gebhart/patrepeval huggingface dataset:
Semiconductor pattern overlay (1994)

Advanced semiconductor manufacturing processes require tight overlay registration tolerances. These strict overlay performance specifications dictate the wafer level overlay metrology performance required. Achieving a high level of performance from overlay metrology equipment requires attention to all aspects of the measurement process. A typical measurement system configuration is reviewed and elements of optical overlay measurement, as they relate to measurement uncertainty, are discussed in detail. Data analysis techniques, used to quantify tool induced measurement uncertainty, are demonstrated with supporting examples. Process and measurement target induced uncertainties are reviewed. Current developments in both target design and measurement algorithms are proposed to address these uncertainties. Measurement optimization and its role in process control applications and future developments in overlay processing are also discussed.
A Xenopus egg factor with DNA-binding properties characteristic of terminus-specific telomeric proteins. (1993)

We have identified a Xenopus laevis protein factor that specifically recognizes vertebrate telomeric repeats at DNA ends. This factor, called Xenopus telomere end factor (XTEF), is detected predominantly in extracts of Xenopus eggs and ovaries, which are estimated to contain sufficient XTEF to bind approximately 3 x 10(7) DNA ends. In contrast, XTEF is much less abundant (approximately 90 per cell) in extracts of somatic cell nuclei. Mobility retardation analysis of the XTEF activity in egg extracts indicates that this factor binds the vertebrate telomeric repeat sequence (TTAGGG)2 when present in a single-stranded 3' overhang. Single-stranded 3' extensions of (TTTGGG)2, (AAAGGG)2, (TTACCC)2, or a nonrepetitive sequence fail to bind XTEF efficiently, whereas changes in the double-stranded sequence 5' to the TTAGGG repeat tail are tolerated. TTAGGG repeats are not recognized at internal position, at a 5' protruding end, or in double-stranded DNA. In addition, the factor does not bind RNA with single-stranded UUAGGG repeats at a 3' end. XTEF-DNA complexes form and are stable in high salt. The DNA-binding properties of XTEF resemble the characteristics of a class of terminus-specific telomere proteins identified previously in hypotrichous ciliates.
Clarification of the Taxonomy of Bacillus mycoides (1995)

Because of the very similar physiological properties and base sequences of the 16S rRNAs of Bacillus cereus, Bacillus mycoides, and Bacillus thuringiensis, some taxonomists question the validity of separating these organisms into distinct species. DNA relatedness studies based on spectrophotometrically measured renaturation rates were carried out to determine the taxonomic relationships of the three species. A study of 58 strains revealed that the levels of relatedness between B. cereus and B. mycoides and between B. cereus and B. thuringiensis ranged from 22 to 44% and from 59 to 69%, respectively. On the basis of the moderately high levels of DNA relatedness which we determined, B. cereus and B. thuringiensis appeared to be genetically related but taxonomically distinct entities. The B. mycoides group was genetically distantly related to the B. cereus group and represented a separate taxon. Furthermore, our data indicated that the B. mycoides group consists of two genetically distinct groups, each of which represents a distinct species. In addition to rhizoidal colonial morphology and lack of motility, the B. mycoides group could be distinguished from B. cereus by differences in fatty acid profiles and acetanilide-producing activities.
A beam steering technique using dielectric wedges (1995)

The thesis describes a method of' beam steering aimed at&#13;\nproducing a useful amount of deflection of an antenna beam&#13;\nfrom boresight, by a simple and Inexpensive method. For&#13;\nlarge antennas, It is difficult, as well as expensive, to&#13;\nsteer the beam by more than a few beamwidths. The method&#13;\nstudied was developed with particular reference to the&#13;\nbeam steering requirements of Direct Broadcast Satellite&#13;\nflat plate antennas.&#13;\nThe method involves two dielectric wedges, having circular&#13;\nfaces, placed In front of the antenna. By adjusting the&#13;\nrelative angular position of the wedges, the beam can be&#13;\nsteered In any direction, up to a maximum value from the&#13;\nantenna boresight direction. The maximum value of the&#13;\ndeflection is determined by the wedge angle and the&#13;\ndielectric constant of the wedge material. This method of&#13;\nbeam steering Is Independent of frequency. Frequency&#13;\nlimitations are, however, set by the need for a matching&#13;\nlayer on the wedge faces to reduce the loss due to&#13;\nreflection and also due to interference of multiple&#13;\nreflection effects on the radiation pattern.&#13;\nExtensive investigations are made (both theoretical and&#13;\nexperimental) to predict the performance of the wedges as&#13;\nthe beam Is steered. The effect of reflection is studied and a new matching technique is devised. Other practical&#13;\nconsiderations for example, stepping the wedges for weight&#13;\nreduction, the effect of loss in the dielectric material&#13;\nand cross polar performance are also taken into account.&#13;\nSome effort is given to explore the possibility of using&#13;\nmetal loaded artificial dielectrics using polyurethane as&#13;\nthe base material.&#13;\nFinally, a number of charts are presented to determine the&#13;\namount of beam steering for an arbitrary position of the&#13;\nwedges.
464. The reactions of certain epoxides in aqueous solutions (1950)

