Miracle-dz/UniFAR-FTUs huggingface dataset:
Fully-Connected CRFs with Non-Parametric Pairwise Potential

Conditional Random Fields (CRFs) are used for diverse tasks, ranging from image denoising to object recognition. For images, they are commonly defined as a graph with nodes corresponding to individual pixels and pairwise links that connect nodes to their immediate neighbors. Recent work has shown that fully-connected CRFs, where each node is connected to every other node, can be solved efficiently under the restriction that the pairwise term is a Gaussian kernel over a Euclidean feature space. In this paper, we generalize the pairwise terms to a non-linear dissimilarity measure that is not required to be a distance metric. To this end, we propose a density estimation technique to derive conditional pairwise potentials in a non-parametric manner. We then use an efficient embedding technique to estimate an approximate Euclidean feature space for these potentials, in which the pairwise term can still be expressed as a Gaussian kernel. We demonstrate that the use of non-parametric models for the pairwise interactions, conditioned on the input data, greatly increases expressive power whilst maintaining efficient inference.
Bridging the Gap between Deterministic and Stochastic Modeling with Automatic Scaling and Conversion

During the past decade, many successful deterministic models of macromolecular regulatory networks have been built. Deterministic simulations of these models can show only average dynamics of the systems. However, stochastic simulations of macromolecular regulatory models can account for behaviors that are introduced by the noisy nature of the systems but not revealed by deterministic simulations. Thus, converting an existing model of value from the most common deterministic formulation to one suitable for stochastic simulation enables further investigation of the regulatory network. Although many different stochastic models can be developed and evolved from deterministic models, a direct conversion is the first step in practice. This conversion process is tedious and error-prone, especially for complex models. Thus, we seek to automate as much of the conversion process as possible. However, deterministic models often omit key information necessary for a stochastic formulation. Specifically, values in the model have to be scaled before a complete conversion, and the scaling factors are typically not given in the deterministic model. Several functionalities helping model scaling and converting are introduced and implemented in the JigCell modeling environment. Our tool makes it easier for the modeler to include complete details as well as to convert the model. Stochastic simulations are known for being computationally intensive, and thus require high performance computing facilities to be practical. With parallel computation on Virginia Tech’s System X supercomputer, we are able to obtain the first stochastic simulation results for realistic cell cycle models. Stochastic simulation results for several mutants, which are thought to be biologically significant, are presented. Successful deployment of the enhanced modeling environment demonstrates the power of our techniques.
Development of System for the Automatic Generation of Unknown Virus Extermination Software

In recent years, there has been a frequent occurrence of virus-related incidents, including cases where a virus infection has caused the unauthorized release of confidential information. Viruses should be considered a society-level security risk. However, the mainstream approach to addressing a virus is basically to implement countermeasures for the virus after the damage has occurred. Some of these countermeasures are unable to keep up with the current pace at which viruses are occurring. To address this problem, in this research, we developed a system to generate unknown virus extermination software automatically, without any manual operations. The developed system is designed to automatically generate software that detects and exterminates an unknown virus, by using both a dynamic heuristic that uses a virtual PC and a technique to automatically generate a signature from header data in the virus executable. We were able to verify the effectiveness of this system when we conducted experiments to check whether or not an actual virus could be exterminated by a vaccine that was automatically created for the virus with the developed system
Correlation Between SAR and Temperature Rise Distributions with Different Masses and Schemes of Averaging, Child Head, Dipole Antenna Radiation at 1800 MHz

This paper attempts to investigate relationship between specific absorption rate (SAR) obtained for different averaging volumes, different averaging schemes and temperature increase based on correlation analysis of their distributions in the child head for the frac14-length dipole antenna radiation at 1800 MHz. Different averaging masses and several SAR averaging procedures are considered. The goal of this investigation is to derive the best SAR related metric that describes the thermal response of the exposed tissue.
An inorganic geochemical argument for coupled anaerobic oxidation of methane and iron reduction in marine sediments

