gebhart/patrepeval huggingface dataset:
Within-Layer Overlay Impact for Design in Metal Double Patterning (2010)

In double patterning lithography (DPL), overlay errors between two patterning steps of the same layer translate into CD variability. Since CD uniformity budget is very tight, meeting requirement of overlay control is one of the biggest challenges for deploying DPL. In this paper, we electrically evaluate overlay errors for back-end-of-line DPL with the goal of studying relative effects of different overlay sources and interactions of overlay control with design parameters. Experimental results show the following: 1) the expected electrical impact of overlay in a path is not significant (<; 6% worst-case RC variation) and should be the basis for determining overlay budget requirement; 2) the worst-case electrical impact of overlay in a single line remains a serious concern (up to 16.6% ΔRC and up to 50 mV increase of peak crosstalk noise); 3) translational overlay error has the largest electrical impact compared to other overlay sources; and 4) overlay in y direction (x for horizontal metallization) has negligible electrical impact and, therefore, preferred routing direction should be taken into account for overlay sampling and alignment strategies. Design methods for reducing overlay electrical impact in wires are then identified. Finally, we explore positive/negative process options from an electrical perspective and conclude that positive process is preferred.
Novel diagnostic microarray assay formats towards comprehensive on-site analysis (2009)

Advances in molecular methods for analyzing DNA, RNA and proteins in humans as well as in other animals, plants, fungi, bacteria or viruses have greatly increased the resolution with which we can study life’s complexity and dynamics on earth. While genomic, transcriptomic and proteomic laboratory tools for molecular diagnosis of disease are rapidly becoming more comprehensive, the access to such advanced yet often expensive and centralized procedures is limited. There is a great need for rapid and comprehensive diagnostic methods in low-resource settings or contexts where a person can not or will not go to a hospital or medical laboratory, yet where a clinical analysis is urgent. In this thesis, results from development and characterization of novel technologies for DNA and protein microarray analysis are presented. Emphasis is on methods that could provide rapid, cost-effective and portable analysis with convenient readout and retained diagnostic accuracy. The first study presents a magnetic bead-based approach for DNA microarray analysis for a rapid visual detection of single nucleotide polymorphisms. In the second work, magnetic beads were used as detection reagents for rapid differential detection of presence of pestiviral family members using a DNA oligonucleotide microarray with read-out by means of a tabletop scanner or a digital camera. In paper three, autoimmune responses from human sera were detected on a protein autoantigen microarray, again by means of magnetic bead analysis. Here, special emphasis was made in comprehensively comparing the performance of the magnetic bead detection to common fluorescence-based detection. In the fourth study, an immunochromatographic lateral flow protein microarray assay is presented for application in the classification of contagious pleuropneumonia from bovine serum samples. The analysis could be performed within 10 minutes using a table top scanner, and the performance of the assay was shown to be comparable to that of a cocktail ELISA. In the fifth paper, the lateral flow microarray framework is investigated in further detail by means of experiments and numerical simulation. It was found that downstream effects play an important role, and the results further suggest that the downstream binding profiles may find use in simple affinity evaluation.
Optimization of the spray drying of a<i>Paenibacillus polymyxa-</i>based biopesticide on pilot plant and production scales (2013)

Spore survival and moisture content are two important properties of biopesticides, and both are related to field biocontrol efficacy and storage shelf life. In this study, Paenibacillus polymyxa (HY96-2) was spray-dried on both pilot plant and production scales, and the effects of inlet and outlet temperatures on spore survival and moisture content were investigated. The results showed that inlet temperatures ranging from 170 to 230 °C (at an outlet temperature of 80 °C) had no obvious effect on the two properties during pilot scale processing, although an inlet temperature of 230 °C resulted in higher feed speed. When the outlet temperature on the pilot scale was reduced from 100 to 80 °C, no obvious variations in spore survival and moisture content were found, while a further reduction from 80 to 65 °C resulted in a decline in spore survival from 81.0 to 67.0% and an increase in moisture content from 2.3 to 31.7%. These results indicate that both outlet temperature and moisture content have an effect on spore survival. Optimum inlet and outlet temperatures for P. polymyxa processing were 230 °C and 85–90 °C on a production scale. Under these conditions, spore survival and moisture content were 83.5–86.6% and 2.73––4.12%, respectively.
Two hypervarlable minisatellite DNA binding proteins (1991)

