gebhart/patrepeval huggingface dataset:
Characterizing fluorocarbon assisted atomic layer etching of Si using cyclic Ar/C4F8 and Ar/CHF3 plasma (2016)

With the increasing interest in establishing directional etching methods capable of atomic scale resolution for fabricating highly scaled electronic devices, the need for development and characterization of atomic layer etching processes, or generally etch processes with atomic layer precision, is growing. In this work, a flux-controlled cyclic plasma process is used for etching of SiO<sub>2</sub> and Si at the Angstrom-level. This is based on steady-state Ar plasma, with periodic, precise injection of a fluorocarbon (FC) precursor (C<sub>4</sub>F<sub>8</sub> and CHF<sub>3</sub>) and synchronized, plasma-based Ar<sup>+</sup> ion bombardment [D. Metzler et al., J. Vac. Sci. Technol., A 32, 020603 (2014) and D. Metzler et al., J. Vac. Sci. Technol., A 34, 01B101 (2016)]. For low energy Ar<sup>+</sup> ion bombardment conditions, physical sputter rates are minimized, whereas material can be etched when FC reactants are present at the surface. This cyclic approach offers a large parameter space for process optimization. Etch depth per cycle, removal rates, and self-limitation of removal, along with material dependence of these aspects, were examined as a function of FC surface coverage, ion energy, and etch step length using in situ real time ellipsometry. The deposited FC thickness per cycle is found to have a strong impact on etch depth per cycle of SiO<sub>2</sub> and Si but is limited with regard to control over material etching selectivity. Ion energy over the 20-30 eV range strongly impacts material selectivity. The choice of precursor can have a significant impact on the surface chemistry and chemically enhanced etching. CHF<sub>3</sub> has a lower FC deposition yield for both SiO<sub>2</sub> and Si and also exhibits a strong substrate dependence of FC deposition yield, in contrast to C<sub>4</sub>F<sub>8</sub>. The thickness of deposited FC layers using CHF<sub>3</sub> is found to be greater for Si than for SiO<sub>2</sub>. X-ray photoelectron spectroscopy was used to study surface chemistry. When thicker FC films of 11 Å are employed, strong changes of FC film chemistry during a cycle are seen whereas the chemical state of the substrate varies much less. On the other hand, for FC film deposition of 5 Å for each cycle, strong substrate surface chemical changes are seen during an etching cycle. The nature of this cyclic etching with periodic deposition of thin FC films differs significantly from conventional etching with steady-state FC layers since surface conditions change strongly throughout each cycle.
Detection of brachytherapy seeds at varying angles with a singular-spectrum-analysis algorithm (2007)

A singular-spectrum-analysis (SSA) algorithm previously was shown to be successful in detecting brachytherapy seeds in B-mode images when seeds were orthogonal to the ultrasound beam. In this study, the algorithm was extended to detect seeds at angles to the beam. The SSA algorithm derives P-values from selected eigenvalue pairs of the autocorrelation matrix of seed echo signals. The P-value indicates the probability of presence of a seed. A seed inserted in a gel pad and another inserted in beef tissue were scanned with a 5-MHz transducer. The seed angle was varied from orthogonal to the beam to 23 deg from orthogonal, using 1-degree increments. Simulations of seed echoes based on empirical data were generated and used to test the algorithm. Success in seed detection was expressed by a score computed from P-values. Scores for simulations decreased from 0.8 to 0.45 as the angle increased from 0 to 12 deg. Scores for experimental data varied from 0.74 at 0 deg to 0.62 at 23 deg; the lowest value was 0.1 at 7 deg. Accordingly, the SSA algorithm was successful in detecting the seed with clinically relevant angles between seed and beam.
Rational design of low-molecular weight heparins with improved <i>in</i> <i>vivo</i> activity (2003)

