Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing Quantum Chemical and Polyparameter Models for Predicting Environmentally Significant Parameters for New Munition Compounds

There is increasing concern about the environmental fate and effects of munition constituents (MCs). Polyparameter linear free energy relationships (pp-LFERs) that employ Abraham solute parameters are available for a variety of parameters that can aid in evaluating the risk of MCs to the environment. However, poor predictions using pp-LFERs and ABSOLV estimated Abraham solute parameters are found for some key physico-chemical properties, particularly for novel MCs. In this work, the Abraham solute parameters of eight MCs and munition-like compounds are determined using experimentally determined partition coefficients in various solvent-water systems. The compounds investigated include hexahydro-1,3,5-trinitro1,3,5-triazacyclohexane (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), Hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX), hexahydro-1,3-dinitroso-5nitro-1,3,5-triazine (DNX), 2,4,6-trinitrotoluene (TNT), 1,3,5-trinitrobenzene (TNB), and 4-nitroanisole (4NAN). The solvents in the solvent-water systems are hexane, dichloromethane, trichloromethane, octanol, and toluene. The measured partition coefficients span a range from -2.19 to 3.17 log units. The only available reported partition coefficients are for octanol-water for some of the investigated compounds and they are in good agreement with the experimental measurements from this study. Correlations of the measured solvent-water partition coefficients for some solute pairs or solvent system pairs indicate the consistency and reliability of the experimental data, and also serve to estimate missing values. The predictions of solvent-water partition coefficients (log KP) using experimentally derived solute parameters have much lower root mean square error of prediction of log KP (RMSE = 0.38) than those using ABSOLV estimated parameters (RMSE = 3.56) for the investigated compounds. Additionally, the predictions for various physico-chemical properties using the solute parameters derived in this study agree with available literature reported values with prediction errors within 0.79 log units except for water solubility of RDX and HMX with errors of 1.48 and 2.16 log units respectively. However, predictions using ABSOLV estimated solute parameters have larger prediction errors of up to 7.68 log units. This large discrepancy is probably due to the missing –R2N-NO2 and –R2N-NO2 functional groups in the ABSOLV fragment database. 2.
Prenylome profiling reveals S-farnesylation is crucial for membrane targeting and antiviral activity of ZAP long-isoform

S-prenylation is an important lipid modification that targets proteins to membranes for cell signaling and vesicle trafficking in eukaryotes. As S-prenylated proteins are often key effectors for oncogenesis, congenital disorders, and microbial pathogenesis, robust proteomic methods are still needed to biochemically characterize these lipidated proteins in specific cell types and disease states. Here, we report that bioorthogonal proteomics of macrophages with an improved alkyne-isoprenoid chemical reporter enables large-scale profiling of prenylated proteins, as well as the discovery of unannotated lipidated proteins such as isoform-specific S-farnesylation of zinc-finger antiviral protein (ZAP). Notably, S-farnesylation was crucial for targeting the long-isoform of ZAP (ZAPL/PARP-13.1/zc3hav1) to endolysosomes and enhancing the antiviral activity of this immune effector. These studies demonstrate the utility of isoprenoid chemical reporters for proteomic analysis of prenylated proteins and reveal a role for protein prenylation in host defense against viral infections.
Aberrant stress‐induced Hsp70 expression in immune cells in multiple sclerosis

Heat shock protein 70 (Hsp70), a prominent member of the heat shock protein family, is a stress‐induced chaperone, contributing to the “protein triage” mechanism. However, we and others have previously shown that chaperonin activity of Hsp70 also promotes immune recognition of protein/peptide antigens, including myelin autoantigens. Hsp70 has been strikingly elevated in multiple sclerosis (MS) lesions. In a search for the mechanism of Hsp70 up‐regulation in MS, we analyzed Hsp70 expression in peripheral blood mononuclear cells (PBMCs) from MS patients (n = 49), healthy controls (n = 40), and patients with rheumatoid arthritis, (RA; n = 13). Hsp70 was detected by Western blot, and Hsp70 levels were quantified by ELISA. We found that Hsp70 was expressed at low levels in ex vivo PBMCs. However, after heat shock, Hsp70 was up‐regulated significantly more (up to sixfold) in MS patients compared with healthy controls. This significant overproduction of Hsp70 was also seen following another stress condition, LPS stimulation. Hsp70 is a product of several independent genes, and we found the HSPA1B gene product to be the major form responsible for Hsp70 protein overexpression in PBMCs. Hsp70 overexpression was preceded by increased nuclear presence of heat shock factor 1 (HSF1). HSF1 activation depends on phosphorylation, and we found that inhibition of the A group of protein kinase C isoenzymes significantly reduced inducible Hsp70 production. These results indicate that immune cells from MS patients are more prone to Hsp70 induction under stress conditions, suggesting a possible link between Hsp70 overexpression and development of autoimmunity. © 2010 Wiley‐Liss, Inc.
Lesbian, Gay, and Bisexual Identity as a Moderator of Relationship Functioning After Sexual Assault