Hypervariable minisatellite DNA sequences are short, tandemly repeated sequences present at numerous loci in eukaryotes. They stimulate intermolecular homologous recombination up to 13-fold in human cells in culture and may be specific sites for the initiation of recombination in the eukaryotic genome (Wahls, W.P., Wallace, L.J., & Moore, P.D. (1990) Cell 60, 95-103). Reported here is the detection and partial purification of two hypervariable minisatellite DNA binding proteins, called Msbp-2 and Msbp-3, present in the nuclear extracts of human HeLa cells. The proteins elute from a gel filtration column with a native mass of 200-250 kDa and have sizes of 77 kDa and 115 kDa respectively.
The alternative splicing of the CD45 tyrosine phosphatase is controlled by negative regulatory trans-acting splicing factors. (1992)

CD45, a receptor-type protein tyrosine phosphatase involved in lymphocyte activation, consists of five isoforms generated by alternative mRNA splicing. The pattern of CD45 splicing depends upon cell type, state of activation, and thymic development. We previously showed that mouse B and thymocyte cell lines transfected with a human CD45 minigene construct appropriately splice the alternative exons, demonstrating the presence of trans-acting tissue-specific splicing factors. To study the regulation of CD45 alternative splicing, cells having different splicing patterns were transiently fused, and mRNA was analyzed using reverse transcription-polymerase chain reaction. Human B cells, normally producing only the largest CD45 mRNAs, could splice out the alternative exons after fusion with mouse thymocytes. In contrast, the splicing pattern of human T cell lines (smaller CD45 isoforms) was unaltered by fusion with mouse B cells. This suggests that cells expressing the smallest CD45 isoform contain negatively acting trans-factor(s) that allow the alternative exons to be skipped, and that the full length isoform containing all three alternative exons is the default pattern of splicing. In agreement, incubation of thymocytes or T cell subsets with cycloheximide increased mRNA corresponding to the larger isoforms. CD45 isoform expression can now be interpreted in terms of the presence or absence of negative regulatory trans-acting splicing factors.
Dynamic Changes in the Recovery after Traumatic Brain Injury in Mice: Effect of Injury Severity on T2-Weighted MRI Abnormalities, and Motor and Cognitive Functions (2008)

Memory and neurobehavioral dysfunctions are among the sequelae of traumatic brain injury (TBI). The Neurological Severity Score (NSS) includes 10 tasks and was previously designed to assess the functional status of mice after TBI. The object recognition task (ORT) measures specific episodic memory and is expressed by the percent time spent by an animal at a novel, unfamiliar object (Discrimination Index [DI]). It is an ideal tool for evaluating cognitive function after TBI. The present study sought to validate the use of the NSS and ORT in severe and mild focal TBI in mice, and to confirm that the spontaneous recovery and the radiological abnormalities, shown by T2-weighted magnetic resonance imaging (MRI), are dependent upon injury severity. Mice were subjected to severe and mild closed head injury (NSS at 1 h 7.52 +/- 0.34 and 4.62 +/- 0.14, respectively). NSS was evaluated for 25 days and showed a decrease by 3.86 +/- 0.26 and 2.54 +/- 0.35 units in the severely and mildly injured mice, respectively. ORT revealed DI in severely injured group of 51.7 +/- 6.15%, (vs approximately 75-80% in uninjured animal) on day 3 and 66.2 +/- 6.81% on day 21. In contrast, the mildly injured mice did not show cognitive impairment throughout the same period. The damage seen by MRI at 24 h after injury, strongly correlated with NSS(1h) (R = 0.87, p < 0.001). We conclude that NSS is a reliable tool for evaluation of neurological damage in head-injured mice, NSS(1h) predicts the motor dysfunction, cognitive damage, and brain-damage characteristics as depicted by T2-weighted MRI. The combined assessment of neurobehavioral and cognitive function along with MRI is most useful in evaluating recovery from injury, especially when testing effectiveness of novel treatments or genetic manipulations.
A Statistical Approach to Mechanized Encoding and Searching of Literary Information (1957)

