gebhart/patrepeval huggingface dataset:
SQL query optimization (1996)

The strength of commercial query optimizers like DB2 comes from their ability to select an optimal order by generating all equivalent reorderings of binary operators. However, there are no known methods to generate all equivalent reorderings for a SQL query containing joins, outer joins, and groupby aggregations. Consequently, some of the reorderings with significantly lower cost may be missed. Using hypergraph model and a set of novel identities, we propose a method to reorder a SQL query containing joins, outer joins, and groupby aggregations. While these operators are sufficient to capture the SQL semantics, it is during their reordering that we identify a powerful primitive needed for a dbms. We report our findings of a simple, yet fundamental operator, generalized selection, and demonstrate its power to solve the problem of reordering of SQL queries containing joins, outer joins, and groupby aggregations.
The capsid determinant of fibrotropism for the MVMp strain of minute virus of mice functions via VP2 and not VP1 (1995)

The minute virus of mice, prototype strain MVMp, productively infects cultured murine fibroblasts but not T cells. The immunosuppressive strain, MVMi, shows the converse tropism. These reciprocal tropisms are mediated by the viral capsids, in which their determinants have been mapped to a few specific amino acids in the primary sequence shared by VP1 and VP2. Which of these proteins is relevant in presenting these determinants during infection is not known. We have approached this question using a recombinant parvovirus system in which a LuIII-derived transducing genome, containing the luciferase reporter in place of viral coding sequences, can be packaged by capsid proteins from separate helper sources. We generated transducing virions by using helper constructs expressing either VP1 or VP2, containing the MVMp or MVMi tropic determinant region, in various combinations. The virions were used to infect human NB324K cells and murine A9 fibroblasts. Transduction of the human cells (permissive for both MVMp and MVMi) required both VP1 and VP2 and was successful with all combinations of these proteins. In contrast, significant transducing activity for A9 cells was detected only with recombinant virions containing VP2 of MVMp, while the use of either source of VP1 had little effect. We conclude that VP2 from MVMp is necessary to enable infection of murine A9 fibroblasts.
Facial selectivity in the addition of nucleophiles to the radical cations of substituted 2-methyleneadamantanes (1998)

The diphenylmethylenecyclohexane, 2, and the substituted 2-methyleneadamantanes, 3-7, have been prepared. The radical cation of each was generated by photochemical oxidation using 1,4-dicyanobenzene as the sensitizer, and their reactivity was examined in methanol-acetonitrile mixtures with added tetraethylammonium cyanide. Although compound 2 reacted only by tautomerization, the other compounds all gave addition products. For the monoaryl alkenes 3, 4, and 5, comparable yields of both methanol and HCN addition products were obtained, resulting from nucleophilic attack at either end of the alkene radical cation. For the diphenylalkenes 6 and 7, the regioselectivity favored nucleophilic attack at the adamantyl carbon, and the addition products were predominantly those of HCN addition. For the 5-methoxy compound 7, HCN addition was facially selective with a syn:anti ratio of 58:42.Key words: methyleneadamantanes, facial selectivity, radical cations.
Methods for reduction of charging emissions (1997)

One of the most critical subjects in coking plants are charging emissions. The paper reviews the systems that have been used over the years to reduce charging emissions. The advantages and disadvantages are summarized for the following systems: Double collecting main with aspiration on both oven sides; Single collecting main with/without aspiration via standpipe, and extraction and cleaning of charging gas on charging car; Single collecting main with aspiration via standpipe and pretreatment of charging gas on the charging car as well as additional stationary exhaust and cleaning of charging gas; Single collecting main with aspiration via single standpipe; and Single collecting main with simultaneous aspiration via two standpipes and a U-tube connecting the oven chamber with the neighboring oven. The paper then briefly discusses prerequisites for reduction of charging emissions.
Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer (2023)

Prostate-specific membrane antigen (PSMA) is an important cell surface target in prostate cancer. There are limited data on the heterogeneity of PSMA tissue expression in metastatic castration-resistant prostate cancer (mCRPC). Furthermore, the mechanisms regulating PSMA expression (encoded by the FOLH1 gene) are not well understood. Here, we demonstrate that PSMA expression is heterogeneous across different metastatic sites and molecular subtypes of mCRPC. In a rapid autopsy cohort in which multiple metastatic sites per patient were sampled, we found that 13 of 52 (25%) cases had no detectable PSMA and 23 of 52 (44%) cases showed heterogeneous PSMA expression across individual metastases, with 33 (63%) cases harboring at least 1 PSMA-negative site. PSMA-negative tumors displayed distinct transcriptional profiles with expression of druggable targets such as MUC1. Loss of PSMA was associated with epigenetic changes of the FOLH1 locus, including gain of CpG methylation and loss of histone 3 lysine 27 (H3K27) acetylation. Treatment with histone deacetylase (HDAC) inhibitors reversed this epigenetic repression and restored PSMA expression in vitro and in vivo. Collectively, these data provide insights into the expression patterns and regulation of PSMA in mCRPC and suggest that epigenetic therapies - in particular, HDAC inhibitors - can be used to augment PSMA levels.
Biochemical characterization of Epstein-Barr virus nuclear antigen 2A (1991)