Heparin and low-molecular weight heparins (LMWHs), complex, sulfated polysaccharides isolated from endogenous sources, are potent modulators of hemostasis. Heparin and LMWHs interact with multiple components of the coagulation cascade to inhibit the clotting process. Pharmaceutical preparations of these complex polysaccharides, typically isolated from porcine intestinal mucosa, are heterogeneous in length and composition and, hence, highly polydisperse. Because of the structural heterogeneity of heparin and LMWHs, correlating their activity with a particular structure or structural motif has been a challenging task. Herein, we demonstrate a practical analytical method that enables the measurement of a structural correlate to in vivo anticoagulant function. With this understanding we have developed LMWHs with increased anticoagulant activity and decreased polydispersity. In addition to the pronounced anti-Xa and anti-IIa activity of these LMWHs, we also demonstrate that they possess desirable in vivo pharmacokinetic properties, the ability to cause the release of tissue factor pathway inhibitor (TFPI) from the endothelium, complete bioavailability through s.c. delivery, and the ability to inhibit both venous and arterial thromboses. Importantly, from a clinical safety point of view, unlike LMWHs presently used in the clinic, we show that these LMWHs are rapidly and completely neutralized by protamine. Together, the findings presented herein demonstrate a facile approach for the creation of designer LMWHs with optimal activity profiles.
CdZnTe semiconductor parallel strip Frisch grid radiation detectors (1998)

CdZnTe wide band gap compound semiconducting material offers promise as a room temperature operated gamma ray spectrometer. Position-dependent free charge carrier losses during transport can prevent efficient charge carrier extraction from semiconductor detectors and severely reduce energy resolution. Hole trapping losses in CdZnTe radiation detectors are far worse than electron trapping losses and resolution degradation in CdZnTe detectors results primarily from severe hole trapping during transport. Coplanar radiation detectors improve energy resolution by sensing the induced charge primarily from the motion of electrons. Demonstrated is an alternative approach to single free charge carrier sensing, in which a parallel strip Frisch grid is fabricated on either side of a parallelepiped block. The detectors are three terminal devices, but require only one preamplifier for the output signal. The prototype devices demonstrate a considerable increase in energy resolution when operated in the true Frisch grid mode rather than the planar mode, with a demonstrated room temperature energy resolution for 662 keV gamma rays of 5.91% at FWHM for a 10 mm/spl times/2 mm/spl times/10 mm device. Presently, high surface leakage currents prevent large voltages from being applied to the devices, which ultimately reduces their maximum achievable energy resolution. Further improvements are expected with the realization of reduced surface leakage currents.
Drug resistance to topoisomerase directed chemotherapy in human multiple myeloma (2008)

Human multiple myeloma is an incurable hematological malignancy characterized by the proliferation of plasma cells in the bone marrow. Myeloma represents approximately 20% of all blood cancers. In this research we have explored examples of both intrinsic and acquired drug resistance in myeloma.\nTopoisomerases are enzymes that are critical for cell division, especially in rapidly dividing cells such as are found in cancer. Topoisomerase poisons are a common group of drugs that are used to treat cancer. Topoisomerase I and II poisons used in the treatment of multiple myeloma include topotecan, mitoxantrone, doxorubicin, and etoposide\nIn order for topoisomerase drugs to be effective, the enzyme must be in direct contact with the DNA. In chapters one and two we examined the export of topoisomerase II alpha from the nucleus as a mechanism of drug resistance. High density cells, similar to those found in the bone marrow, export topoisomerase II alpha from the nucleus to the cytoplasm, rendering the cell drug resistant. We found that blocking nuclear export using the CRM1 inhibitor ratjadone C, or CRM1 specific siRNA, could sensitize high density cells to topoisomerase drugs. Sensitization to topoisomerase inhibitors was correlated with increased topoisomerase/DNA complexes and increased DNA strand breaks. This method of sensitizing human myeloma cells suggests a new therapeutic approach to this disease.\nIn chapter three we examined the role of the molecular transporter ABCG2 in drug resistance in multiple myeloma. We found that ABCG2 expression in myeloma cell lines increased after exposure to topotecan or doxorubicin. Myeloma patients treated with topotecan had an increase in ABCG2 mRNA and protein expression after drug treatment and at relapse. We found that expression of ABCG2 is regulated, at least in part, by promoter methylation both in cell lines and in patient plasma cells. Demethylation of the promoter increased ABCG2 mRNA and protein expression. These findings suggest that ABCG2 is expressed and functional in human myeloma cells, regulated by promoter methylation, affected by cell density, upregulated in response to chemotherapy, and may contribute to drug resistance.
Generalized theoretical treatment and numerical method of time-resolved radially dependent laser pulses interacting with multiphoton absorbers (2006)