W. C. J. Ross, J. Chem. Soc., 1950, 2257 DOI: 10.1039/JR9500002257
Chemoselective and Position Specific Methylation of tert‐Alkyl Halides with Methyltitanium(IV) Chlorides (1980)

Methylation with methyltitanium reagents promises to have a wide range of application, not least because of its chemoselectivity. In the tert ‐alkyl chlorides studied, which additonally contained a primary ‐or sec ‐alkyl chloride unit or an olefinic double bond, only the tert ‐C‐atom was methylated under favorable conditions.
A Conformational Study of the Human and Rat Encephalitogenic Myelin Oligodendrocyte Glycoprotein Peptides 35–55 (1997)

Myelin oligodendrocyte glycoprotein (MOG), is considered an important central-nervous system-specific target autoantigen for primary demyelination in autoimmune diseases like multiple sclerosis. We have recently demonstrated that MOG or its derived peptide, MOG-(35-55)-peptide, are able to produce in animals, clinicopathologic signs that mimic multiple sclerosis. The rat MOG sequence spanning amino acids 35-55 [rMOG-(35-55)-peptide] differs from the human sequence [hMOG-(35-55)-peptide] by a single amino acid substitution, i.e. Pro42-->Ser. Mice injected with rMOG-(35-55)-peptide showed severe inflammation and demyelination throughout the central nervous system but, interestingly, mice injected with hMOG-(35 -55)-peptide showed only a few foci of mild inflammation with no demyelination. Circular dichroism and nuclear magnetic resonance spectroscopy have been used to structurally characterise the bioactive peptides hMOG-(35-55)-peptide and rMOG-(35-55)-peptide. In 0.1 M K2HPO4/KOH, 90% H2O/D2O solutions, these derived peptides have been shown, by NMR spectroscopy, to adopt detectable levels of short-range structure in equilibrium with unfolded conformers. On addition of 2,2,2-trifluoro-(2H3)ethanol, rMOG-(35-55)-peptide and hMOG-(35-55)-peptide adopt folded structures which have nuclear Overhauser enhancements characteristic of a poorly defined alpha-helix over residues 44-51. There are some indications of secondary structure also evident in the N-terminal region of rMOG-(35-55)-peptide. CD spectroscopy has revealed that in aqueous solution both peptides are unfolded but in 2.2.2-trifluoroethanol and, at micellar concentrations of sodium dodecyl sulfate, rMOG-(35-55)-peptide and, to a lesser extent, hMOG-(35-55)-peptide adopt helical conformations. In contrast, at non-micellar concentrations of SDS rMOG-(35-55)-peptide and hMOG-(35-55)-peptide adopt, according to CD spectroscopy, a beta-structure indicating that the peptides change conformation depending on the microenvironment of the amino acids.
Molecular requirements for the interaction of thrombospondin with thrombin-activated human platelets: modulation of platelet aggregation (1992)