Sexual assault is unfortunately common, especially among lesbian, gay, and bisexual (LGB) individuals. Yet, the associations of such victimization have not yet been extensively established in the areas of sexual identity and romantic relationship functioning. Accordingly, the present study examined the associations between lifetime sexual assault, LGB identity, and romantic relationship functioning in a sample of 336 LGB individuals. A history of sexual assault was associated with attachment anxiety and several sexual identity components (i.e., higher levels of acceptance concerns, identity uncertainty, internalized homonegativity, and identity superiority). Furthermore, an association of sexual assault and attachment avoidance was moderated by internalized homonegativity. Finally, a more secure LGB identity was associated with healthier romantic relationship functioning. Collectively, these findings are applicable to services for LGB sexual assault victims, suggesting the incorporation of treatment that bolsters LGB identity and couple functioning. Limitations and future directions are discussed.
The application of probability density estimation to text-independent speaker identification

Most text-independent speaker identification methods to date depend on the use of some distance metric for classification. In this paper we develop the use of probability density function (pdf) estimation for text-independent speaker identification. We compare the performance of two parametric and one non-parametric pdf estimation methods to one distance classification method that uses the Mahalanobis distance. Under all conditions tested, the pdf estimation methods performed substantially better than the Mahalanobis distance method. The best method is a non-parametric pdf estimation method.
Generalized Stacking Fault Energies of Aluminum Alloys–Density Functional Theory Calculations

Generalized stacking fault energies of aluminum alloys were calculated using density functional theory. Stacking fault energy of aluminum alloys was correlated with the d-electrons number of transition metal alloying elements. The tendency to twinning is also modified by the presence of the alloying element in the deformation plane. Our results suggest that Al alloys, with such elements as Zr, Nb, Y, Mo, Ta, and Hf, are expected to exhibit a strong work hardening rate due to emission of the partial dislocations.
Implementation techniques for evolvable HW systems: virtual VS. dynamic reconfiguration

Adaptive hardware requires some reconfiguration capabilities. FPGAs with native dynamic partial reconfiguration (DPR) support pose a dilemma for system designers: whether to use native DPR or to build a virtual reconfigurable circuit (VRC) on top of the FPGA which allows selecting alternative functions by a multiplexing scheme. This solution allows much faster reconfiguration, but with higher resource overhead. This paper discusses the advantages of both implementations for a 2D image processing matrix. Results show how higher operating frequency is obtained for the matrix using DPR. However, this is compensated in the VRC during evolution due to the comparatively negligible reconfiguration time. Regarding area, the DPR implementation consumes slightly more resources due to the reconfiguration engine, but adds further more capabilities to the system.
Expressive Description Logics

This chapter covers extensions of the basic Description Logics introduced in Chapter 2 by very expressive constructs that require advanced reasoning techniques. In particular, we study reasoning in Description Logics that include general inclusion axioms, inverse roles, number restrictions, reflexive-transitive closure of roles, fixpoint constructs for recursive definitions, and relations of arbitrary arity. The chapter will also address reasoning w.r. t. knowledge bases including both a TBox and an ABox, and discuss more general ways to treat objects. Since the logics considered in the chapter lack the finite model property, finite model reasoning is of interest and will also be discussed. Finally, we mention several extensions to Description Logics that lead to undecidability, confirming that the expressive Description Logics considered in this chapter are close to the boundary between decidability and undecidability.
Genome Architecture and Its Roles in Human Copy Number Variation

Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.
Chromosomal map location of the alpha-hemolysin structural gene in Staphylococcus aureus NCTC 8325

The alpha-hemolysin structural gene, hly+, previously cloned, insertionally inactivated, and introduced into the chromosome by allele replacement (M.O. O'Reilly, J.C.S. De Azavedo, S. Kennedy, and T.J. Foster, Microb. Pathog. 1:125-138, 1986), was shown by protoplast fusion and transformation to be in the gene order purC-hly-uraB-omega[chr::Tn916]1101-thrB on the chromosome of Staphylococcus aureus NCTC 8325. This location is clearly distinct from that of the agr determinant, a regulatory gene affecting several extracellular proteins, including alpha-hemolysin, located between tmn and ilv.
Translation of Central Nervous System Occupancy from Animal Models: Application of Pharmacokinetic/Pharmacodynamic Modeling

