gebhart/patrepeval huggingface dataset:
Identification of Messenger RNAs and MicroRNAs Associated With Fragile X Mental Retardation Protein (2006)

Fragile X syndrome, a common form of inherited mental retardation, is caused by the loss of the Fragile X mental retardation protein (FMRP). FMRP, which may regulate translation in neurons, not only associates with specific messenger RNAs (mRNAs) and with microRNAs (miRNAs), but also associates with the components of the miRNA pathway, including the Dicer and Argonaute proteins. It has been proposed that FMRP regulates the translation of its mRNA targets through miRNAs. In this chapter, we describe the protocol to identify the mRNAs and miRNAs associated with FMRP in vivo. The same method could also be applied to other RNA-binding proteins interacting with specific mRNAs or miRNAs.
Specific Activities of Dolastatin 10 and Peptide Derivatives against <i>Cryptococcus neoformans</i> (1998)

The biosynthetic peptide dolastatin 10 is currently in phase I and II cancer clinical trials. We evaluated the antifungal spectrum of dolastatin 10 and four structural modifications. In broth macrodilution assays, the peptides were fungicidal for American Type Culture Collection strains and clinical isolates (including fluconazole-resistant strains) of Cryptococcus neoformans but no other yeasts or filamentous fungi examined. Specificity for C. neoformans was also demonstrated in the solid-phase disk diffusion assay, and fungicidal activity was confirmed in time-kill experiments. For a methyl ester modification, the MICs at which 50 and 90% of 19 clinical isolates were inhibited (MIC50 and MIC90, respectively) were 0.195 and 0.39 microg/ml, respectively. The MFC50 (50% minimum fungicidal concentration) for this peptide was 0.39 microg/ml, and the MFC90 was 0.78 microg/ml. MICs and MFCs were identical or lower in the presence of human serum but increased with lowered pH. These peptides should be pursued as potential chemotherapeutics for C. neoformans, a leading cause of infection and mortality in immunocompromised patients.
Structure-activity relations in cephalosporins prepared from penicillins. 2. Analogs of cephalexin substituted in the 3-methyl group (1977)

A previously outlined general procedure for preparing various 3-substituted cephalosporins from the penicillin nucleus has been used, with modifications where required, to prepare a series of analogues of cephalexin with various substituents in the 3-methyl group. The 3-substituents most conducive to broad-spectrum antibacterial activity were 3-pyridylmethyl and m- or p-carboxybenzyl. The compounds were only poorly absorbed by the oral route in mice, but the 3-(carboxybenzyl) compounds gave more prolonged useful serum levels than the usual cephalosporins.
Accurate localisation of ground faults in non-solidly earthed networks based on transients analysis (2017)

In this study, the authors present a new approach for localising ground faults, using transients in the currents and voltages. The authors' approach is based on the double sided estimation of the transient voltage at an unknown ground fault location. It is assumed that the calculated transient profile from both sides of the line is comparable for a known fault location. For better accuracy, an existing higher frequency spectrum is used, and through that, redundant information from each existing frequency is extracted. The precise idea, accuracy analysis, as well as further relevant benefits of our method will be thoroughly described in this study.
A multiplication-free approximate algorithm for the inverse discrete cosine transform (1999)

A fast multiplication-free algorithm for the inverse discrete cosine transform (IDCT) is developed. This algorithm is an approximation to the IDCT and is applicable in implementations of compression standards such as JPEG, MPEG-1, MPEG-2 H.263. The proposed algorithm is 32% faster than its exact counterpart. For low bit-rate video codecs, the quantization effects introduced by the multiplier-free approach is considerably lower than the distortion introduced by the quantizer settings of the video codec and thus the overall PSNR loss is well within 1 dB for the proposed multiplier-free approach. If DCT data sparseness is taken into account, compared with other recently developed fast approximate DCT and IDCT methods, the proposed scheme provides significant reductions in computation complexity. The approach described here can be easily adapted for the forward DCT.
Directed test generation for effective fault localization (2010)

Fault-localization techniques that apply statistical analyses to execution data gathered from multiple tests are quite effective when a large test suite is available. However, if no test suite is available, what is the best approach to generate one? This paper investigates the fault-localization effectiveness of test suites generated according to several test-generation techniques based on combined concrete and symbolic (concolic) execution. We evaluate these techniques by applying the Ochiai fault-localization technique to generated test suites in order to localize 35 faults in four PHP Web applications. Our results show that the test-generation techniques under consideration produce test suites with similar high fault-localization effectiveness, when given a large time budget. However, a new, "directed" test-generation technique, which aims to maximize the similarity between the path constraints of the generated tests and those of faulty executions, reaches this level of effectiveness with much smaller test suites. On average, when compared to test generation based on standard concolic execution techniques that aims to maximize code coverage, the new directed technique preserves fault-localization effectiveness while reducing test-suite size by 86.1% and test-suite generation time by 88.6%.
A decimal floating-point fused-multiply-add unit (2010)