Here, we present results from sediments collected in the Argentine Basin, a non‐steady state depositional marine system characterized by abundant oxidized iron within methane‐rich layers due to sediment reworking followed by rapid deposition. Our comprehensive inorganic data set shows that iron reduction in these sulfate and sulfide‐depleted sediments is best explained by a microbially mediated process—implicating anaerobic oxidation of methane coupled to iron reduction (Fe‐AOM) as the most likely major mechanism. Although important in many modern marine environments, iron‐driven AOM may not consume similar amounts of methane compared with sulfate‐dependent AOM. Nevertheless, it may have broad impact on the deep biosphere and dominate both iron and methane cycling in sulfate‐lean marine settings. Fe‐AOM might have been particularly relevant in the Archean ocean, >2.5 billion years ago, known for its production and accumulation of iron oxides (in iron formations) in a biosphere likely replete with methane but low in sulfate. Methane at that time was a critical greenhouse gas capable of sustaining a habitable climate under relatively low solar luminosity, and relationships to iron cycling may have impacted if not dominated methane loss from the biosphere.
Dietary Patterns and Trends in the United States: The UNC-CH Approach

Over the past 2 decades our group of nutrition and economics researchers at the University of North Carolina at Chapel Hill has used a wide array of methods to study eating patterns and dietary trends. Our focus has been on characterising the way diet has changed over time and identifying some of the major factors underlying these trends. The complexity of this undertaking has led us to develop a number of unique systems for classifying foods and assessing the overall quality of diet. We have also addressed the challenges that exist when measuring changes in both the food supply and food-related behaviors over time. This paper summarises some of the methodological work related to food grouping, overall diet quality indices, and trends research as well as the challenges we still face in this arena.
Ordering the Cell Death Pathway

Previous studies indicate that activation of c-Jun kinase (JNK) is necessary for apoptosis of trophic factor-deprived PC12 cells and that death in this system is suppressed by multiple agents, including BCL2, inhibitors of the interleukin-1-converting enzyme (ICE) family of proteases, blockers of transcription, and a variety of small molecules with differing modes of action. Here, we determine the order in which these agents block apoptosis relative to JNK activation. Overexpression of BCL2 promotes PC12 cell survival and blocks JNK activation caused by trophic factor withdrawal. Similarly, the survival-promoting agents aurintricarboxylic acid, N-acetylcysteine, the nitric oxide generator diethylenetriamine nitric oxide, 8-bromo-cGMP, and 8-(4-chlorophenylthio)-cAMP act upstream to inhibit JNK activation. In contrast, zVAD-fluoromethylketone (a permeant ICE family inhibitor), actinomycin D, and the G1/S cell cycle inhibitor deferoxamine, all promote survival after trophic factor withdrawal, but do not affect JNK activation. These findings are consistent with the presence of an ordered cell death pathway triggered by trophic factor deprivation in which 1) BCL2 and a number of survival-promoting agents act upstream of JNK, 2) ICE family protease actions, regulated genes required for cell death, and certain cell cycle blockers lie either downstream of JNK or on independent pathways required for apoptotic death.
Sampling and Variance Analysis for Monte Carlo Integration in Spherical Domain. (Analyse de Variance et Échantillonnage pour l'intégration Monte Carlo sur la sphère)