The Epstein-Barr virus nuclear antigen 2A (EBNA-2A) was immunoprecipitated from latently Epstein-Barr virus-infected lymphocytes with a polyclonal serum raised against the EBNA-2A C terminus. The nucleus contained three subfractions of EBNA-2A which could be distinguished by their resistance to salt extraction: (i) a nucleoplasmatic fraction that was solubilized at 50 mM NaCl, (ii) a chromatin-associated fraction extractable at 1.5 M NaCl, and (iii) a nuclear matrix-associated fraction solubilized only by boiling with buffer containing 2% sodium dodecyl sulfate. The three subfractions were phosphorylated; it was demonstrated that the nucleoplasmatic and the chromatin-associated fractions were phosphorylated at serine and threonine residues. The half-life of the EBNA-2A protein was determined by cycloheximide treatment and by pulse-chase experiments and was found to be at least 24 h. The turnover of the phosphate residues bound to the two salt-soluble subfractions was determined to be approximately 6 to 9 h, suggesting a possible role of the phosphorylation in the regulation of the biological activity of EBNA-2A. Dephosphorylation of EBNA-2A resulted in an increased mobility of the protein during sodium dodecyl sulfate-polyacrylamide gel electrophoresis and indicated the presence of differentially phosphorylated subclasses of the protein. Analysis of EBNA-2A by sucrose gradient centrifugation revealed the existence of two subclasses of complexed molecules which exhibited sedimentation coefficients of approximately 13S and 34S.
Development of Pressure Standard up to 1 GPa using a Precise Pressure Multiplier (2006)

The pressure standard up to 1 GPa using a precise pressure multiplier and a pressure balance has been developed. The multiplying ratio of the pressure multiplier, which is the ratio of high pressure to low pressure, is about 10. The pressure multiplier has low and high pressure ports and is capable of generating pressure of 1 GPa at the high pressure port when pressure of 100 MPa is applied to the low pressure port. The pressure for the low pressure port can be applied accurately using a pressure balance. The multiplying ratio of the multiplier was precisely measured as a function of pressure by applying known pressures to both the ports. Using the multiplying ratio measured, the pressure generated at the high pressure port was calculated up to 1 GPa. In this paper, the methods for evaluating the multiplying ratio of the multiplier and for calculating the pressure generated using the pressure multiplier up to 1 GPa with its uncertainty are described in detail. Also, the characteristics of some pressure transducers evaluated using the pressure standard developed are shown
Self‐Diffusion of Er in Pure and HfO 2 ‐Doped Polycrystalline Er 2 O 3 (1979)

Using a tracer sectioning technique, the self‐diffusion of Er in pure and HfO 2 ‐doped polycrystalline Er 2 O 3 was measured at 1614° to 1900°C. Up to ≊ 10 mol% HfO 2 dopant level, the Er self‐diffusion coefficients followed a relation based on cation vacancies as the principal mobile defects present and available for cation diffusion. Above 10 mol% HfO 2 , deviation from this relation occurred, apparently due to clustering of cation vacancies and oxygen interstitials around the dopant hafnium ions. The activation energy for the self‐diffusion of Er in pure Er 2 O 3 was 82.2 kcal/mol and increased with the HfO 2 dopant level present.
Extended-field confocal imaging for 3D surface sensing (2004)

A novel optoelectronic set up based on a confocal extended field proprietary design has been developed for high resolution 3D surface sensing as well as for roughness and surface flaw characterization. The classical optical sectioning property of the basic confocal imaging design assumes that a monochromatic light beam is propagating forth and back from the elementary point source to the spatial filtering pinhole. When using a polychromatic light source, the residual chromatic aberration of the optical system reduces the optical sectioning global performance by enlarging the axial resolution (optical sectioning) by a quantity almost equal to the length of the axial chromatic aberration. When dealing with 3D surface sensing of the axial chromatic aberration can be considered as generating a highly accurate axial color coding, provided that an adequate color decoding of the backreflected light beam is realized. Consequently, it appears that it is possible to design customized confocal extended field point sensors with depths of field ranging from a few tens of microns (with subnanometric axial resolution) up to tens of millimeters (with micrometric axial resolution). Owing to the large Numerical Aperture of the confocal imaging set up perfectly specular optical surfaces can be easily captured with this type of instrument. Examples of Metrological 3D surface sensing of aspheric ophtalmic progressive lenses, small lens arrays and MOEMS will be presented and discussed.
Production of cloned pigs expressing human thrombomodulin in endothelial cells (2012)