This paper presents the first hardware implementation of a fully parallel decimal floating-point fused-multiply-add unit performing the operation ± (A × B) ± C on decimal floating-point operands. The proposed design is fully compliant with the IEEE 754-2008 standard and supports the two standard formats decimal64 and decimal128. Furthermore, the proposed design may be controlled to perform the multiplication or the addition/subtraction as standalone operations. Our decimal floating-point FMA may be pipelined so that a complete resultant decimal floating-point is available each clock cycle.
Light-propagation management in coupled waveguide arrays: Quantitative experimental and theoretical assessment from band structures to functional patterns (2012)

We assess the band structure of arrays of coupled optical waveguides both by ab initio calculations and by experiments, with an excellent quantitative agreement without any adjustable physical parameter. The band structures we obtain can deviate strongly from the expectations of the standard coupled mode theory approximation, but we describe them efficiently by a few parameters within an extended coupled mode theory. We also demonstrate that this description is in turn a firm and simple basis for accurate beam management in functional patterns of coupled waveguides, in full accordance with their design.
Nature and origin of asphaltenes in processsed coals. Volume 2. The chemistry and mechanisms of coal conversion to clean fuel. Final report, March 1977-January 1979 (1979)

Studies have been undertaken to develop a fundamental understanding of the chemistry of coal and coal liquefaction products and the mechanisms involved in the conversion of coal to soluble products under typical solvent refining conditions. Specil emphasis has been placed on the importance and reactions of various solvent components (especially hydroaromatics and phenols), the composition of SRC's, the significance of coal type, the chemistry involved in the formation of insoluble residues, the effects of coal mineral matter, and temperature and contact time variation, especially very short times. A variety of materials were investigated ranging in rank from peat to a low volatile B bituminous coal. Reactions were conducted in stirred autoclaves at contact times of 0.25 to 400 minutes using process-derived and synthetic-recycle solvents. Other reaction variables included temperature, atmosphere, catalysts, and coal pretreatments to alter the mineral constituents. Reactions were also run with coal liquid fractions and model compounds. Solvents included process-derived recycle solvents and chemical fractions isolated from them, as well as synthetic mixtures formulated to elucidate the effects of the nature and concentration of various hydroaromatics and phenols, and the effects of added hydrogen-consuming components. SRC's and solvents were studied by new analytical and preparative liquid chromatographic methods, in addition to a variety of wet chemical and spectroscopic techniques. The compositions of solvents, SRC's and residues were also studied by Field Ionization Mass Spectroscopy, CP-/sup 13/C-NMR, Polarography, Selective Oxidation, and Optical Microscopy.
Carbocyclic analog of 3-deazaadenosine: a novel antiviral agent using S-adenosylhomocysteine hydrolase as a pharmacological target (1982)

The carbocyclic analogue of 3-deazaadenosine (3-deaza-C-Ado) has been synthesized and found to have antiviral activity in cell culture against herpes simplex virus type 1, vaccinia virus, and HL-23 C-type virus. It is relatively noncytotoxic at effective antiviral concentrations and is not subject to deamination or phosphorylation. It acts as a competitive inhibitor of S-adenosyl-L-homocysteine hydrolase, is at best a poor substrate, and does not inactivate the enzyme significantly. 3-Deaza-C-Ado may cause a selective inhibition of the methylation of the polynucleotide 5' cap of viral mRNA via higher cellular concentrations of S-adenosyl-L-homocysteine, resulting from the inhibition of S-adenosylhomocysteine hydrolase in infected cells, since increases in the intracellular level of S-adenosylhomocysteine, but no effects on DNA or RNA synthesis, were observed after incubation of these cells with it.
A stable room-temperature sodium–sulfur battery (2016)