This dissertation introduces a theoretical framework to study different sampling patterns in the spherical domain and their effects in the evaluation of global illumination integrals. Evaluating illumination (light transport) is one of the most essential aspect in image synthesis to achieve realism which involves solving multi-dimensional space integrals. Monte Carlo based numerical integration schemes are heavily employed to solve these high dimensional integrals. One of the most important aspect of any numerical integration method is sampling. The way samples are distributed on an integration domain can greatly affect the final result. For example, in images, the effects of various sampling patterns appear in the form of either structural artifacts or completely unstructured noise. In many cases, we may get completely false (biased) results due to the sampling pattern used in integration. The distribution of sampling patterns can be characterized using their Fourier power spectra. It is also possible to use the Fourier power spectrum as input, to generate the corresponding sample distribution. This further allows spectral control over the sample distributions. Since this spectral control allows tailoring new sampling patterns directly from the input Fourier power spectrum, it can be used to improve error in integration. However, a direct relation between the error in Monte Carlo integration and the sampling power spectrum is missing. In this work, we propose a variance formulation, that establishes a direct link between the variance in Monte Carlo integration and the power spectra of both the sampling pattern and the integrand involved. To derive our closed-form variance formulation, we use the notion of homogeneous sample distributions that allows expression of error in Monte Carlo integration, only in the form of variance. Based on our variance formulation, we develop an analysis tool that can be used to derive theoretical variance convergence rates of various state-of-the-art sampling patterns. Our analysis gives insights to design principles that can be used to tailor new sampling patterns based on the integrand
Measurement of Elastic Constants of Nanohoneycomb Structures

Five engineering constants of transversely isotropic nanohoneycomb material are obtained, using one tensile test, two bending tests, and two indentation tests. The advantage is that all these tests can be carried out using only simple beam shape specimens. In all but the tensile test, a desired material constant is to be extracted from mixed materials constants. A disadvantage is that the deviation of the desired material constants are increased by the deviation of other related material constants. This is the first attempt to measure mechanical properties of microscopic specimens of brittle transversely isotropic material. It is intended to lay the foundation for easy and simple measurement of complex material constants of microscopic specimens.
Molecular dynamics simulation of a binary mixture lubricant for use in hard disk interfaces

In Hard Disk Drives (HDD), it is necessary to decrease the Flying Height (FH) between the head and the disk (currently, FH is around 3-5 nm) so as to increase recording densities. Retaining the solid lubricant has become a difficult proposition owing to intermittent contact between the surfaces. ZTMD and Z are used as solid lubricant to lubricate these interfaces. In this paper, the behavior of the binary mixture lubricant such as ZTMD & Z is modeled and analyzed using Molecular Dynamics (MD) simulation with the help of GROMACS software. It can be observed from simulation studies that ZTMD has poor replenishment performance although it possesses good retention properties. Addition of Z molecules improves replenishment performance of whole system. When ZTMD molecules alone are modeled, final structure attains stable state only at -4800 kJmol -1 . After the addition of Z molecules, final structure (ZTMD+Z) attains more stable state at -6950 kJ mol -1 . When compared to ZTMD, binary mixture lubricants (ZTMD + Z) are considered as more stable and for use in HDDs for their efficient operation.
Estradiol Metabolites Inhibit Endothelin Synthesis by an Estrogen Receptor-Independent Mechanism

Estradiol inhibits endothelin-1 synthesis, an effect that may contribute to the cardiovascular protective effects of estradiol. Recent findings that estradiol inhibits neointima formation in mice lacking estrogen receptors suggests that the cardiovascular protective effects of estradiol may be mediated by means of an estrogen receptor-independent mechanism. Because 2-hydroxyestradiol and 2-methoxyestradiol, metabolites of estradiol with little/no affinity for estrogen receptors, are more potent than estradiol in inhibiting vascular smooth muscle cell growth, we investigated whether these metabolites also inhibit endothelin-1 synthesis by means of an receptor-independent mechanism. Treatment of porcine coronary artery endothelial cells for 4 to 24 hours with 0.001 to 1 &mgr;mol/L of estradiol, 2-hydroxyestradiol, or 2-methoxyestradiol concentration-dependently inhibited basal as well as serum-induced (2.5%), TNF&agr;-induced (10 ng/mL), angiotensin II–induced (100 nmol/L), and thrombin-induced (4 U/mL) endothelin-1 synthesis. Estradiol, 2-hydroxyestradiol, and 2-methoxyestradiol also inhibited serum-induced mitogen-activated protein kinase activity. As compared with estradiol, its metabolites were more potent in inhibiting endothelin-1 secretion and mitogen activated protein kinase activity. The inhibitory effects of 2-hydroxyestradiol and 2-methoxyestradiol on endothelin-1 release and mitogen-activated protein kinase activity were not blocked by ICI182780 (50 &mgr;mol/L), an estrogen receptor antagonist. Our findings indicate that the estradiol metabolites 2-hydroxyestradiol and 2-methoxyestradiol potently inhibit endothelin-1 synthesis by means of an estrogen receptor-independent mechanism. This effect of estradiol metabolites may be mediated by inhibition of mitogen activated protein kinase activity and may contribute to the cardioprotective effects of estradiol.
Post-Transcriptional and Epigenetic Regulation of Antigen Processing Machinery (APM) Components and HLA-I in Cervical Cancers from Uighur Women