Translation of central nervous system receptor occupancy from animal models to humans has been elusive for many therapeutic targets. However, this may represent a valuable link to clinical efficacy for drugs acting within the brain and spinal cord. The introduction of positron emission tomography marked a significant noninvasive advance in determination of target engagement in the central nervous system. Pharmacokinetic/pharmacodynamic (PK/PD) modeling represents a valuable tool to translate ex vivo receptor occupancy from relevant animal models to humans. Whereas PK properties usually are reasonably scaled across species using standard allometric principles, PD properties related to receptor occupancy are usually species-independent. The translational value and applicability of PK/PD approaches are more directly evident when comparable modeling assumptions and mathematical model structures are employed across experiments and analyses. The purpose of this article is to review the basic principles of PK/PD analysis of receptor occupancy determined using noninvasive positron emission tomography imaging and first principles of allometric PK scaling and PD prediction based on animal data. By use of the data from the area of pain management, we also provide a case study of PK/PD analysis showcasing the importance of PK/PD model assumptions in predicting receptor occupancy in humans based on data from animal models.
Sprint and Vertical Jump Performances Are Not Affected by Six Weeks of Static Hamstring Stretching

The purpose of this study was to investigate whether 6 weeks of static hamstring stretching effects range of motion (ROM), sprint, and vertical jump performances in athletes. Twenty-one healthy division III women's track and field athletes participated in the study. Subjects were tested for bilateral knee ROM; 55-m sprint time; and vertical jump height before, at 3 weeks, and after the 6-week flexibility program. Subjects were randomly assigned to treatment and control groups and warmed up with a 10-minute jog on a track before a hamstring stretching protocol. The stretching protocol consisted of four repetitions held for 45 seconds, 4 days per week. Four variables (left and right leg ROM, 55-m sprint time, vertical jump) were analyzed using a repeated-measures analysis of variance design. No significant differences (P ≤ 0.05) were found with any of the four variables between the stretching and control groups. Six weeks of a static hamstring stretching protocol did not improve knee ROM or sprint and vertical jump performances in women track and field athletes. The use of static stretching should be restricted to post practice or competition because of the detrimental effects reported throughout the literature. Based on the current investigation, it does not seem that chronic static stretching has a positive or negative impact on athletic performance. Thus, the efficacy of utilizing this practice is questionable and requires further investigation.
Abstract 545: Suppression of Atherosclerosis by Synthetic REV-ERB Agonist

Background: Development of atherosclerosis is a complex process that involves both hyperlipidemia and inflammation. Therapies that can target both metabolic and inflammatory aspect of this disease have significant potential in the treatment of cardiovascular diseases. The nuclear receptors for heme, REV-ERBα and REV-ERBβ, play important roles in regulation of metabolism and inflammation. Recently it was demonstrated that knock-down of REV-ERBα in hematopoetic cells in LDL receptor null mice led to increased atherosclerosis. We sought to determine if synthetic REV-ERB agonists that we have developed might have the ability to suppress atherosclerosis in this model. Methods and Results: A previously characterized synthetic REV-ERB agonist, SR9009, was used to determine if activation of REV-ERB activity would affect atherosclerosis in LDL receptor deficient mice. Eight-week-old mice with deficient LDL receptor were fed high cholesterol diet and treated with vehicle or REV-ERB agonist, SR9009 (100mg/kg, I.P.) for a period of eight weeks. Atherosclerotic plaque size was significantly reduced in mice administered SR9009 compared to control mice. In another study plasma lipid levels were monitored every two weeks for eight weeks. We demonstrate that SR9009 significantly reduced plasma lipid levels in these mice. To determine the role of REV-ERB in macrophage differentiation and polarization bone-marrow derived macrophages (BMDM) were treated with SR9009 in vitro. SR9009 treatment of BMDM reduced the polarization of BMDM to proinflammatory M1 macrophage. Gene expression of markers of M1 polarization as well as pro-inflammatory cytokine secretion was reduced in macrophages treated with SR9009. Conclusions: We demonstrate that REV-ERB targets multiple processes involved in atherosclerosis. Our results suggest that pharmacological targeting of REV-ERBs may be a viable therapeutic option for treatment of atherosclerosis.
Biomolecular Coronas Provide the Biological Identity of Nanomaterials