High-energy rechargeable batteries based on earth-abundant materials are important for mobile and stationary storage technologies. Rechargeable sodium-sulfur batteries able to operate stably at room temperature are among the most sought-after platforms because such cells take advantage of a two-electron-redox process to achieve high storage capacity from inexpensive electrode materials. Here we report a room-temperature sodium-sulfur battery that uses a microporous carbon-sulfur composite cathode, and a liquid carbonate electrolyte containing the ionic liquid 1-methyl-3-propylimidazolium-chlorate tethered to SiO2 nanoparticles. We show that these cells can cycle stably at a rate of 0.5 C (1 C=1675, mAh g(-1)) with 600 mAh g(-1) reversible capacity and nearly 100% Coulombic efficiency. By means of spectroscopic and electrochemical analysis, we find that the particles form a sodium-ion conductive film on the anode, which stabilizes deposition of sodium. We also find that sulfur remains interred in the carbon pores and undergo solid-state electrochemical reactions with sodium ions.
Empirical Differential Privacy (2019)

We show how to achieve differential privacy with no or reduced added noise, based on the empirical noise in the data itself. Unlike previous works on noiseless privacy, the empirical viewpoint avoids making any explicit assumptions about the random process generating the data.
High-Ge-Content SiGe Alloy Single Crystals Using the Nanomembrane Platform (2020)

The growth of single crystals of Ge-rich SiGe alloys in an extended composition range is demonstrated using the nanomembrane (NM) platform and III-V growth substrates. Thin films of high-Ge-content SiGe films are grown on GaAs(001) to below the kinetic critical thickness and released from the growth substrate by selectively etching a release layer to relax the strain. The resulting crystalline nanomembranes at the natural lattice constant of the alloy are transferred to a new host and epitaxially overgrown at similar compositions to make a thicker single crystal. Straightforward critical-thickness calculations demonstrate that a very wide range of group IV alloys, including those involving Sn, can be fabricated using the NM platform and the proper choice of III-V substrate. Motivations for making new group IV alloys center on band gap engineering for the development of novel group IV optoelectronic structures and devices.
Detection of Human Cytomegalovirus in Clinical Specimens by DNA-DNA Hybridization (1984)

A diagnostic assay has been developed to detect human cytomegalovirus (HCMV) DNA in clinical specimens with 32P-labeled cloned fragments of HCMV strain AD169. The labeled probe can detect 10 pg of HCMV DNA and fails to hybridize to DNA from other herpesviruses or human DNA. The assay correctly identified 22 (92%) of 24 coded urine specimens culture positive for HCMV and 23 (88%) of 26 urine specimens culture negative for HCMV. In a prospective study of 67 buffy-coat specimens from recipients of bone marrow transplants HCMV DNA was detected in 13 (93%) of 14 culture-positive samples. Of 53 buffy-coat specimens culture negative for HCMV, 32 were hybridization negative for HCMV DNA. However, in 20 of 21 buffy-coat specimens positive for HCMV by hybridization but negative by culture there was evidence that the hybridization assay was correct and more sensitive than currently available tissue culture techniques.
Rectifying rolling shutter video from hand-held devices (2010)

This paper presents a method for rectifying video sequences from rolling shutter (RS) cameras. In contrast to previous RS rectification attempts we model distortions as being caused by the 3D motion of the camera. The camera motion is parametrised as a continuous curve, with knots at the last row of each frame. Curve parameters are solved for using non-linear least squares over inter-frame correspondences obtained from a KLT tracker. We have generated synthetic RS sequences with associated ground-truth to allow controlled evaluation. Using these sequences, we demonstrate that our algorithm improves over to two previously published methods. The RS dataset is available on the web to allow comparison with other methods.
Low temperature atomic layer deposition of highly photoactive hematite using iron(iii) chloride and water (2013)

Nanostructured hematite (α-Fe2O3) has been widely studied for use in a variety of thin film applications including solar energy conversion, water oxidation, catalysis, lithium-ion batteries, and gas sensing. Among established deposition methods, atomic layer deposition (ALD) is a leading technique for controlled synthesis of a wide range of nanostructured materials. In this work, ALD of Fe2O3 is demonstrated using FeCl3 and H2O precursors at growth temperatures between 200 and 350 °C. Self-limiting growth of Fe2O3 is demonstrated with a growth rate of ∼0.6 Å per cycle. As-deposited, films are nanocrystalline with low chlorine impurities and a mixture of α- and γ-Fe2O3. Post-deposition annealing in O2 leads to phase-pure α-Fe2O3 with increased out-of-plane grain size. Photoelectrochemical measurements under simulated solar illumination reveal high photoactivity toward water oxidation in both as-deposited and post-annealed films. Planar films deposited at low temperature (235 °C) exhibit remarkably high photocurrent densities ∼0.71 mA cm−2 at 1.53 V vs. the reversible hydrogen electrode (RHE) without further processing. Films annealed in air at 500 °C show current densities of up to 0.84 mA cm−2 (1.53 V vs. RHE).
A Micro-Optical Wall Shear Stress Sensor Concept Based on Whispering Gallery Mode Resonators (2008)