Written communication of ideas is carried out on the basis of statistical probability in that a writer chooses that level of subject specificity and that combination of words which he feels will convey the most meaning. Since this process varies among individuals and since similar ideas are therefore relayed at different levels of specificity and by means of different words, the problem of literature searching by machines still presents major difficulties. A statistical approach to this problem will be outlined and the various steps of a system based on this approach will be described. Steps include the statistical analysis of a collection of documents in a field of interest, the establishment of a set of “notions” and the vocabulary by which they are expressed, the compilation of a thesaurus-type dictionary and index, the automatic encoding of documents by machine with the aid of such a dictionary, the encoding of topological notations (such as branched structures), the recording of the coded information, the establishment of a searching pattern for finding pertinent information, and the programming of appropriate machines to carry out a search.
A 2.5 V 50 MHz IF-sampling ΔΣ-modulator for digital cellular telephones (2002)

This paper discusses the design of a 50 MHz IF-sampling switched-capacitor /spl Delta//spl Sigma/-modulator with a 2.5 V supply voltage implemented in a 0.5 /spl mu/m BiCMOS process. The problems caused by the low analog supply voltage are addressed with special biasing and common-mode arrangements. Simulation results verifying a peak SNDR of 83 dB for a baseband signal are presented.
Putative Role of the Orphan Nuclear Receptor SXR (Steroid and Xenobiotic Receptor) in the Mechanism of CYP3A4 Inhibition by Xenobiotics (2002)

Cytochrome P450 monooxygenase 3A4 (CYP3A4) is responsible for the metabolism of endogenous steroids and drugs in liver. Many inducers of human CYP3A4, such as rifampicin, bind to the orphan nuclear receptor SXR (steroid and xenobiotic receptor) as ligands and stimulate transcription on xenobiotic response elements located in the CYP3A4 promoter. Conversely, it is not known whether SXR mediates the transcriptional repression. We thus examined transcriptional repression of SXR and its interaction with corepressors, NCoR (nuclear receptor corepressor) and SMRT (silencing mediator for retinoid and thyroid receptors) using reporter assays in the absence and presence of ligand. Cotransfection of SMRT, but not NCoR, inhibited not only basal but also rifampicin-induced transcriptional activity of SXR on the CYP3A4 promoter through specific SMRT-SXR interaction in HepG2 cells. Interestingly, rifampicin also increased the interaction of SXR with SMRT as well as with coactivator SRC-1. On the other hand, the anti-fungal agent ketoconazole decreased SXR interaction with both SRC-1 and SMRT. Ketoconazole partially inhibited corticosterone-induced SXR-mediated transcription on the CYP3A4 promoter. Taken together, our results suggest that the differential interaction of coactivators and corepressors induced by various xenobiotics may alter SXR-mediated transcription. Further, the effects of ketoconazole on the CYP3A4 gene suppression may explain, in part, drug-induced inhibition of the CYP3A4 action at the transcriptional level.
Fringe Rate Demodulator For Fiber Optic Interferometric Sensors (1988)

Fiber optic interferometric sensors can be extremely sensitive. A sensor that operates in the 1 to 10K radian regime has been developed at the Naval Postgraduate School. Present demodulators operate over a 10 microradian to .1 radian range. Therefore a different approach to demodulation is required for this sensor. A fringe rate scheme is described here. The output of an optical shaft encoder driven by a pendulum resembles the fringe pattern produced by a fiber optic interferometric sensor in response to a sinusoidal perturbation. The HEDS 6000 shaft encoder used in this project provides both in-phase and quadrature waveforms --both are required for demodulation. This simulates the two waveforms provided by an interferometer with a 3X3 coupler. The well behaved outputs of the shaft encoder were used to test the fringe rate demodulator circuit. The cicuitry that reconstructs the analog signal from the in-phase and quadrature signals must do two things: convert the interferometric fringe rate to a proportional voltage level and determine whether this level should remain positive or be inverted. A frequency-to-voltage converter chip (SK9209) accomplishes the first task. Since the chip is based on a charge pump/RC integrator there are some trade-offs for noise vs. slew-rate. A possible solution is a digital frequency-to-voltage circuit, i.e. a digital counter and a D/A converter. The up/down decision can be made by determining which waveform (in-phase or quadrature) is leading. This is accomplished by a JK flip-flop and edge detector circuitry. The flip-flop output controls a switch which is the converting element in a voltage follower/inverting amplifier. The output of the circit is a waveform which indicates particle velocity.
Photo-triggered solvent-free metamorphosis of polymeric materials (2017)

