gebhart/patrepeval huggingface dataset:
Antenna theory and design (1981)

Antenna Fundamentals and Definitions. Some Simple Radiating Systems and Antenna Practice. Arrays. Line Sources. Resonant Antennas: Wires and Patches. Broadband Antennas. Aperture Antennas. Antenna Synthesis. Antennas in Systems and Antenna Measurements. CEM for Antennas: The Method of Moments. CEM for Antennas: Finite Difference Time Domain Method. CEM for Antennas: High-Frequency Methods. Appendices. Index.
WSXM: A software for scanning probe microscopy and a tool for nanotechnology (2007)

In this work we briefly describe the most relevant features of WSXM, a freeware scanning probe microscopy software based on MS-Windows. The article is structured in three different sections: The introduction is a perspective on the importance of software on scanning probe microscopy. The second section is devoted to describe the general structure of the application; in this section the capabilities of WSXM to read third party files are stressed. Finally, a detailed discussion of some relevant procedures of the software is carried out.
Reconfigurable flight control of a high incidence research model using predictive control (1998)

This paper describes a scheme for fault-tolerant control of an aircraft with a high angle of incidence. The scheme is an example of a generic scheme proposed in (Maciejowski, 1997), adapted to the particular needs of this application. It combines the use of a high-fidelity model of the aircraft with model predictive control, and assumes the availability of information about the fault which has occurred from an FDI system. This paper examines the performance of the proposed fault-tolerant scheme in the presence of severe failures of control surfaces and of the aircraft structure. It contains details of a modelling methodology which enables updating of the model with failure information, and of a methodology for on-line re-linearisation. The modelling methodology follows the introduced in (Huzmezan and Maciejowski, 1998).
Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing (2009)

Novel massively parallel sequencing technologies provide highly detailed structures of transcriptomes and genomes by yielding deep coverage of short reads, but their utility is limited by inadequate sequencing quality and short-read lengths. Sequencing-error trimming in short reads is therefore a vital process that could improve the rate of successful reference mapping and polymorphism detection. Toward this aim, we herein report a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each "child" sequence is considered to be stochastically derived from its more abundant "parent" sequence with one mutation through sequencing errors. The root node is the most frequently observed sequence that represents all erroneous reads in the entire tree, allowing the alignment of the reliable representative read to the genome without the risk of mapping erroneous reads to false-positive positions. This method complements base calling and the error correction of making direct alignments with the reference genome, and is able to improve the overall accuracy of short-read alignment by consulting the inherent relationships among the entire set of reads. The algorithm runs efficiently with a linear time complexity. In addition, an error rate evaluation model can be derived from bacterial artificial chromosome sequencing data obtained in the same run as a control. In two clustering experiments using small RNA and 5'-end mRNA reads data sets, we confirmed a remarkable increase ( approximately 5%) in the percentage of short reads aligned to the reference sequence.
Generalized architecture for simultaneous localization, auto-calibration, and map-building (2003)

This paper discusses the design of a very general architectural framework for navigation and tracking systems that fuse dead-reckoning sensors (e.g. inertial or encoders) with environment-referenced sensors, such as ultrasonic, optical, magnetic, or RF sensors. The framework enables systems that simultaneously track themselves, construct a map of landmarks in the environment, and calibrate sensor intrinsic and extrinsic parameters. The goals of the architecture are to permit easy configuration of numerous sensor combinations including IMUs, GPS, range sensors, inside-out bearing sensors, outside-in bearing sensors, etc., and to provide compatibility with multiple sensor networking standards, distributed sensor fusion algorithms, and implementation strategies. A decentralized Kalman filter based on Carlson's federated filter algorithm (1990) is used to decouple the auto-mapping, auto-calibration and navigation filters to produce a more flexible and modular architecture.
Joint destruction in rheumatoid arthritis: biological bases. (1997)

