution of the expected utility estimate because it describes the uncertainty in the estimate. The distributions of the expected utility estimates can also be used to compare models, for example, by computing the probability of one model having a better expected utility than some other model. We propose an approach using cross-validation predictive densities to obtain expected utility estimates and Bayesian bootstrap to obtain samples from their distributions. We also discuss the probabilistic assumptions made and properties of two practical cross-validation methods, importance sampling and k-fold cross-validation. As illustrative examples, we use multilayer perceptron neural networks and gaussian processes with Markov chain Monte Carlo sampling in one toy problem and two challenging real-world problems.
Researching Genetic Versus Nongenetic Determinants of Disease: A Comparison and Proposed Unification

Current research designs that dissociate genetic and nongenetic measurements are reaching their limits. Research standards deviate in genetic versus nongenetic epidemiology. Besides some immutable differences, such as the correlation pattern between variables, these divergent research standards can converge considerably. Current research designs that dissociate genetic and nongenetic measurements are reaching their limits. Studies are needed that massively measure genotypes, nongenetic exposures, and outcomes concurrently.
The effect of muscle relaxants on cricothyroid muscle: a report of three cases.

The speed of onset and recovery rate from muscle relaxants depends on the potency of the drug, the dose of the drug, and the muscle group that is monitored. The diaphragm and the laryngeal muscles are more resistant to the effects of muscle relaxants than the more frequently monitored muscles of the hand, such as the adductor pollicis, which is innervated by the ulnar nerve. Several studies have been performed using electromyographic (EMG) responses of the diaphragm and transgastric pressure changes after stimulation of the phrenic nerve (1-7). Other studies have measured the response of the laryngeal muscles to neuromuscular blocking drugs by measuring tracheal tube cuff pressures after stimulation of the recurrent laryngeal nerve (8-10). The conclusion from all of these studies has been that the diaphragm and laryngeal muscles are more resistant to the effects of muscle relaxants, demonstrate the effects of the relaxant more rapidly, and have faster recovery than muscles of the hand. Despite these aforementioned studies, direct EMG measurement of the effects of muscle relaxants on the function of the cricothyroid muscle has not been previously reported. This article reports the electromyographic responses of the cricothyroid muscle to succinylcholine in one patient and to mivacurium in two patients undergoing modified bilateral radical neck dissection for malignant head and neck tumors. None of the patients received muscle relaxants after tracheal intubation until the motor nerves were identified prior to surgical resection. Body temperature was maintained between 35.5 and 37.0°C with the aid of forced air warming blankets in all three patients.
Asynchronous data fusion for AUV navigation via heuristic fuzzy filtering techniques

This paper presents a heuristic fuzzy position estimation technique for autonomous underwater vehicle navigation. The heuristic estimator performs asynchronous data fusion of all sensor measurements based on their relative confidence levels, and then nonlinearly combines the fused information with the INS estimates via fuzzy filtering techniques. In this paper, the basis and implementation of the estimator will be described, and navigation results will be presented based on the heuristic estimator. In addition, performance comparison based on the heuristic estimator and those based on extended Kalman filters will be reported in our companion paper, and the results are expected to provide insights into the pros and cons of individual methods in terms of computational cost, steady-state and convergence characteristics for bias estimation.
Correlation of DNA Methylation with Histone Modifications Across the HNRPA2B1-CBX3 Ubiquitously-Acting Chromatin Open Element (UCOE)