Liquefaction and solidification of materials are the most fundamental changes observed during thermal phase transitions, yet the design of organic and polymeric soft materials showing isothermal reversible liquid-nonliquid conversion remains challenging. Here, we demonstrate that solvent-free repeatable molecular architectural transformation between liquid-star and nonliquid-network polymers that relies on cleavage and reformation of a covalent bond in hexaarylbiimidazole. Liquid four-armed star-shaped poly(n-butyl acrylate) and poly(dimethyl siloxane) with 2,4,5-triphenylimidazole end groups were first synthesized. Subsequent oxidation of the 2,4,5-triphenylimidazoles into 2,4,5-triphenylimidazoryl radicals and their coupling with these liquid star polymers to form hexaarylbiimidazoles afforded the corresponding nonliquid network polymers. The resulting nonliquid network polymers liquefied upon UV irradiation and produced liquid star-shaped polymers with 2,4,5-triphenylimidazoryl radical end groups that reverted to nonliquid network polymers again by recoupling of the generated 2,4,5-triphenylimidazoryl radicals immediately after terminating UV irradiation.The design of organic and polymeric soft materials showing isothermal reversible liquid-nonliquid conversion is challenging. Here, the authors show solvent-free repeatable molecular architectural transformation between liquid-star and non-liquid-network polymers by the cleavage and reformation of covalent bonds in the polymer chain.
DInSAR estimation of land motion using intermittent coherence with application to the South Derbyshire and Leicestershire coalfields (2013)

Differential interferometric synthetic aperture radar (DInSAR) is a recognized remote-sensing method for measuring the land motion occurring between two satellite radar acquisitions. Advanced DInSAR techniques such as persistent scatterers and small baseline methods are excellent over urban and rocky environments but generally poor over more rural and natural terrain where the signal can be intermittently good and bad. Here, we describe the Intermittent Small Baseline Subset (ISBAS) method, which appears to improve results over natural, woodland and agricultural terrain. This technique uses a multi-looked, low-resolution approach, which is particularly suitable for deriving the linear components of subsidence for large-scale deformations. Application of the ISBAS method over a coal mining area in the UK indicates that it is able to significantly improve upon a standard small baseline approach.
High efficiency polymer solar cells with internal quantum efficiency approaching 100% (2009)

We report the fabrication and measurement of solar cells with 6% power conversion efficiency using the alternating copolymer, poly[N-9''-hepta-decanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole), PCDTBT, in bulk heterojunction (BHJ) composites with the fullerene derivative [6,6]-phenyl C<sub>70</sub>-butyric acid methyl ester (PC<sub>70</sub>BM). The PCDTBT/PC<sub>70</sub>BM solar cells exhibit the best performance of any BHJ system studied to date; J<sub>sc</sub> = 10.6 mA/cm<sup>2</sup>, V<sub>oc</sub> = 0.88 V, FF = 0.66 and η<sub>e</sub> = 6.1% under air mass 1.5 global (AM 1.5G) irradiation of 100 mW/cm<sup>2</sup>. The internal quantum efficiency (IQE) is close to 100%, implying that essentially every absorbed photon results in a separated pair of charge carriers and that all photogenerated carriers are collected at the electrodes.
Experimental Field Test Results on Feasibility of Declarative Spectrum Management (2008)

We describe the design and report on experience fielding an end-to-end framework for declarative spectrum management of frequency agile wireless communication devices. As part of the Defense Advanced Research Projects Agency NeXt Generation communication program, we developed a distributed, policy-driven system that restricts spectrum access based on spectral, temporal and geospatial context. We report on our field framework experimentation, illustrating the capability offered to wireless systems, their command & control management, and individual radios for enforcing spectrum access policies while enabling the radios to fully utilize available spectrum in comparison to traditional, static-assignment spectrum access methods.
Synergistic effects of tacrolimus and azole antifungal compounds in fluconazole-susceptible and fluconazole-resistant Candida glabrata isolates (2015)