We introduce a generalized numerical method to calculate short-pulsed laser propagation in a wide class of multiphoton absorbing materials. The method has no restrictions on the input pulse widths varying from nanosecond to femtosecond, and its numerical solution is both radially and temporarily dependent, enabling us to check numerically the validity of assuming radially constant solutions, which ensures that the true peak intensity falls below the damage causing level. A new feature of our technique enables us to determine quantitatively the contributions to the total absorption due to every electronic energy level. We found excellent agreement between our calculations and experiments using sample materials ranging from reverse saturable absorbers, two-photon absorbers with excited-state absorption to three-photon absorbers. We applied our technique to a two-photon absorber with excited-state absorption and found approximately 1 order of magnitude increase in the absorption when femtosecond pulses were used in place of nanosecond pulses.
MRI quantification of non‐Gaussian water diffusion by kurtosis analysis (2010)

Quantification of non-Gaussianity for water diffusion in brain by means of diffusional kurtosis imaging (DKI) is reviewed. Diffusional non-Gaussianity is a consequence of tissue structure that creates diffusion barriers and compartments. The degree of non-Gaussianity is conveniently quantified by the diffusional kurtosis and derivative metrics, such as the mean, axial, and radial kurtoses. DKI is a diffusion-weighted MRI technique that allows the diffusional kurtosis to be estimated with clinical scanners using standard diffusion-weighted pulse sequences and relatively modest acquisition times. DKI is an extension of the widely used diffusion tensor imaging method, but requires the use of at least 3 b-values and 15 diffusion directions. This review discusses the underlying theory of DKI as well as practical considerations related to data acquisition and post-processing. It is argued that the diffusional kurtosis is sensitive to diffusional heterogeneity and suggested that DKI may be useful for investigating ischemic stroke and neuropathologies, such as Alzheimer's disease and schizophrenia.
Secure RAID schemes for distributed storage (2016)

We propose secure RAID, i.e., low-complexity schemes to store information in a distributed manner that is resilient to node failures and resistant to node eavesdropping. We generalize the concept of systematic encoding to secure RAID and show that systematic schemes have significant advantages in the efficiencies of encoding, decoding and random access. For the practical high rate regime, we construct three XOR-based systematic secure RAID schemes with optimal encoding and decoding complexities, from the EVENODD codes and B codes, which are array codes widely used in the RAID architecture. These schemes optimally tolerate two node failures and two eavesdropping nodes. For more general parameters, we construct efficient systematic secure RAID schemes from Reed-Solomon codes. Our results suggest that building “keyless”, information-theoretic security into the RAID architecture is practical.
Human Ehrlichiosis in the United States, 1985 to 1990 (1994)

The findings of this study are primarily representative of more seriously ill patients with human ehrlichiosis. Although rates are low, ehrlichiosis is found in many areas of the United States. Patients with a history of tick exposure, acute febrile illness, decreasing leukocyte counts, and decreasing platelet counts may have ehrlichiosis. Prompt treatment with tetracycline or chloramphenicol markedly decreases the morbidity.
Kinetic Studies on the Hydrogenation of Curcuminoids Isolated from Curcuma Longa by LC/MS (2015)

In the present study, we investigated the catalytic palladium hydrogenation of curcuminoids, the major constituent isolated from Turmeric root (Curcuma longa) at various time intervals and monitored by LC/MS. The study revealed that the most of the curcuminoids hydrogenated within two hours period and gave the corresponding tetra, hexa and octa-hydrocurcuminoids at different ratio except bisdemethoxycurcumin, which gave only hexa-hydrogenated derivative. Even though, Palladiumcarbon catalyst does not favour the reduction of carbonyl group, due to the presence of the conjugated double bonds hydrogenation occurred.
22.1: PH‐VAN System Design for High Contrast Rub‐Free Microdisplays (2001)

Abstract If circular polarizers are incorporated into a microdisplay system, a Vertically Aligned Nematic (VAN) cell design with perfect homeotropic alignment can be used. This alignment is easy to achieve and removes the rubbing step from the manufacturing process. Perfect Homeotropic VAN (PH‐VAN) cells have the performance advantage of ultra high contrast.
Synthesis and antiviral activity of some phosphates of the broad-spectrum antiviral nucleoside, 1-.beta.-D-ribofuranosyl-1,2,4-triazole-3-carboxamide (ribavirin) (1978)