The methylation-free CpG island encompassing the divergently transcribed promoters of the HNRPA2B1 and CBX3 housekeeping genes possesses a dominant ubiquitously-acting chromatin opening element (UCOE) capability. This element allows reproducible and stable transgene expression including from within centromeric heterochromatin. We present an investigation of DNA methylation and histone modification marks across the HNRPA2B1-CBX3 locus in primary peripheral blood mononuclear cells (PBMCs) to characterise the chromatin structure that underlies UCOE activity. The CpG methylation-free region associated with the UCOE extends into the central areas of HNRPA2B1 and CBX3, with a total length of ~5kb. However, the DNA in the 3’ half of both genes is methylated. Histone H4 lysine (K) acetylation shows a broad distribution across both genes, whilst histone H3 lysine acetylation peaks around the transcriptional start sites and drops to background levels at the 3’ ends. Higher levels of H3K4 di-methylation are present at the 3’ end of the genes in contrast to H3K4 tri-methylation which peaks around the transcriptional start sites. Therefore, methylated DNA in transcribed regions of these genes has been shown here to co-exist with active histone modification marks, indicating that these functionally opposing epigenetic signatures can overlap. This suggests that an extended large region of unmethylated DNA in combination with distinct histone modification patterns are at the basis of UCOE function.
DEEP CONVECTIVE TRANSPORT AND WET SCAVENGING IN DIFFERENT CONVECTIVE REGIMES DURING THE DC3 FIELD CAMPAIGN

Title of Dissertation: DEEP CONVECTIVE TRANSPORT AND WET SCAVENGING IN DIFFERENT CONVECTIVE REGIMES DURING THE DC3 FIELD CAMPAIGN Yunyao Li, Doctor of Philosophy, 2018 Dissertation directed by: Research Professor Kenneth E. Pickering Department of Atmospheric and Oceanic Science Deep convective transport of surface moisture and pollution from the planetary boundary layer to the upper troposphere and lower stratosphere affects the radiation budget and climate. Firstly, I analyzed the deep convective transport through cloudresolved simulations of three different convective regimes from the 2012 Deep Convective Clouds and Chemistry (DC3) field campaign: an airmass thunderstorm, a supercell storm, and a mesoscale convective system (MCS). Analysis of vertical flux divergence shows that deep convective transport in the supercell case is the strongest per unit area, while transport of boundary layer insoluble trace gases is relatively weak in the MCS due to the injection of clean air into the mid-troposphere by a strong rear inflow jet. Additionally, forward and backward trajectories are used to determine the source of the upper-level detrained air. My second focus is using of cloud parameterized Weather Research and Forecasting model coupled with chemistry (WRF-Chem) simulations to analyze the subgrid deep convective transport in the supercell case and MCS case. Based on the precipitation results, the best WRF simulation of these storms was obtained with use of the GrellFreitas (GF) convective scheme. The default subgrid convective transport scheme was replaced with a scheme to compute convective transport within the GF subgrid cumulus parameterization, which resulted in improved transport simulations. The results demonstrate the importance of having subgrid convective transport consistent with the convective parameterization in regional models. Moreover, the subgrid scale convective transport played a more significant role in the supercell case than the MCS case. I evaluated the model-simulated subgrid wet scavenging of soluble trace gases (such as HNO3, CH2O, CH3OOH, H2O2, and SO2) in the supercell case, and improved subgrid wet scavenging by determining appropriate ice retention factors, and by adjusting the conversion rate of cloud water to rain water. The introduction of the ice retention factors greatly improved the model simulation of less soluble species (e.g. decreased the CH2O simulation error by 12 % and decreased the CH3OOH simulation error by 63%). Finally, I conducted a > 24-hour long simulation to examine downwind ozone production and its sensitivity to the ice retention factors. DEEP CONVECTIVE TRANSPORT AND WET SCAVENGING IN DIFFERENT CONVECTIVE REGIMES DURING THE DC3 FIELD CAMPAIGN
Application of the Spatial Database for Shoreline Change Analysis and Visualisation: Example from the Western Polish Coast, Southern Baltic Sea

