gebhart/patrepeval huggingface dataset:
Molecular analysis of Fanconi anemia: the experience of the Bone Marrow Failure Study Group of the Italian Association of Pediatric Onco-Hematology (2014)

Fanconi anemia is an inherited disease characterized by congenital malformations, pancytopenia, cancer predisposition, and sensitivity to cross-linking agents. The molecular diagnosis of Fanconi anemia is relatively complex for several aspects including genetic heterogeneity with mutations in at least 16 different genes. In this paper, we report the mutations identified in 100 unrelated probands enrolled into the National Network of the Italian Association of Pediatric Hematoly and Oncology. In approximately half of these cases, mutational screening was carried out after retroviral complementation analyses or protein analysis. In the other half, the analysis was performed on the most frequently mutated genes or using a next generation sequencing approach. We identified 108 distinct variants of the FANCA, FANCG, FANCC, FANCD2, and FANCB genes in 85, 9, 3, 2, and 1 families, respectively. Despite the relatively high number of private mutations, 45 of which are novel Fanconi anemia alleles, 26% of the FANCA alleles are due to 5 distinct mutations. Most of the mutations are large genomic deletions and nonsense or frameshift mutations, although we identified a series of missense mutations, whose pathogenetic role was not always certain. The molecular diagnosis of Fanconi anemia is still a tiered procedure that requires identifying candidate genes to avoid useless sequencing. Introduction of next generation sequencing strategies will greatly improve the diagnostic process, allowing a rapid analysis of all the genes.
Proposal of SDMA configuration adopting directivity and polarization control (2006)

Abstract In this paper, a new SDMA (Space Division Multiple Access) configuration is proposed in which the number of multitudes of SDMA can be increased by using dual polarization antennas at both the smart antenna base stations and the mobile terminals. In the proposed configuration, the smart antennas at the base stations constantly monitor the mutual correlations between the mobile terminals at the time of reception. Then, the polarization (vertical or horizontal) to be transmitted by each mobile terminal is determined in such a way that the mutual correlation between the mobile terminals connected at the same time is minimized. The mobile terminal used in the proposed system has a configuration in which the antennas with vertical and horizontal polarizations can be switched for transmission. Transmission is carried out with the polarization specified by the base station. The proposed configuration is expected not only to improve spatial division capability of SDMA by the smart antenna base station with vertical and horizontal polarizations but also to compensate the deterioration of the transmission quality along with the increase of multiplicity of SDMA by means of the switching configuration of the transmission polarization of the mobile terminal while the interference between the mobile terminals is taken into account. The proposed configuration can be applied to the uplinks in the TDD or FDD channels. By means of the numerical simulation, the basic characteristics of the proposed configuration are clarified in the case where the cross polarization discrimination (XPD) and the number of mobile terminals vary. In this way, it is demonstrated that the mobile terminal discrimination capability is improved over the conventional SDMA with the vertical polarization and the system is useful for increased multiplicity of SDMA. Further, the propagation characteristics (amplitude and phase) of the vertical and horizontal polarizations are obtained when the base station antenna and the mobile terminal antenna are placed on a steel tower and on a vehicle, respectively. The characteristics of the proposed configuration are presented where several mobile terminals exist. Usefulness of the proposed configuration in an actual environment for increased multiplicity of SDMA is presented. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(2): 33–45, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecja.20287
Novel Modified Optical Fibers for High Temperature In-Situ Miniaturized Gas Sensors in Advanced Fossil Energy Systems (2014)

This report covers the technical progress on the program “Novel Modified Optical Fibers for High Temperature In-Situ Miniaturized Gas Sensors in Advanced Fossil Energy Systems”, funded by the National Energy Technology Laboratory of the U.S. Department of Energy, and performed by the Materials Science & Engineering and Electrical & Computer Engineering Departments at Virginia Tech, and summarizes technical progress from July 1st, 2005 –June 30th, 2014. The objective of this program was to develop novel fiber materials for high temperature gas sensors based on evanescent wave absorption in optical fibers. This project focused on two primary areas: the study of a sapphire photonic crystal fiber (SPCF) for operation at high temperature and long wavelengths, and a porous glass based fiber optic sensor for gas detection. The sapphire component of the project focused on the development of a sapphire photonic crystal fiber, modeling of the new structures, fabrication of the optimal structure, development of a long wavelength interrogation system, testing of the optical properties, and gas and temperature testing of the final sensor. The fabrication of the 6 rod SPCF gap bundle (diameter of 70μm) with a hollow core was successfully constructed with lead-in and lead-out 50μm diameter fiber along with transmission and gas detection testing. Testing of the sapphire photonic crystal fiber sensor capabilities with the developed long wavelength optical system showed the ability to detect CO2 at or below 1000ppm at temperatures up to 1000°C. Work on the porous glass sensor focused on the development of a porous clad solid core optical fiber, a hollow core waveguide, gas detection capabilities at room and high temperature, simultaneous gas species detection, suitable joining technologies for the lead-in and lead-out fibers and the porous sensor, sensor system sensitivity improvement, signal processing improvement, relationship between pore structure and fiber geometry to optical properties, and the development of a sensor packaging prototype for laboratory testing. Analysis and experiments determined that a bonding technique using a CO2 laser is the most suitable joining technique. Pore morphology alteration showed that transmission improved with increasing annealing temperature (producing smaller pores), while the sensor response time increased and the mechanical strength decreased with increasing annealing temperature. Software was developed for data acquisition and signal processing to collect and interpret spectral gas absorption data. Gas detection on porous glass sensors was completed and the detection limit was evaluated using acetylene and was found to be around 1- 200ppm. A complete materials package for porous glass sensors was manufactured for testing.
Synthesis and crystal chemistry of Fe3+-bearing (Mg,Fe3+)(Si,Fe3+)O3 perovskite (2012)