1-beta-D-Ribofuranosyl-1,2,4-triazole-3-carboxamide 5'-phosphate (2) was prepared and converted into the following derivatives: the 5'-phosphoramidate 3, the 5'-diphosphate 4, the 5'-triphosphate 5, and the cyclic 3',5'-phosphate 6. The cyclic 2',3'-phosphate 7 was prepared from the parent nucleoside, 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide (1), and was opened to the 2'(3')-phosphate 8. These compounds were found to exhibit significant antiviral activity against several viruses in cell culture. Ribavirin 5'-phosphate (2) was shown to be effective when tested against lethal infections in mice caused by influenza A2, influenza B, and murine hepatitis viruses.
Reactions of Hydrogen Peroxide with Familial Amyotrophic Lateral Sclerosis Mutant Human Copper-Zinc Superoxide Dismutases Studied by Pulse Radiolysis (1998)

Mutations in copper-zinc superoxide dismutase (CuZn-SOD) have been implicated in the familial form of the motor neuron disease amyotrophic lateral sclerosis (Lou Gehrig's disease). We have expressed and purified recombinant human wild type (hWT) and G93A (hG93A) CuZn-SOD, and we have used pulse radiolysis to measure their superoxide dismutase activities and their rates of deactivation upon exposure to hydrogen peroxide or heat. Both hG93A and hWT CuZn-SOD were found to have high SOD activities in their copper and zinc containing as-isolated forms as well as when remetallated entirely with copper (CuCu). Rates of deactivation by hydrogen peroxide of the as-isolated hWT and hG93A enzymes were determined and were found to be similar, suggesting that the FALS mutant enzyme is not inactivated at a higher rate than wild type by generation of and subsequent reaction with hydroxyl radical, .OH, when it is in the CuZn form. However, rates of deactivation by hydrogen peroxide of the CuCu derivatives of both hWT and hG93A were significantly greater than those of the copper and zinc containing as-isolated enzymes. Rates of thermal deactivation were also similar for the mutant and hWT as-isolated CuZn forms but were greater for the CuCu derivatives of both enzymes. Reactions of hydrogen peroxide with the Cu(II)Cu(II) derivative of the WT enzyme demonstrate that the copper ion in the copper site is reduced much more rapidly than the copper in the zinc site, leading to the conclusion that reaction of hydrogen peroxide with Cu(I) in the copper site is the source of deactivation in the CuCu as well as the CuZn enzymes.
Characterization of a Human Cytomegalovirus Glycoprotein Complex (gcI) (1988)

Three distinct families of glycoprotein complexes present in the envelopes of human cytomegalovirus and designated gcI, gcII and gcIII have been described recently. The synthesis of the gcI family was analysed using either inhibitors of glycoprotein processing and transport or endoglycosidase treatments of purified glycoproteins. The initial step in gcI synthesis involved the glycosylation of a 95K protein (p95) to form a high-mannose, simple N-linked glycoprotein of Mr 158K (gp158), which was detected only in the presence of the glycoprotein processing inhibitor castanospermine. This intermediate was rapidly trimmed in the virus-infected cell to form a more stable simple N-linked precursor glycoprotein of Mr 138K (gp138). Treatment of either gp158 or gp138 with endoglycosidase H produced p95. Both molecules, gp158 and gp138, were found in disulphide-linked complexes which are presumably infected cell precursors to gcI since they were not found in virions. The processing of these complexes involved complete cleavage of gp138 and conversion of some but not all of its oligosaccharide to complex N-linked chains. Both processing events were inhibited by the ionophore monensin. Mature gcI contained the gp138 cleavage product, gp93-130. The latter glycoprotein could be separated into two electrophoretic forms, gp93 and gp130. The deglycosylated form of gp55 had a discrete banding pattern with an apparent Mr of 46K (p46). In contrast, the deglycosylated forms of gp93 and gp130 had diffuse banding patterns with apparent Mr values of 46K to 56K (p46-56) and 60K to 70K (p60-70) respectively. Peptide profiles comparing gp93 with gp130 indicated that they have highly similar polypeptide backbones. Since the deglycosylated forms of gp55 and gp130, 46K and 60K to 70K, respectively, together exceed the 95K precursor/deglycosylated intermediate in Mr, we propose that the above glycoproteins are derived by an alternative proteolytic cleavage of the precursor. The heterogeneous electrophoretic properties of the deglycosylated forms of gp93 and gp130 may be due to additional post-translational modifications other than glycosylation.
The role of the <i>C</i> state in the XeF laser (1979)