We have investigated the molecular requirements for thrombospondin (TSP) to bind to the platelet surface and to support the subsequent secretion-dependent platelet aggregation. For this, we used two distinct murine monoclonal antibodies (MoAbs), designated MAI and MAII, raised against human platelet TSP, and three polyclonal antibodies, designated R3, R6, and R5, directed against fusion proteins containing the type 1 (Gly 385-Ile 522), type 2 (Pro 559-Ile 669), and type 3 (Asp 784-Val 932) repeating sequences, respectively. Among them, R5 and R6, but not R3, inhibited thrombin-induced aggregation of washed platelets and the concomitant secretion of serotonin. These antibodies, however, did not inhibit the expression of TSP on thrombin-activated platelets, as measured by the binding of a radiolabeled MoAb to TSP, suggesting that they may inhibit platelet aggregation by interfering with a physiologic event subsequent to TSP binding. In contrast, MoAb MAII, which reacts with an epitope located within the heparin-binding domain of TSP, inhibited both TSP surface expression and platelet aggregation/secretion induced by thrombin. In addition, this MoAb inhibited in a dose-dependent manner (IC50 approximately 0.5 mumol/L) the interaction of 125I-TSP with immobilized fibrinogen and platelet glycoprotein IV, both potential physiologic receptors for TSP on thrombin-activated platelets. These results indicate that the interaction of TSP with the surface of activated platelets can be modulated at the level of a specific epitope located within the amino terminal heparin-binding domain of the molecule. Thus, selective inhibition of the platelet/TSP interaction may represent an alternative approach to the inhibition of platelet aggregation.
The Inheritance of Resistance Alleles in Multiple Sclerosis (2007)

Multiple sclerosis (MS) is a complex trait in which alleles at or near the class II loci HLA-DRB1 and HLA-DQB1 contribute significantly to genetic risk. HLA-DRB1*15 and HLA-DRB1*17-bearing haplotypes and interactions at the HLA-DRB1 locus increase risk of MS but it has taken large samples to identify resistance HLA-DRB1 alleles. In this investigation of 7,093 individuals from 1,432 MS families, we have assessed the validity, mode of inheritance, associated genotypes, and the interactions of HLA-DRB1 resistance alleles. HLA-DRB1*14-, HLA-DRB1*11-, HLA-DRB1*01-, and HLA-DRB1*10-bearing haplotypes are protective overall but they appear to operate by different mechanisms. The first type of resistance allele is characterised by HLA-DRB1*14 and HLA-DRB1*11. Each shows a multiplicative mode of inheritance indicating a broadly acting suppression of risk, but a different degree of protection. In contrast, a second type is exemplified by HLA-DRB1*10 and HLA-DRB1*01. These alleles are significantly protective when they interact specifically in trans with HLA-DRB1*15-bearing haplotypes. HLA-DRB1*01 and HLA-DRB1*10 do not interact with HLA-DRB1*17, implying that several mechanisms may be operative in major histocompatibility complex-associated MS susceptibility, perhaps analogous to the resistance alleles. There are major practical implications for risk and for the exploration of mechanisms in animal models. Restriction of antigen presentation by HLA-DRB1*15 seems an improbably simple mechanism of major histocompatibility complex-associated susceptibility.
Expression cloning and functional characterization of the kidney cortex high-affinity proton-coupled peptide transporter. (1996)

The presence of a proton-coupled electrogenic high-affinity peptide transporter in the apical membrane of tubular cells has been demonstrated by microperfusion studies and by use of brush border membrane vesicles. The transporter mediates tubular uptake of filtered di- and tripeptides and aminocephalosporin antibiotics. We have used expression cloning in Xenopus laevis oocytes for identification and characterization of the renal high-affinity peptide transporter. Injection of poly(A)+ RNA isolated from rabbit kidney cortex into oocytes resulted in expression of a pH-dependent transport activity for the aminocephalosporin antibiotic cefadroxil. After size fractionation of poly(A)+ RNA the transport activity was identified in the 3.0- to 5.0-kb fractions, which were used for construction of a cDNA library. The library was screened for expression of cefadroxil transport after injection of complementary RNA synthesized in vitro from different pools of clones. A single clone (rPepT2) was isolated that stimulated cefadroxil uptake into oocytes approximately 70-fold at a pH of 6.0. Kinetic analysis of cefadroxil uptake expressed by the transporter's complementary RNA showed a single saturable high-affinity transport system shared by dipeptides, tripeptides, and selected amino-beta-lactam antibiotics. Electrophysiological studies established that the transport activity is electrogenic and affected by membrane potential. Sequencing of the cDNA predicts a protein of 729 amino acids with 12 membrane-spanning domains. Although there is a significant amino acid sequence identity (47%) to the recently cloned peptide transporters from rabbit and human small intestine, the renal transporter shows distinct structural and functional differences.
Induction of tumor cell death by high hydrostatic pressure as a novel supporting technique in orthopedic surgery (2003)