We have synthesized magnesium-iron silicate perovskites with the general formula Mg1-xFe3+x+ySi1-y O3, in which the iron cation is exclusively trivalent. To investigate the crystal chemistry of Fe3+-bearing perovskite, six samples (both with and without Al) were analyzed using scanning electron microscopy, electron microprobe, X-ray diffraction, and Mössbauer spectroscopy. Results indicate that Fe3+ substitutes significantly into both the octahedral and dodecahedral sites in the orthorhombic perovskite structure, but prefers the octahedral site at Fe3+ concentrations between 0.04 and 0.05 Fe per formula unit, and the dodecahedral site at higher Fe3+ concentrations. We propose a model in which Fe3+ in the A/B site (in excess of that produced by charge coupled substitution) is accommodated by Mg/O vacancies. Hyperfine parameters refined from the Mössbauer spectra also indicate that a portion of dodecahedral sites undergo significant structural distortion. The presence of Fe3+ in the perovskite structure increases the unit-cell volume substantially compared to either the Mg end-member, or Fe2+-bearing perovskite, and the addition of Al did not significantly alter the volume. Implications for increased compressibility and a partially suppressed spin transition of Fe3+ in lower mantle perovskite are also discussed.
Structural basis for the emission of violet bioluminescence from a W92F obelin mutant (2001)

Mutation of the Trp92 that is known to lie within the active site of the photoprotein obelin from Obelia longissima, results in a shift of the bioluminescence color from blue (lambda(max)=485 nm) to violet. The corrected spectrum shows a new band with lambda(max)=410 nm now contributing equally to the one at longer wavelength. The crystal structure of this W92F obelin determined at 1.72 A resolution shows that there is no significant change in the dimensions of the active site between WT obelin (recombinant Ca2+-regulated photoprotein from Obelia longissima) and the mutant. It is proposed that the bioluminescence spectral shift results from removal of a hydrogen bond from the indole of W92 nearby a hydroxyl belonging to the 6-phenyl substituent of the substrate coelenterazine. Propagation of this change through a conjugated bond system in the excited state of the product coelenteramide affects the coupling of the N1-position and the hydrogen-bonded Y138.
Cell-Cycle Analysis of Drug-Treated Cells (2003)

A variety of flow cytometric methods have been developed over the past 25 yr to study how treatment with chemotherapeutic agents affects cell-cycle progression. One of the most commonly used measurements relies on a singletime analysis of the DNA distribution of a cell population (1). This analysis may also be multivariate, for instance, when another cell feature is measured in addition to DNA. The additional feature(s) often provides information about a particular metabolic or molecular feature of the cell that often correlates with the rate of cell progression through the cycle or cell quiescence. Therefore, although such measurements per se cannot reveal whether or not the cell actually progresses through the cycle, the kinetic information is inferred from the DNA content (cell-cycle position) and from the metabolic or molecular profile of that cell.
Selective Catalytic Hydrogenation of Organic Compounds in Supercritical Fluids as a Continuous Process (1998)

We report a new method for continuous hydrogenation in supercritical fluids (CO2 or propane) using heterogeneous noble metal catalysts on Deloxan aminopolysiloxane supports. The method has considerable promise both for laboratory-scale hydrogenation and for the industrial production of fine chemicals. It can be applied to a wide range of organic compounds including alkenes, alkynes, aliphatic and aromatic ketones and aldehydes, epoxides, phenols, oximes, nitrobenzenes, Schiff bases, and nitriles. Conversion of starting materials, product selectivity, and space−time yields of the catalyst are all high, and the reactors themselves are very small (5- and 10-mL volume). Supercritical hydrogenation enables the reaction parameters to be controlled very precisely. Results are presented for a series of different reactions showing product distributions, which are dependent on temperature, pressure, H2 concentration, and the loading and nature of the catalyst. The hydrogenation of cyclohexene has been studied in some detail, and our results are related to the phase diagrams of the ternary system cyclohexane + CO2 + H2, which we present in a novel way, more suited to continuous reactors. Finally, we report that the supercritical hydrogenation of isophorone has advantages over conventional methods.
Numerical Simulations of Strong Shock and Disturbance Interactions Using High-Order Shock-Fitting Algorithms (2008)