Title Biomolecular coronas provide the biological identity of nanosized materials Authors(s) Monopoli, Marco P.; Åberg, Christoffer; Salvati, Anna; Dawson, Kenneth A. Publication date 2012-12-05 Publication information Nature nanotechnology, 7 (12): 779-786 Publisher Nature Publishing Group Item record/more information http://hdl.handle. net/10197/4572 Publisher's version (DOI) 10.1038/nnano.2012. 207
Analytical Methodology for Determination of Trace Cu in Hydrated Alcohol Fuel

Ethyl alcohol (ethanol) is considered to be a highly viable alternative fuel. Its production from biomass means that it can provide a source of energy that is both clean and renewable. The in‐ clusion of ethanol as a component of gasoline can help to reduce problems of pollution in many regions, since it eliminates the needto use tetraethyl lead (historically notorious as a highly tox‐ ic trace component of the atmosphere in major cities) as an anti-knock additive.
Chiral sculptured thin films as circular Bragg supermirrors

The planewave re ection/transmission characteristics of a chiral sculptured thin film (CSTF) were investigated numerically. The helical nanowires of the CSTF were taken to be made from a dissipative material while the void regions between the nanowires were filled with an active material. Theory showed that the CSTF can simultaneously amplify left-circularly-polarized incident light and attenuate right-circularly-polarized incident light, or vice versa depending upon the handedness of the CSTF. The presence of both dissipative and active materials allows the high reflectance to exceed unity for incident light of one circular polarization state across a substantial portion of the circular Bragg spectral regime but not for incident light of the other circular polarization state. That is, the chosen CSTF is a circular Bragg supermirror for one, and only one, circular polarization state.
Effect of prenatal auditory stimulation on numerical synaptic density and mean synaptic height in the posthatch Day 1 chick hippocampus

Previous studies on prenatal auditory stimulation by species‐specific sound or sitar music showed enhanced morphological and biochemical changes in chick hippocampus, which plays an important role in learning and memory. Changes in the efficiency of synapses, synaptic morphology and de novo synapse formation affects learning and memory. Therefore, in the present study, we set out to investigate the mean synaptic density and mean synaptic height at posthatch Day 1 in dorsal and ventral part of chick hippocampus following prenatal auditory stimulation. Fertilized 0 day eggs of domestic chick incubated under normal conditions were exposed to patterned sounds of species‐specific and sitar music at 65 dB levels for 15 min/h round the clock (frequency range: 100–6300 Hz) from embryonic Day 10 till hatching. The synapses identified under transmission electron microscope were estimated for their numerical density by physical disector method and also the mean synaptic height calculated. Our results demonstrate a significant increase in mean synaptic density with no alterations in the mean synaptic height following both types of auditory stimulation in the dorsal as well as ventral part of the hippocampus. The observed increase in mean synaptic density suggests enhanced synaptic substrate to strengthen hippocampal function. Synapse 63:152–159, 2009. © 2008 Wiley‐Liss, Inc.
Deficiency of Mbd2 Attenuates Wnt Signaling

ABSTRACT We have previously shown that deficiency of the methyl binding domain protein Mbd2 dramatically reduces adenoma burden on an ApcMin/+ background. To investigate the mechanism underlying this phenomenon, we have determined the effect of Mbd2 deficiency upon the phenotypes imposed by the conditional deletion of Apc in the small intestine. Microarray analysis demonstrated a partial suppression of the Wnt pathway in the absence of Mbd2. Mbd2 deficiency also influenced one immediate cellular consequence of Apc loss, with normalization of Paneth cell positioning. From a mechanistic perspective, we show that deficiency of Mbd2 elevates levels of the known Wnt target Lect2, and we confirm here that Mbd2 binds the Lect2 promoter in association with NuRD. Furthermore, we show that Lect2 is capable of functioning as a Wnt pathway repressor. These results therefore provide a mechanistic basis for the epigenetic control of adenoma formation mediated through Mbd2.
A NUMERICAL APPLICATION TO PREDICT THE RESISTANCE AND WAVE PATTERN OF KRISO CONTAINER SHIP

In this study, the computational results for KRISO Container Ship (KCS) are presented. CFD analyses are performed to simulate free surface flow around KCS by using RANS approach with success. Also the complicated turbulent flow zone behind the ship is well simulated. The RANS equations and the non-linear free surface boundary conditions are discretized by means of a finite volume scheme. The numerical methodology is found to be appropriate for simulating the turbulent flow around a ship in order to estimate ship total resistance and free surface. By the numerical results, total resistance is calculated for the ship model and the result is satisfactory with regard to the experimental one. As a result of well captured free surface, the wave elevation on/around the hull is compared with the experimental results.