The pathogenesis of rheumatoid arthritis (RA) can be explained through two main hypotheses: macrophage-fibroblast and macrophage-T cell interactions. The interplay between the various populations is influenced by a strong genetic component, which determines the severity of the disease in some cohorts of patients attending referral centers. The key question of the nature of the antigen(s) driving joint inflammation still remains unsolved. Exogenous antigens such as viruses or bacteria have long been searched for in the synovial fluids as well as in tissues, but convincing evidence of their pathogenic role are lacking. Data have been accumulated on the possible role of autoantigens, such as the spliceosomes, filaggrin, calpastatin, type II collagens, or other endogenous peptides, but no definite role regarding their potential contribution to the activation of T cells has been established. Once the process starts, a progressive recruitment of inflammatory T cells and macrophages into the joints occurs through a complex series of adhesion and migratory events. The key driving steps leading to synovial inflammation and cartilage destruction, along with the potential contribution of some key molecules, have been described, thus opening possible perspectives for a therapeutic approach.
Glycoproteins (1972)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Specificity of cell–cell adhesion by classical cadherins: Critical role for low-affinity dimerization through β-strand swapping (2005)

Cadherins constitute a family of cell-surface proteins that mediate intercellular adhesion through the association of protomers presented from juxtaposed cells. Differential cadherin expression leads to highly specific intercellular interactions in vivo. This cell-cell specificity is difficult to understand at the molecular level because individual cadherins within a given subfamily are highly similar to each other both in sequence and structure, and they dimerize with remarkably low binding affinities. Here, we provide a molecular model that accounts for these apparently contradictory observations. The model is based in part on the fact that cadherins bind to one another by "swapping" the N-terminal beta-strands of their adhesive domains. An inherent feature of strand swapping (or, more generally, the domain swapping phenomenon) is that "closed" monomeric conformations act as competitive inhibitors of dimer formation, thus lowering affinities even when the dimer interface has the characteristics of high-affinity complexes. The model describes quantitatively how small affinity differences between low-affinity cadherin dimers are amplified by multiple cadherin interactions to establish large specificity effects at the cellular level. It is shown that cellular specificity would not be observed if cadherins bound with high affinities, thus emphasizing the crucial role of strand swapping in cell-cell adhesion. Numerical estimates demonstrate that the strength of cellular adhesion is extremely sensitive to the concentration of cadherins expressed at the cell surface. We suggest that the domain swapping mechanism is used by a variety of cell-adhesion proteins and that related mechanisms to control affinity and specificity are exploited in other systems.
Overexpression ofHtrA1and Exposure to Mainstream Cigarette Smoke Leads to Choroidal Neovascularization and Subretinal Deposits in Aged Mice (2014)

The HtrA1 overexpression and mainstream cigarette smoke can independently lead to CNV. The HtrA1 gene is a strong risk factor for wet AMD, but not all of the HtrA1 Tg mice developed CNV, suggesting that CNV development depends on multiple risk factors.
Rapid assembly of the bacteriophage T4 core replication complex on a linear primer/template construct. (1993)

DNA synthesis on a primed DNA substrate by bacteriophage T4 requires the assembly of a core replication complex consisting of the T4 DNA polymerase, a single-stranded binding protein (32 protein), and the accessory proteins 44/62 and 45. In this paper, we demonstrate the successful assembly of this core complex on a short linear primer/template system at levels of accessory proteins equivalent to the concentration of primer 3' ends. The key to this assembly is the presence of streptavidin molecules bound at each end of the DNA substrate via biotin moieties incorporated into the template strand. Streptavidin serves to block the ends of the primer/template, thus preventing translocation of the accessory proteins away from the site of assembly and their subsequent dissociation from the ends of the primer/template. Complex assembly on this substrate requires ATP and the presence of both the 44/62 and 45 proteins. The time required for assembly of a full enzyme equivalent of complex in our system is approximately 2 s.
Limitation of transpiration by hydraulic conductance and xylem cavitation in Betula occidentalis (1993)