High order methods that can solve flows involving interactions of flow-disturbances with shock waves are critical for reliable numerical simulation of strong-shock and turbulence interaction problems. Such problems are not well understood due to limitations of numerical methods. For numerical simulation of compressible flows, shock capturing schemes have been the most popular choice. However, most of such methods are inherently dissipative and may incur numerical oscillations near the shock. Present paper focuses on developing and implementing new algorithms based on shock-fitting and front-tracking methodology which can solve the flow with high-order accuracy near as well as away from the shocks. The shock-fitting algorithm avoids dissipation and possible numerical oscillations incurred in shock-capturing methods by treating shocks sharply. We explore two ways for shock-fitting: conventional moving grid set-up and a new fixed grid set-up with front tracking. Conventionally, shock fitting is implemented on moving grid while shock forms a boundary of the computational domain. However, shock-fitted grid generation can be tedious for large and complex motions of the shock-front. Hence, we have also worked on developing a fixed grid set-up for shock-fitting method where shock is tracked using Lagrangian points and is free to move across underlying fixed grid. Using these shock-fitting algorithms we have solved one and two dimensional interactions of shock and vorticity/entropy disturbance waves and results have been found to be very satisfactory. We have also carried out a rate of convergence study to establish that, unlike shock-capturing schemes, the shock-fitting methods are high-order accurate near the shock. Although problems considered in this paper are relatively simple, the quality of results obtained from shock-fitting method provides good motivation to pursue it further for the problems of shock-turbulence interactions. In future, fixed grid shock-fitting methodology will be further developed with Immersed interface method of Zhong [1, 2] and more robust front-tracking algorithms so that more complex shock-turbulence interaction problems can be considered.
Ten-Step Minimally Invasive Cervical Decompression via Unilateral Tubular Laminotomy: Technical Note and Early Clinical Experience (2019)

In our early clinical experience, minimally invasive cervical ULBD is safe and effective. Adherence to the presented 10-step technique will allow surgeons to safely address bilateral cervical pathology while avoiding complications.
Dynamically formed heterogeneous robot teams performing tightly-coordinated tasks (2006)

As we progress towards a world where robots play an integral role in society, a critical problem that remains to be solved is the pickup team challenge; that is, dynamically formed heterogeneous robot teams executing coordinated tasks where little information is known a priori about the tasks, the robots, and the environments in which they would operate. Successful solutions to forming pickup teams would enable researchers to experiment with larger numbers of robots and enable industry to efficiently and cost-effectively integrate new robot technology with existing legacy teams. In this paper, we define the challenge of pickup teams and propose the treasure hunt domain for evaluating the performance of pickup teams. Additionally, we describe a basic implementation of a pickup team that can search and discover treasure in a previously unknown environment. We build on prior approaches in market-based task allocation and plays for synchronized task execution, to allocate roles amongst robots in the pickup team, and to execute synchronized team actions to accomplish the treasure hunt task
Inhibiting Drivers of Non-mutational Drug Tolerance Is a Salvage Strategy for Targeted Melanoma Therapy (2016)

Once melanomas have progressed with acquired resistance to mitogen-activated protein kinase (MAPK)-targeted therapy, mutational heterogeneity presents a major challenge. We therefore examined the therapy phase before acquired resistance had developed and discovered the melanoma survival oncogene MITF as a driver of an early non-mutational and reversible drug-tolerance state, which is induced by PAX3-mediated upregulation of MITF. A drug-repositioning screen identified the HIV1-protease inhibitor nelfinavir as potent suppressor of PAX3 and MITF expression. Nelfinavir profoundly sensitizes BRAF and NRAS mutant melanoma cells to MAPK-pathway inhibitors. Moreover, nelfinavir is effective in BRAF and NRAS mutant melanoma cells isolated from patients progressed on MAPK inhibitor (MAPKi) therapy and in BRAF/NRAS/PTEN mutant tumors. We demonstrate that inhibiting a driver of MAPKi-induced drug tolerance could improve current approaches of targeted melanoma therapy.
Method for Processing of Periodic Images at Reduced Levels of Electron Irradiation (1971)