Abstract The main aim of the study was to introduce a spatial database application for the estimation of changes in shoreline position. The open-source PostgreSQL database system with the PostGIS spatial extension was used as the data store for digitalised shorelines. The solution to calculations of the shoreline changes was based on the functions written in the PL/SQL language and geospatial functions provided by the PostGIS extension. The traditional baseline and transects method was used to quantify the distances and rate of shoreline movement. Outputs of the calculations were stored in the database table and simply visualised using graphical functions in the R software environment or in GIS Desktop software. The advantage of presented method is the application of SQL language in the analysis of the relation between the geometry of shorelines stored in the database table, which, compared to other similar solutions, gives the user fully open, simple analytical code and enable selecting custom parameters of analysis, modifying code and performing additional calculations.
Shear Bond Strength of Al2O3 Sandblasted Y-TZP Ceramic to the Orthodontic Metal Bracket

As the proportion of adult orthodontic treatment increases, mainly for aesthetic reasons, orthodontic brackets are directly attached to yttria-stabilized tetragonal zirconia polycrystal (Y-TZP) restorations. This, study analyzed the shear bond strength (SBS) between various surface treated Y-TZP and orthodontic metal brackets. The Y-TZP specimens were conditioned by 110 μm Al2O3 sandblasting, or sandblasting followed by coating with one of the primers (silane, MDP, or an MDP-containing silane primer). After surface treatment, the orthodontic metal bracket was bonded to the specimen using a resin cement, and then 24 h storage in water and thermal cycling (5000 cycles, 5–55 °C), SBS was measured. Surface roughness was analyzed for surface morphology, and X-ray photoelectron spectroscopy (XPS) was employed for characterization of the chemical bond between the Y-TZP and the MDP-based primers (MDP, MDP containing silane primer). It was found that after surface treatment, the surface roughness of all groups increased. The groups treated with 110 μm Al2O3 sandblasting and MDP, or MDP-containing silane primer showed the highest SBS values, at 11.92 ± 1.51 MPa and 13.36 ± 2.31 MPa, respectively. The SBS values significantly decreased in all the groups after thermal cycling. Results from XPS analysis demonstrated the presence of chemical bonds between Y-TZP and MDP. Thus, the application of MDP-based primers after Al2O3 sandblasting enhances the resin bond strength between Y-TZP and the orthodontic metal bracket. However, bonding durability of all the surface-treated groups decreased after thermal cycling.
Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.
Inhibition of Human Cytomegalovirus DNA Polymerase by C-Terminal Peptides from the UL54 Subunit

ABSTRACT In common with other herpesviruses, the human cytomegalovirus (HCMV) DNA polymerase contains a catalytic subunit (Pol or UL54) and an accessory protein (UL44) that is thought to increase the processivity of the enzyme. The observation that antisense inhibition of UL44 synthesis in HCMV-infected cells strongly inhibits viral DNA replication, together with the structural similarity predicted for the herpesvirus processivity subunits, highlights the importance of the accessory protein for virus growth and raises the possibility that the UL54/UL44 interaction might be a valid target for antiviral drugs. To investigate this possibility, overlapping peptides spanning residues 1161 to 1242 of UL54 were synthesized and tested for inhibition of the interaction between purified UL54 and UL44 proteins. A peptide, LPRRLHLEPAFLPYSVKAHECC, corresponding to residues 1221 to 1242 at the very C terminus of UL54, disrupted both the physical interaction between the two proteins and specifically inhibited the stimulation of UL54 by UL44. A mutant peptide lacking the two carboxy-terminal cysteines was markedly less inhibitory, suggesting a role for these residues in the UL54/UL44 interaction. Circular dichroism spectroscopy indicated that the UL54 C-terminal peptide can adopt a partially α-helical structure. Taken together, these results indicate that the two subunits of HCMV DNA polymerase most likely interact in a way which is analogous to that of the two subunits of herpes simplex virus DNA polymerase, even though there is no sequence homology in the binding site, and suggest that the UL54 peptide, or derivatives thereof, could form the basis for developing a new class of anti-HCMV inhibitors that act by disrupting the UL54/UL44 interaction.