For long-term xenograft survival, coagulation control is one of the remaining critical issues. Our attention has been directed toward human thrombomodulin (hTM), because it is expected to exhibit the following beneficial effects on coagulation control and cytoprotection: (i) to solve the problem of molecular incompatibility in protein C activation; (ii) to exert a role as a physiological regulator, only when thrombin is formed; (iii) to suppress direct prothrombinase activity; and (iv) to have anti-inflammatory properties. hTM gene was transfected into pig (Landrace/Yorkshire) fibroblasts using pCAGGS expression vector and pPGK-puro vector. After puromycin selection, only fibroblasts expressing a high level of hTM were collected by cell sorting and then applied to nuclear transfer. Following electroactivation and subsequent culture, a total of 1547 cleaved embryos were transferred to seven surrogate mother pigs. Two healthy cloned piglets expressing hTM were born, successfully grew to maturity and produced normal progeny. Immunohistochemical staining of organs from F1 generation pigs demonstrated hTM expression in endothelial cells as well as parenchymal cells. High expression was observed particularly in endothelial cells of kidney and liver. Aortic endothelial cells from cloned pigs were found to express hTM levels similar to human umbilical vein endothelial cells (HUVEC) and to make it possible to convert protein C into activated protein C. The blockade of human endothelial cell protein C receptor (hEPCR) significantly reduced APC production in HUVEC, but not in hTM-PAEC. Although no bleeding tendency was observed in hTM-cloned pigs, activated partial thromboplastin time (APTT) was slightly prolonged and soluble hTM was detected in pig plasma. hTM was expressed in platelets and mononuclear cells, but not in RBC. Cloned pigs expressing hTM in endothelial cells at a comparable level to HUVEC were produced. As complete suppression of antigen-antibody reaction in the graft is essential for accurate assessment of transgene related to coagulation control, production of genetically engineered pigs expressing hTM and complement regulatory protein based on galactosyltransferase knockout is desired.
Genomic distribution and functions of uptake signal sequences in Actinobacillus actinomycetemcomitans (2006)

Actinobacillus actinomycetemcomitans is naturally competent for transformation, with a transformation system similar to that of Haemophilus influenzae that preferentially takes up DNA bearing uptake signal sequences (USS) with the same 9-base USS core. This study examined the function of the extended 29-base USS, which comprises a highly conserved 1st region (containing the 9-base core) and 2nd and 3rd semi-conserved AT-rich regions, in transformation of A. actinomycetemcomitans. Transformation frequency was not affected by either location (in middle or at 5' end) or quantity (one or two) of USS in donor DNA. Relative transformation efficiencies (in comparison to the positive control) were 28-67 % for linear DNA with single-base mutations in the USS 1st region, and 47 % and 73 %, respectively, for linear DNA with USS that contained either a non-consensus 2nd or a non-consensus 3rd region. Plasmids with a stand-alone 1st or a stand-alone 2nd-3rd region exhibited 21 % and 6 % relative transformation efficiencies, respectively. It was also noted that A. actinomycetemcomitans and H. influenzae were similar in the frequencies and distribution patterns of USS in their genomes. In conclusion, all three regions of the extended 29-base USS are required for optimum transformation in A. actinomycetemcomitans.
The Protective Effect of Febuxostat on Chronic Tacrolimus-Induced Nephrotoxicity in Rats (2016)

Fx is effective in controlling hyperuricemia and in preventing Tac-induced renal injury, via a reduction of oxidative stress. Therefore, a targeted therapy aimed at inhibiting uric acid by Fx may be a useful approach in the management of the progression of nephropathy in renal transplant patients treated with Tac.
Industrial MOF Synthesis (2011)

This chapter contains sections titled: Introduction Raw Materials Synthesis Shaping Applications Conclusion and Outlook References
Slip length of water on graphene: Limitations of non-equilibrium molecular dynamics simulations (2012)

Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is "not practical, if not impossible" based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition.
Scale invariance of a diodelike tunnel junction (2013)