As vegetative forms of microorganisms are impaired by high hydrostatic pressure (HHP) in the range of 400-600 MPa, the non-thermal inactivation of vegetative bacteria, yeasts, and moulds present in foods such as jams, fruit juices, and dressings by HHP is now well-established. Eukaryotic cells, when subjected to HHP are also damaged. In the present study, the effect of HHP on cell viability of human osteoblasts (HOB), human fibroblasts (HFB), and different tumor cell lines such as osteosarcoma cells SAOS-2, human histiocytic leukemia cells U-937, and the ovarian cancer cell line OV-MZ-6 was investigated. Therefore the different cell lines were subjected to pressures between 50 and 400 MPa and tested for viability. At HHP of 100 MPa (10 min) about 80% of the various cell lines were still alive. At 350 MPa all of the cells were damaged and dead. The three tumor cell lines investigated were slightly more resistant to HHP (50% dead at 170-193 MPa) than HOB and HFB (50% dead at 130-145 MPa). The present study demonstrates that both normal cells and tumor cells are rapidly inactivated by HHP treatment.
Identifying mild and severe preeclampsia in asymptomatic pregnant women by levels of cell‐free fetal DNA (2013)

Women with cffDNA levels below the 5th percentile and above the 90th percentile quantified at 25 weeks' gestation are at increased risk of developing preeclampsia. Adding PAPP-A levels to the analysis did not increase the DR of preeclampsia.
An Introduction to the Conjugate Gradient Method Without the Agonizing Pain (1994)

The Conjugate Gradient Method is the most prominent iterative method for solving sparse systems of linear equations. Unfortunately, many textbook treatments of the topic are written so that even their own authors would be mystified, if they bothered to read their own writing. For this reason, an understanding of the method has been reserved for the elite brilliant few who have painstakingly decoded the mumblings of their forebears. Nevertheless, the Conjugate Gradient Method is a composite of simple, elegant ideas that almost anyone can understand. Of course, a reader as intelligent as yourself will learn them almost effortlessly. The idea of quadratic forms is introduced and used to derive the methods of Steepest Descent, Conjugate Directions, and Conjugate Gradients. Eigenvectors are explained and used to examine the convergence of the Jacobi Method, Steepest Descent, and Conjugate Gradients. Other topics include preconditioning and the nonlinear Conjugate Gradient Method. I have taken pains to make this article easy to read. Sixty-two illustrations are provided. Dense prose is avoided. Concepts are explained in several different ways. Most equations are coupled with an intuitive interpretation.
Treatment of Infections Caused by Metronidazole-ResistantTrichomonas vaginalis (2004)

Infections with the sexually transmitted protozoan Trichomonas vaginalis are usually treated with metronidazole, a 5-nitroimidazole drug derived from the antibiotic azomycin. Metronidazole treatment is generally efficient in eliminating T. vaginalis infection and has a low risk of serious side effects. However, studies have shown that at least 5% of clinical cases of trichomoniasis are caused by parasites resistant to the drug. The lack of approved alternative therapies for T. vaginalis treatment means that higher and sometimes toxic doses of metronidazole are the only option for patients with resistant disease. Clearly, studies of the treatment and prevention of refractory trichomoniasis are essential. This review describes the mechanisms of metronidazole resistance in T. vaginalis and provides a summary of trichomonicidal and vaccine candidate drugs.
Chemical disinfection of hepatitis A virus on environmental surfaces (1990)

Hepatitis A virus disinfection was assessed on contaminated stainless-steel disks. Ten microliters of fecally suspended hepatitis A virus was deposited on the center of each disk, dried for 20 min, and then covered with 20 microliters of the test product for 1 min. Of the 20 formulations tested, only 2% glutaraldehyde, a quaternary ammonium formulation containing 23% HCl (toilet bowl cleaner), and sodium hypochlorite (greater than 5,000 ppm [greater than 5,000 micrograms/ml] of free chlorine) reduced the virus titer by greater than 99.9%; phenolics, iodine-based products, alcohols, and solutions of acetic, peracetic, citric, and phosphoric acids were unable to do so.
QSAR Models of the in vitro Estrogen Activity of Bisphenol A Analogs (2003)