In vitro interaction between tacrolimus (FK506) and four azoles (fluconazole, ketoconazole, itraconazole and voriconazole) against thirty clinical isolates of both fluconazole susceptible and -resistant Candida glabrata were evaluated by the checkerboard microdilution method. Synergistic, indifferent or antagonism interactions were found for combinations of the antifungal agents and FK506. A larger synergistic effect was observed for the combinations of FK506 with itraconazole and voriconazole (43%), followed by that of the combination with ketoconazole (37%), against fluconazole-susceptible isolates. For fluconazole-resistant C. glabrata , a higher synergistic effect was obtained from FK506 combined with ketoconazole (77%), itraconazole (73%), voriconazole (63%) and fluconazole (60%). The synergisms that we observed in vitro , notably against fluconazole-resistant C. glabrata isolates, are promising and warrant further analysis of their applications in experimental in vivo studies.
Photopatternable Conductive PDMS Materials for Microfabrication (2008)

Abstract Conductive photodefinable polydimethylsiloxane (PDMS) composites that provide both high electrical conductivity and photopatternability have been developed. The photosensitive composite materials, which consist of a photosensitive component, a conductive filler, and a PDMS pre‐polymer, can be used as a negative photoresist or a positive photoresist with an additional curing agent. A standard photolithographic approach has been used to fabricate conductive elastomeric microstructures. Feature sizes of 60 µm in the positive photoresist and 10 µm in the negative photoresist have been successfully achieved. Moreover, as the conductive filler, silver powders significantly improve the electrical conductivity of the PDMS polymer, but also provide enhanced mechanical and thermal properties as well as interesting biological properties. The combined electrical, mechanical, thermal, and biological properties along with photopatternability make the PDMS‐Ag composite an excellent processable and structural material for various microfabrication applications.
Chemoselective and Continuous Flow Hydrogenations in Thin Films Using a Palladium Nanoparticle Catalyst Embedded in Cellulose Paper (2018)

Cellulose immobilized palladium (0) nanoparticles (PdNPs) were prepared for the use in scalable catalytic reactions in flow. Preparation of the catalyst is remarkably simple and fast, where a palladium acetate solution is drop-casted onto cellulose paper and then exposed to 1 atm of hydrogen for a mere 90 s to produce embedded Pd(0) nanoparticles. This catalyst system is efficient in the hydrogenation of alkenes, nitroarenes, ketones, and enamides, with products formed in high yields, under ambient pressure and temperature. The system is also effective for transfer hydrogenation using ammonium formate as an alternative hydrogen source. A high catalyst stability and reusability are demonstrated along with the chemoselective and scalable synthesis of industrially important fine chemicals, including the biobased molecule cyrene.
Expression of a Chimeric Tobacco Peroxidase Gene in Transgenic Tomato Plants (1992)

Tomato plants (Lycopersicon esculentum cv. OH 7814) were transformed via Agrobacterium tumefaciens with a chimeric tobacco anionic peroxidase (EC 1.11.1.7) gene joined to the cauliflower mosaic virus (CaMV) 35S promoter. Transgenic plants obtained by selection on kanamycin were found to have more than five times the total leaf peroxidase activity of control plants. Transformed tomato plants chronically wilted upon reaching sexual maturity. Two independently selected transformants were self-fertilized, and progeny were obtained that were homozygous for the foreign gene. Isoelectric focusing gels stained for peroxidase activity revealed a new tomato leaf peroxidase isoenzyme with a pI of 3.75, which is similar to that seen in Nicotiana sylvestris L. Mature tomato fruit were found to have up to 1600-fold higher peroxidase activity in transformants expressing the tobacco anionic peroxidase (TobAnPOD) than control plants. Tissue blots showed the tobacco enzyme evenly distributed throughout the tomato fruit tissue. Progeny plants possessing the tobacco peroxidase gene (now homozygous) showed stunting, and fruit size was reduced by >80%. However, fruit set was normal and the rate of ripening was not altered from control plants. Fruit from transformed plants were found to have normal pigmentation, but the soluble solids concentration was 400% higher than in control tomato fruit. This result was predicted from the peroxidase-induced water stress. Possible roles for the tobacco anionic peroxidase in growth, development, and stress resistance are discussed.
Contemporary Communication Systems Using MATLAB (1999)

Signals and linear systems random processes analog communications analog-to-digital conversion baseband digital transmission channel equalization carrier modulation systems channel capacity and coding spread spectrum communications.