ABSTRACT The extent to which stomatal conductance ( g s ) was capable of responding to reduced hydraulic conductance ( k )and preventing cavitation‐inducing xylem pressures was evaluated in the small riparian tree, Betula occidentalis Hook. We decreased k by inducing xylem cavitation in shoots using an air‐injection technique. From 1 to 18 d after shoot injection we measured midday transpiration rate (E), g s , and xylem pressure (Ψ p‐xylem ) on individual leaves of the crown. We then harvested the shoot and made direct measurements of k from the trunk (2–3 cm diameter) to the distal tip of the petioles of the same leaves measured for E and g s . The k measurement was expressed per unit leaf area ( k l , leaf‐specific conductance). Leaves measured within 2 d of shoot injection showed reduced g s and E relative to non‐injected controls, and both parameters were strongly correlated with k l At this time, there was no difference in leaf Ψ p‐xylem between injected shoots and controls, and leaf Ψ p‐xylem was not significantly different from the highest cavitation‐inducing pressure (Ψ p‐cav ) in the branch xylem (‐1.43 ± 0.029 MPa, n=8). Leaves measured 7–18 d after shoots were injected exhibited a partial return of g s and E values to the control range. This was associated with a decrease in leaf Ψ p‐xylem below Ψ p‐cav and loss of foliage. The results suggest the stomata were incapable of long‐term regulation of E below control values and that reversion to higher E caused dieback via cavitation.
Functional Characterization of Bacterial Oligosaccharyltransferases Involved in O-Linked Protein Glycosylation (2007)

Protein glycosylation is an important posttranslational modification that occurs in all domains of life. Pilins, the structural components of type IV pili, are O glycosylated in Neisseria meningitidis, Neisseria gonorrhoeae, and some strains of Pseudomonas aeruginosa. In this work, we characterized the P. aeruginosa 1244 and N. meningitidis MC58 O glycosylation systems in Escherichia coli. In both cases, sugars are transferred en bloc by an oligosaccharyltransferase (OTase) named PglL in N. meningitidis and PilO in P. aeruginosa. We show that, like PilO, PglL has relaxed glycan specificity. Both OTases are sufficient for glycosylation, but they require translocation of the undecaprenol-pyrophosphate-linked oligosaccharide substrates into the periplasm for activity. Whereas PilO activity is restricted to short oligosaccharides, PglL is able to transfer diverse oligo- and polysaccharides. This functional characterization supports the concept that despite their low sequence similarity, PilO and PglL belong to a new family of "O-OTases" that transfer oligosaccharides from lipid carriers to hydroxylated amino acids in proteins. To date, such activity has not been identified for eukaryotes. To our knowledge, this is the first report describing recombinant O glycoproteins synthesized in E. coli.
Reversible shutdown of replicon initiation by transient hypoxia in Ehrlich ascites cells (1992)

The O2-dependent regulation of replication in Ehrlich ascites cells, characterized by a reversible shutdown of replicon initiation during hypoxia, was scrutinized with respect to the involvement of gene expression. Synchronous and asynchronous cells were subjected to transient hypoxia and examined for expression of selected 'late' growth-regulated mRNA and for the influence of inhibitors of transcription and translation on DNA replication. Irrespective of whether replicon initiation was suppressed by hypoxia or retriggered by reoxygenation, the levels of thymidine kinase mRNA and of proliferating cell-nuclear antigen/cyclin mRNA were as high as in untreated replicating cells. The level of histone H3.1 mRNA followed, with a distinct delay, the replicative activity of the cells governed by the imposed changes of pO2. The response of replication to inhibition of transcription and translation was virtually the same as to hypoxia, i.e. a selective suppression of replicon initiation. It was demonstrated that replicon initiation depends on one or several short-lived protein(s) (lifetime about 5 min) which is (are) formed under hypoxic conditions as well. The lifetime of the corresponding RNA message(s) is in the range of several hours. It is suggested that the expression of genes conditioning resting cells for DNA replication remains unaffected by hypoxia or by restoring the normal pO2. Hypoxic cell appear to rest in a state fully prepared for entering DNA replication, but a yet unknown event essential for replicon initiation is blocked. This event depends on a critical oxygen tension as well as on short-lived protein(s).
Amino acid sequence of a human leukocyte interferon. (1981)