Abstract Bisphenol A is a monomer constituent of epoxy and polycarbonate resins used in consumer products. Many studies have shown that bisphenol A is a weak estrogen receptor agonist with endocrine disrupting potential in exposed organisms. Presented here is a series of quantitative structure‐activity relationship models to describe the in vitro hormone activity (estrogen receptor binding, reporter gene induction, and cell proliferation) of bisphenol A and 24 of its analogs. The hormone activity ranged over four orders of magnitude, with bisphenol A displaying intermediate activity. Comparative molecular field analysis, comparative molecular similarity indices, and hologram quantitative structure activity models were generated using SYBYL 6.8. Bisphenols with optimal estrogen activity contained two unencumbered phenolic groups in the para orientation, and multiple alkyl substituents extending from the carbon linking phenolic rings. Bisphenols with methyl group hydrogens replaced by halogens also produced strong estrogenic analogs. These studies suggest that it may be possible to use such structure activities to develop bisphenols that are useful monomers with reduced hormone activity.
Successful Subretinal Delivery and Monitoring of MicroBeads in Mice (2013)

The accessibility for routine surgery and its immune privileged state make the eye an ideal target for release system implants for therapeutic substances, including neurotrophic and anti-angiogenic compounds or protein based biosimilars. Microencapsulated human stem cells (MicroBeads) promise to overcome limitations inherent with single factor release systems, as they are able to produce physiologic combinations of bioactive compounds.
Regenerative Biomaterials that “Click”: Simple, Aqueous-Based Protocols for Hydrogel Synthesis, Surface Immobilization, and 3D Patterning (2011)

The click chemistry era has generated a library of versatile "spring-loaded" reactions that offer high yields, regio- and stereospecificity, and outstanding functional group tolerance. These powerful transformations are particularly advantageous for the design of sophisticated biomaterials that require high levels of precision and control, namely, materials that promote tissue regeneration such as hydrogels, 2D functionalized substrates, and 3D biomimetic scaffolds. In this review, the synthesis and application of regenerative biomaterials via click chemistry are summarized. Particular emphasis is placed on the copper(I)-catalyzed alkyne-azide cycloaddition, Diels-Alder cycloadditions, and thiol-click coupling.
Oncolytic herpes simplex virus-1 lacking ICP34.5 induces p53-independent death and is efficacious against chemotherapy-resistant ovarian cancer. (2000)

Replication-restricted herpes simplex virus-1 (HSV-1) strains lacking ICP34.5 are emerging as powerful anticancer agents against several solid tumors including epithelial ovarian cancer (EOC). Although chemotherapy-resistant tumors would be likely candidates for treatment with HSV-1 mutants lacking ICP34.5, the efficacy of these mutants on such tumors is unknown. In the present study, we investigated whether chemotherapy resistance affects the response of ovarian cancer cells to HSV-R3616, an ICP34.5-deficient, replication-restricted HSV-1. Primary EOC cultures obtained from patients who varied in their responses to platinum/paclitaxel induction chemotherapy displayed similar sensitivity to HSV-R3616. Similarly, chemotherapy-sensitive ovarian cancer cells A2780 and PA-1, possessing wild-type p53, and their respective chemotherapy-resistant clones A2780/200CP, lacking p53 function, and PA-1/E6, permanently expressing the HPV E6 gene, were equally sensitive to HSV oncolysis. Because wild-type HSV can kill cells by apoptosis and nonapoptotic mechanisms, we investigated the involvement of apoptosis and the role of the p53 tumor suppressor gene in oncolysis induced by HSV-R3616. Infection of ovarian cancer cell lines by HSV-R3616 was followed by cell death via apoptosis or nonapoptotic mechanisms as noted by morphology, cell cycle analysis, and in situ TUNEL assay. p53 protein levels remained unchanged, and Bax protein levels decreased in cells possessing intact p53 and that mainly underwent HSV-induced apoptosis. Loss of p53 function did not affect the frequency or rate of apoptosis or the sensitivity of EOC cells to the oncolytic effect of HSV-R3616. These results suggest that recombinant HSV-1 lacking ICP34.5 is capable of killing ovarian cancer cells that lack p53 function, resist apoptosis, and/or are chemotherapy resistant. These data support the hypothesis that HSV-based oncolytic therapy may be efficacious in chemotherapy-resistant tumors, including tumors that are deficient in p53.