Meaningful high resolution microscope of specimens that are sensitive to radiation damage is limited in resolution by considerations of statistics and contrast in the image. The product of contrast, C, and resolution, d, must satisfy the inequality where S/n is the minimum acceptable ratio of real contrast to statistical fluctuations in intensity, f is the fraction of electrons incident upon the specimen that actually contribute to image formation, and D min is the minimum dose or exposure that causes structural disorder at the resolution, d. While the value of S/N must be approximately 5 for visual perception of structure, a very much smaller value can be made acceptable by spatial superposition or “averaging” of similar images. In most circumstances this is practical only for objects with a determinable spatial redundancy. We report here on the construction of an experimental system for (1) recording statistically noisy images, (2) determining the image redundancy, and (3) executing the desired spatial averaging.
Use of Cell-Penetrating-Peptides in Oligonucleotide Splice Switching Therapy (2012)

The hydrophobic plasma membrane constitutes an indispensable barrier for cells, allowing influx of essential molecules while preventing access to other macromolecules. Although pivotal for the maintenance of cells, the inability to cross the plasma membrane is one of the major obstacles toward current drug development. Oligonucleotides (ONs) are a group of substances that display great therapeutic potential to interfere with gene expression. Several classes of ONs have emerged either based on double stranded RNAs, such as short interfering RNAs that are utilized to confer gene silencing, or single stranded ONs of various chemistries for antisense targeting of small regulatory micro RNAs or mRNAs. In particular the use of splice switching oligonucleotides (SSOs) to manipulate alternative splicing, by targeting pre-mRNA, has proven to be a highly promising therapeutic strategy to treat various genetic disorders, including Duchenne muscular dystrophy and spinal muscular atrophy. Despite being efficient compounds to alter splicing patterns, their hydrophilic macromolecular nature prohibits efficient cellular internalization.Various chemical drug delivery vehicles have been developed aiming at improving the bioavailability of nucleic acid-based drugs. In the context of SSOs, one group of peptidebased delivery vectors, i.e. cell-penetrating peptides (CPPs), display extremely high potency. CPPs have a remarkable ability to convey various, otherwise impermeable, macromolecules across the plasma membrane of cells in a relatively non-toxic fashion. This review provides insight into the application of CPPs and ONs in gene regulation with particular focus on CPP-assisted delivery of therapeutic SSOs.
The Catalytic Activity of some EDA Complexes for the Hydrogen Exchange Reaction and the Electronic Structures of the Aromatic Anions (1973)

Article The Catalytic Activity of some EDA Complexes for the Hydrogen Exchange Reaction and the Electronic Structures of the Aromatic Anions was published on March 1, 1973 in the journal Zeitschrift für Physikalische Chemie (volume 84, issue 1-4).
Optical matched filtering for character recognition (1983)

An ordinary matched filter responds with a peak signal to the input. The peak corresponds to the location of a target. In some pattern recognition tasks it is desirable not to find the location of a target but to identify it (for example, a printed character). It is therefore proposed that the concept of a matched filter is modified in such a way that the output pattern consists of vertical fringes. These fringes are quite suitable as a recognition signature because the now uninteresting vertical position of the input character becomes irrelevant: when the input is moving horizontally, the output fringes move correspondingly. A slit detector will therefore produce an electronic single-frequency signal. An even better performance can be expected from a detector with a fringe mask in front of it. Such a detector system is tuned resonantly to a particular moving fringe pattern. This modified matched filtering concept may incorporate such properties as multiplexing, principal component recognition, pupil replication, and incoherent inputs.
Fault Identification of Discrete Event Systems Modeled by Petri Nets With Unobservable Transitions (2017)

This paper deals with the identification problem of faulty behavior in a discrete event system, assuming that the fault-free model of a system is given in terms of Petri nets, where the set of transitions is divided into two disjoint subsets: 1) observable and 2) unobservable ones. The observed system output is defined as a transition-marking sequence, i.e., each transition is followed by a marking. First, a nonlinear integer programming model that characterizes the faults modeled by fault transitions is built according to the abnormal behavior extracted from the observed sequence. Then, it is converted into an integer linear programming (ILP) problem and a faulty net that preserves the structure of the fault-free one is obtained by solving this ILP model. In addition, an algorithm is developed to ensure acyclicity of the resulting unobservable subnet whose transition set is composed of the unobservable transitions of the fault-free net and the identified fault transitions.
Data-Driven Identification of Parametric Partial Differential Equations (2019)

In this work we present a data-driven method for the discovery of parametric partial differential equations (PDEs), thus allowing one to disambiguate between the underlying evolution equations and their parametric dependencies. Group sparsity is used to ensure parsimonious representations of observed dynamics in the form of a parametric PDE, while also allowing the coefficients to have arbitrary time series, or spatial dependence. This work builds on previous methods for the identification of constant coefficient PDEs, expanding the field to include a new class of equations which until now have eluded machine learning based identification methods. We show that group sequentially thresholded ridge regression outperforms group LASSO in identifying the fewest terms in the PDE along with their parametric dependency. The method is demonstrated on four canonical models with and without the introduction of noise.