The primary structures of three major species of human leukocyte interferon differ from the structure predicted from the DNA sequence of recombinants containing leukocyte interferon-coding regions. Compared to the recombinant interferon produced in bacteria, three of the purified natural proteins isolated from leukocytes lack the 10 COOH-terminal amino acids suggested by the DNA sequence.
Graft-Versus-Tumor Effects After Allogeneic Hematopoietic Cell Transplantation With Nonmyeloablative Conditioning (2005)

New approaches aimed at reducing the incidence of grade 2 to 4 acute GVHD might improve survival after allogeneic HCT after nonmyeloablative conditioning.
Line length: an efficient feature for seizure onset detection (2005)

A signal feature with low computational burden is presented as an efficient tool for seizure onset detection. The feature was evaluated over a total of. 1,215 hours of intracranial EEG signal from 10 patients. Results confirmed this feature as being useful for seizure onset detection yielding an average delay of 4.1 seconds, 0.051 false positives per hour, and one false negative on a subclinical seizure out of 111 seizures analyzed of which 23 were subclinical.
Global interactions in the early modern age, 1400-1800 (2011)

Introduction: the global integration of space 1. European states and overseas empires 2. Asian states and territorial empires 3. International markets and global exchange networks 4. The movement of peoples and diffusion of cultures 5. The formation of new demographic and ecological structures 6. The transmission of religion and culture Conclusion: the landscapes of an altered world.
The design and implementation of a three degree of freedom force output joystick (1990)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1990.
Maximum achievable aspect ratio in deep reactive ion etching of silicon due to aspect ratio dependent transport and the microloading effect (2005)

When etching high-aspect-ratio silicon features using deep reactive ion etching (DRIE), researchers find that there is a maximum achievable aspect ratio, which we define as the critical aspect ratio, of an etched silicon trench using a DRIE process. At this critical aspect ratio, the apparent etch rate (defined as the total depth etched divided by the total elapsed time) no longer monotonically decreases as the aspect ratio increases, but abruptly drops to zero. In this paper, we propose a theoretical model to predict the critical aspect ratio and reveal its causal mechanism. The model considers aspect ratio dependent transport mechanisms specific to each of the reactant species in the three subprocesses of a time-multiplexed etch cycle: deposition of a fluorocarbon passivation layer, etching of the fluorocarbon polymer at the bottom of the trench, and the subsequent etching of the underlying silicon. The model predicts that the critical aspect ratio is defined by the aspect ratio at which the polymer etch rate equals the product of the deposition rate and the set time ratio between the deposition and etching phases for the time-multiplexed process. Several DRIE experiments were performed to qualitatively validate the model. Both model simulations and experimental results demonstrate that the magnitude of the critical aspect ratio primarily depends on (i) the relative flux of neutral species at the trench opening, i.e., the microloading effect, and (ii) aspect ratio dependent transport of ions during the polymer etching subprocess of a DRIE cycle.
Dystrophin in frameshift deletion patients with Becker muscular dystrophy. (1992)