We measure the current vs voltage (I-V) characteristics of a diodelike tunnel junction consisting of a sharp metallic tip placed at a variable distance d from a planar collector and emitting electrons via electric-field assisted emission. All curves collapse onto one single graph when I is plotted as a function of the single scaling variable Vd^{-λ}, d being varied from a few mm to a few nm, i.e., by about six orders of magnitude. We provide an argument that finds the exponent λ within the singular behavior inherent to the electrostatics of a sharp tip. A simulation of the tunneling barrier for a realistic tip reproduces both the scaling behavior and the small but significant deviations from scaling observed experimentally.
Impact of Physics on Medical Sciences andApplications: Lasers and Nanotechnology (2016)

This review article focuses on the latest advances in medical sciences that followed recent developments in physics. The focus here will be on the developments in those disciplines of physics namely; lasers and nanotechnology that are related to the research at the Laboratory of Lasers and New Materials (LLNM) of Cairo University and have direct connection to the field of Medical Physics. Laser induced breakdown spectroscopy (LIBS) has proven to be a powerful technique as a rapid and accurate tool for the identification and the analysis of microorganisms and human clinical specimens. It was applied in (LLNM) for the diagnosis and classification of liver cancer. New short wave length laser lines have been identified in (LLNM) which are important for the development of X-ray lasers that will have great impact on medical sciences and applications. Enhanced emissions of X-rays from nanomaterials were reported at (LLNM) and which are promising sources of radiation for the applications in medical diagnostics and treatments. The recent developments in lasers and nanotechnology have revolutionized both the research in biomedical science and the methods for medical diagnostics and treatments.
The singularity loci of two triangular parallel manipulators (2002)

We study the Jacobian of spatial parallel manipulators that have triangular base and top platform architectures with 2-2-2 and 3-2-1 actuator configurations. The Jacobian matrix is formulated using dual quaternion coordinates. The zero locus of the determinant of the resulting Jacobian is what we refer to as the singularity loci. The result is an eighth order polynomial in the dual quaternion coordinates. The loci of singular positions for a fixed orientation for the 2-2-2 actuator arrangement is a cubic surface. The loci of singular positions for the 3-2-1 actuator arrangement is also a cubic surface, which factors into three planes.
Cardioversion of atrial fibrillation: how and when? (2003)

European Heart Journal Supplements (
Proteomic Profiling of Mouse Helper T Cell Differentiation (2019)

Helper T cell differentiation is a key process in the regulation of adaptive immune responses. Here, mouse Th1 and Th2 cells are profiled using high-throughput proteomics to increase the understanding of the molecular biology of Th differentiation to support the design of prophylactic and therapeutic intervention strategies for (infectious) diseases. Protein profiling of Th1/Th2 differentiated cells results in the quantification of almost 6000 proteins of which 41 are differentially expressed at FDR < 0.1, and 19 at the FDR < 0.05 level, respectively. Differential protein expression analysis identifies a number of the expected canonical Th differentiation markers, and gene set analysis using the REACTOME database and a hypergeometric test (FDR < 0.05) confirms that helper T cell pathways are the top sets that are differentially expressed. Additionally, by network analysis, many differentially expressed proteins are associated with the Th1 and Th2 pathways. Data are available via PRIDE database with identifier PXD004532.
Gating of a Molecular Transistor:  Electrostatic and Conformational (2004)

We derive a general result that can be used to evaluate and compare the transconductance of different field-effect mechanisms in molecular transistors, both electrostatic and conformational. The electrostatic component leads to the well-known thermal limit in the absence of tunneling. We show that in a standard three-terminal geometry and in the absence of strong electron−phonon coupling, the conformational component can lead to significant advantages only if the molecular dipole moment μ is comparable to etox, tox being the thickness of the oxide. Surprisingly, this conclusion is independent of the “softness” of the conformational modes involved or other geometrical factors. Detailed numerical results for specific examples are presented in support of the analytical results.
Crowd Detection from Still Images (2008)

The analysis of human crowds has widespread uses from law enforcement to urban engineering and traffic management. All of these require a crowd to first be detected, which is the problem addressed in this paper. Given an image, the algorithm we propose segments it into crowd and non-crowd regions. The main idea is to capture two key properties of crowds: (i) on a narrow scale, its basic element should look like a human (only weakly so, due to low resolution, occlusion, clothing variation etc.), while (ii) on a larger scale, a crowd inherently contains repetitive appearance elements. Our method exploits this by building a pyramid of sliding windows and quan-tifying how “crowd-like ” each level of the pyramid is using an underlying statistical model based on quantized SIFT features. The two aforementioned crowd properties are captured by the resulting feature vector of window re-sponses, describing the degree of crowd-like appearance around an image location as the surrounding spatial extent is increased. 1