Normal function of human leukocyte antigen class I (HLA-I) and antigen processing machinery (APM) proteins is required for T cell-mediated anti-tumor or antiviral immunity, whereas the tumor survival indicates a failure of the host in immune surveillance associated with the dysfunction in antigen presentation, mainly due to the deregulation in HLA-I and APM expression or function. The posttranscriptional regulation of HLA-I and APM expression may associate with epigenetic modifications in cancer development which was not described so far. Here we showed that the development of cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (CSCC) in Uighur women was accompanied with the partial or total loss of protein expression of HLA-I, ß2-m and APM components, including the transporter associated with antigen processing (TAP1/2), low molecular mass protein (LMP2, LMP7), endoplasmic reticulum aminopeptidase 1(ERAP1), chaperone molecules include calreticulin (CLR), calnexin (CNX) and ERp57, and this was proved again by analysis of transcription of the same genes in addition to three genes HLA-A, B and C coding for HLA-I. By bisulfite sequencing approach, we identified target CpG islands methylated at the gene promoter region of TAP1, TAP2, LMP7, tapasin and ERp57 in cervical carcinoma cells. Further analysis of CpG site specific methylation of these genes in cases of CSCC and CIN demonstrated an inverse correlation of altered CpG island methylation of TAP1, LMP7, and ERp57 with changes in protein expression. Moreover, promoter methylation of these genes was significantly higher in cases positive for human papillomavirus 16 (HPV 16) than negative ones. Our results suggested that epigenetic modifications are responsible for the aberrant expression of certain HLA-I and APM genes, and may help to understand unrevealed mechanisms of tumor escape from immune surveillance in cervical carcinogenesis.
The middle evoked response components and schizophrenia.

In a subject sitting quietly without a specific task, the largest evoked potential (EP) components are the middle three—a positive, negative, positive sequence occurring at 50-100, 110-140, and 160-200 milliseconds. These components, termed P100, N140, and P200 in this review, were initially observed in the raw electroencephalogram (EEG) in a few subjects before the advent of signal averaging (Davis 1939). The now widespread agreement that the N140 peak is a correlate of selective attention and the many findings relating P200 to habituation and/or novelty effects—all psychological phenomena possibly associated with deficits in schizophrenia—recommend the study of these components. Other factors as well appear to make the study of these EP components especially suitable. Perceptual and cognitive abnormalities in schizophrenics are not specific to one sensory modality; and while P100 seems to occur earlier with auditory than visual stimuli, N140 and P200 have very similar configurations across auditory, visual, and somatosensory stimuli when recorded at vertex (which generally yields the largest amplitudes as well). The size and frequency of the components make them somewhat more immune to artifacts of eye movement, myogenic components, muscle contamination, or electronic interference than early or late components.
Reducing Travel Time by Incident Reporting via CrowdSourcing