Ne/Xe/NF3 mixtures were irradiated by a cold-cathode e-beam, and the fluorescence yields of the B and C states of XeF were measured as a function of neon pressure from 200 to 5300 Torr. At low neon pressures, the fluorescence yield of the B state corresponds to one photon emitted for each neon ion formed. As the neon pressure is increased the fluorescence yield of the B state decreases, but the ratio of the C emission to B emission approaches unity. If the C is formed through a channel which is independent of the B state, then the ultimate efficiency of the XeF laser is severely limited. However, analysis of the data with a XeF kinetics model indicates that the enhanced C emission results from two-body quenching of the B state by neon. We conclude that the XeF laser performance has been limited by other processes, namely, incomplete vibrational relaxation and ground-state bottlenecking.
<i>BIN2</i>, a New Brassinosteroid-Insensitive Locus in Arabidopsis (2001)

Brassinosteroids (BRs) play important roles throughout plant development. Although many genes have been identified that are involved in BR biosynthesis, genetic approaches in Arabidopsis have led to the identification of only one gene, BRI1, that encodes a membrane receptor for BRs. To expand our knowledge of the molecular mechanism(s) of plant steroid signaling, we analyzed many dwarf and semidwarf mutants collected from our previous genetic screens and identified a semidwarf mutant that showed little response to exogenous BR treatments. Genetic analysis of the bin2 (BR-INSENSITIVE 2) mutant indicated that the BR-insensitive dwarf phenotype was due to a semidominant mutation in the BIN2 gene that mapped to the middle of chromosome IV between the markers CH42 and AG. A direct screening for similar semidwarf mutants resulted in the identification of a second allele of the BIN2 gene. Despite some novel phenotypes observed with the bin2/+ mutants, the homozygous bin2 mutants were almost identical to the well-characterized bri1 mutants that are defective in BR perception. In addition to the BR-insensitive dwarf phenotype, bin2 mutants exhibited BR insensitivity when assayed for root growth inhibition and feedback inhibition of CPD gene expression. Furthermore, bin2 mutants displayed an abscisic acid-hypersensitive phenotype that is shared by the bri1 and BR-deficient mutants. A gene dosage experiment using triploid plants suggested that the bin2 phenotypes were likely caused by either neomorphic or hypermorphic gain-of-function mutations in the BIN2 gene. Thus, the two bin2 mutations define a novel genetic locus whose gene product might play a role in BR signaling.
Automating mode detection for travel behaviour analysis by using global positioning systems-enabled mobile phones and neural networks (2010)

Travel surveys collect trip data such as origin, destination, mode, duration, distance and purpose of trips, as well as socioeconomic and demographic data for analysis. Transportation planners, policymakers, state departments of transportation, metropolitan planning organisations, industry professionals and academic researchers use survey data to better understand the current demand and performance of the transportation infrastructure, and to plan in preparation for future growth. Next-generation travel surveys will utilise global positioning systems (GPS) to collect trip data with minimal input from survey participants. Owing to their ubiquity, GPS-enabled mobile phones are developing into a promising survey tool. TRAC-IT is a mobile phone application that collects real-time GPS data and requires minimal input from the user for data such as trip purpose, mode and vehicle occupancy. To ease survey burden on participants and enable real-time, mode-specific location-based services, new techniques must be explored to derive more information directly from GPS data. As part of travel survey collection, TRAC-IT is able to passively determine trip mode using GPS-enabled mobile phones and neural networks. The mode detection technique presented in this article can be optimised using a critical point, pre-processing algorithm to reduce the size of required GPS datasets obtained from GPS-enabled mobile phones, thus reducing data collection costs while conserving precious mobile phone resources such as battery life.