In a previous study we identified 14 cases with Duchenne muscular dystrophy (DMD) or its milder variant, Becker muscular dystrophy (BMD), with a deletion of exons 3-7, a deletion that would be expected to shift the translational reading frame of the mRNA and give a severe phenotype. We have examined dystrophin and its mRNA from muscle biopsies of seven cases with either mild or intermediate phenotypes. In all cases we detected slightly lower-molecular-weight dystrophin in 12%-15% abudance relative to the normal. By sequencing amplified mRNA we have found that exon 2 is spliced to exon 8, a splice that produces a frameshifted mRNA, and have found no evidence for alternative splicing that might be involved in restoration of dystrophin mRNA reading frame in the patients with a mild phenotype. Other transcriptional and posttranscriptional mechanisms such as cryptic promoter, ribosomal frameshifting, and reinitiation are suggested that might play some role in restoring the reading frame.
Solid-Phase Synthesis of 3H-Quinazolin-4-ones Based on an Aza Wittig-Mediated annulation Strategy (1998)

Aza Wittig-mediated annulation provides a highly efficient and straightforward strategy for the parallel synthesis of 3H-quinazolin-4-ones on solid support. The products were recovered in good yields and exhibited excellent purities.
Designing nanosensors based on ion channel-forming derivatives of Gramicidin A (2008)

This dissertation will focus on detecting analytes in aqueous solution that chemically react with or bind to functional groups near the opening of synthetic ion channels derived from gramicidin A (gA). Detection is achieved when a measurable change in the conductance of ions across the ion channel is produced after the analyte interacts with the channel. Ion channel sensors have great potential for achieving ultrasensitive detection since a single chemical modification near the lumen of the channel can lead to detectable changes in channel conductance. The dissertation will specifically focus on: (1) the development of design parameters to improve sensing with gA-based nanosensors; (2) the demonstration of sensing analytes in aqueous solution by manipulating the charge of a chemical group near the pore of gA (charge-based sensing); (3) the chemistry for producing reactive building blocks of gA for developing robust and diverse gA -based nanosensors; (4) the detection of enzyme activity using our charge-based sensing approach to achieve picomolar limits of detection; and (5) the small structural changes that can be introduced to the peptide near the lumen of the channel to control conductance
<title>Effects of higher order aberrations on the process window</title> (1991)

High-quality imaging is essential for having the largest available process window for the various lithographic mask features, particularly those at the resolution limit of the lens. While lithographic lenses are designed to be 'diffraction limited,' shortcomings in the manufacturing process can introduce aberrations which affect imaging. The effects of such aberrations are explored via computer simulation, using exposure-defocus (E-D) diagrams and plots of linewidth versus focus for isolated and grouped lines. Data from a variety of lithographic lenses and the criteria for measuring lens performance are discussed.
A GRIM fate for human neutrophils in airway disease (2018)

Abstract A neutrophil culture method recapitulates their phenotypic plasticity and may accelerate development of drugs that target pathological subsets in airway disease.
Novel Prodrug Approach for Tertiary Amines:  Synthesis and Preliminary Evaluation of N-Phosphonooxymethyl Prodrugs (1999)

The synthesis and preliminary evaluation of a novel prodrug approach for improving the water solubility of drugs containing a tertiary amine group are reported. The prodrug synthesis involves a nucleophilic substitution reaction between the parent tertiary amine and a novel derivatizing reagent, di-tert-butyl chloromethyl phosphate, resulting in formation of the quaternary salt. The tertiary butyl groups are easily removed under acidic conditions with trifluoroacetic acid giving the N-phosphonooxymethyl prodrug in the free phosphoric acid form, which can subsequently be converted to the desired salt form. The synthesis was successfully applied to a model compound (quinuclidine) and to three tertiary amine-containing drugs (cinnarizine, loxapine, and amiodarone). The prodrugs were designed to undergo a two-step bioreversion process. The first step was an enzyme-catalyzed rate-determining dephosphorylation followed by spontaneous chemical breakdown of the N-hydroxymethyl intermediate to give the parent drug. Selected prodrugs were shown to be substrates for alkaline phosphatase in vitro. A preliminary in vivo study confirmed the ability of the cinnarizine prodrug to be rapidly and completely converted to cinnarizine in a beagle dog following iv administration.