The contribution of this work is the creation of a novel system that enables motorists who witness incidents to submit reports to our system via the web. These reports are aggregated, validated and verified automatically. Then, they are used to update the road network graph. In this work, we designed and implemented an incident reporting system whereby users can report an incident such as an accident or construction on a road network. We extended the FreeSim simulator to accommodate our incident reporting system. Experimental results showed that our system is capable of reducing the travel time of users. We also presented our verification algorithms that are used to verify that reports are fact. Current approaches to congestion detection such as loop detectors probe vehicles, and video image detection may not be available on arterial streets. These technologies may not be available in countries whose transportation budget is low. Our model is less expensive, easy to implement and can work in any environment (e.g. extreme weather). This work is dependent on people’s incident response input and not from sensor signals converted to traffic measurements. To the best of our knowledge, this approach is the first to consider web-based incident Crowd Sourcing with automatic incident verification. Other driver based models are telephoned based.
PRA 1 Inhibits the Extraction of Membrane-bound Rab GTPase by GDI 1 *

Rab is a family of small Ras-like GTPases regulating intracellular vesicle transport. We have previously reported that prenylated Rab acceptor or PRA1 interacts with Rab GTPases and vesicle-associated membrane protein (VAMP2). Structural prediction programs suggest that PRA1, with its two extensive hydrophobic domains, is likely to be an integral membrane protein. However, subcellular fractionation and immunocytochemical analyses indicated that PRA1 is localized both in the cytosol and tightly associated with the membrane compartment. The membrane-bound form can be partially extracted with physiological buffer and urea, suggesting that PRA1 is an extrinsic membrane protein. Deletion of the carboxyl-terminal domain resulted in a protein that behaved as an integral membrane protein, indicating that this domain plays an essential role in maintaining PRA1 in a soluble state. PRA1 can also bind weakly to GDP dissociation inhibitor (GDI), a protein involved in the solubilization of membrane-bound Rab GTPases. Addition of PRA1 inhibited the extraction of membrane-bound Rab3A by GDI, suggesting that membrane localization of Rab GTPases is dependent on the opposing action of PRA1 and GDI. The binding of Rab and VAMP2 to PRA1 is mutually exclusive such that Rab3A can displace VAMP2 in a preformed VAMP2PRA1 complex.
Sequential Roles for Phosphatidylinositol 3-Phosphate and Rab5 in Tethering and Fusion of Early Endosomes via Their Interaction with EEA1* 210

Early endosome antigen 1 (EEA1) is a 170-kDa polypeptide required for endosome fusion in mammalian cells. The COOH terminus of EEA1 contains a FYVE domain that interacts specifically with phosphatidylinositol 3-phosphate (PtdIns-3-P) and a Rab5 GTPase binding region adjacent to the FYVE domain. The dual interaction of EEA1 with both PtdIns-3-P and Rab5 has been hypothesized to provide the specificity required to target EEA1 to early endosomes. To test this hypothesis, we generated truncated (amino acids 1277–1411) and full-length EEA1 constructs containing point mutations in the COOH terminus that impair Rab5 but not PtdIns-3-P binding. These constructs localized to endosomes in intact cells as efficiently as their wild-type counterparts. Furthermore, overexpression of the truncated constructs, both wild-type and mutated, impaired the function of endogenous EEA1 resulting in the accumulation of small, untethered endosomes. These results suggest that association with Rab5 is not necessary for the initial binding and tethering functions of EEA1. A role for Rab5 binding was revealed, however, upon comparison of endosomes in cells expressing full-length wild-type or mutated EEA1. The mutant full-length EEA1 caused the accumulation of endosome clusters and suppressed the enlargement of endosomes caused by a persistently active form of Rab5 (Rab5Q79L). In contrast, expression of wild-type EEA1 with Rab5Q79L enhanced this enlargement. Thus, endosome tethering depends on the interaction of EEA1 with PtdIns-3-P, and its interaction with Rab5 appears to regulate subsequent fusion.