In this paper we discuss a novel micro optical wall shear stress sensor concept based on whispering gallery mode (WGM) shifts of dielectric resonators. The optical resonator, which is a sphere with a diameter of several hundred microns, serves as the sensing element. The wall shear force acting on a moveable plate is transmitted mechanically to the microsphere. As a result of the applied force, the morphology (both shape and refractive index) of the resonator is perturbed leading to a shift of the optical resonance (WGM). By monitoring the shifts to WGMs, measurement of the wall shear stress is accomplished. Shape perturbations of the order of a nanometer can be detected with this optical method. Therefore, the whole sensor system is essentially rigid. Preliminary experiments using a prototype sensor design show promise.
Biological based routing algorithm for mobile ad-hoc networks (2005)

This research introduces the application of a probabilistic-based Ant Routing Algorithm for Mobile Ad-hoc networks (ARAMA) that is inspired from the ant colony's life. Mobile Ad-Hoc networks (MANETs) are highly dynamic, self-configured and self-built networks. Hence, MANETs require a special type of routing algorithms to operate efficiently in such dynamic environment. These algorithms should be able to manage efficiently the usage of the limited network resources across the network nodes (i.e., node's energy, bandwidth, processing power, etc.).
The goal of this research is to present ARAMA ability to route data and manage the network resources while considering the dynamic characteristics of MANETs and the need for low control overheads. The description of the algorithm is provided, which uses a probabilistic search for the near best route in the entire network concentrating in the best routes region. The nodes' and links' parameters are measured and collected in the nodes' indices. A path index is used to measure the path parameters and serves to minimize the forward control packet (ant) size. The concept of negative backward ant is introduced to aid in avoiding unwanted behavior (i.e., looping and link failures, etc.), and to speed up the fault detection and recovery process. Further, the concept of destination trail ants is introduced to dramatically minimize the initialization (learning/optimization) time as well as the connection setup time. A methodology to update the link grade is presented. 
The simulation results show the potential of the algorithm. The results show that ARAMA finds the best/near best path and responds well to node unavailability and the energy level changes in the network nodes. In addition, ARAMA achieves a fairness of node energy usage across the network nodes as an example of the network resource management, which helps in avoiding early node failure because of energy depletion. More, The results show the ability of the algorithm to optimize more than one parameter. In addition, a comparison between ARAMA and Ad hoc On Demand Distance Vector algorithm AODV is presented to show the potential of ARAMA.
Epitaxial-side-down-mounted interband cascade lasers (2012)

A rapid series of recent performance advances have established the interband cascade laser (ICL) as a practical midwave infrared (mid-IR) diode source that may be expected to find broad use in a variety of applications ranging from infrared countermeasures to chemical spectroscopy. The ICL is effectively a hybrid of the conventional diode laser, in that injected electrons and holes recombine to create photons, and the quantum cascade laser (QCL), in that a multi-stage staircase of active quantum wells is connected in series. The ICL also differs from both, however, in that most of the electrons and holes needed for lasing are created internally at semimetallic interfaces separating the stages rather than being injected from the contacts. The ICL performance recently improved dramatically when “carrier rebalancing”, via heavy n-type doping of the electron injector regions, was introduced to equalize the electron and hole populations in the active quantum wells [1]. Recent publications have reported cw operation up to 109°C, cw output power up to 158 mW at room temperature (RT, taken here to be 25°C), RT cw wallplug efficiency up to 13.5%, RT cw drive power as low as 29 mW (more than 20 times lower than the best QCLs results reported to date), and RT cw operation to wavelengths as long as 5.7 μm [1,2]. Here we discuss further improvements of the lasing characteristics that occur when the ICLs are mounted epitaxial-side-down (epi-down), using a proprietary NRL procedure that combines high performance with high processing yield.
Development and Optimization of Gas-Assisted Gravity Drainage (GAGD) Process for Improved Light Oil Recovery (2006)

This is the final report describing the evolution of the project ''Development and Optimization of Gas-Assisted Gravity Drainage (GAGD) Process for Improved Light Oil Recovery'' from its conceptual stage in 2002 to the field implementation of the developed technology in 2006. This comprehensive report includes all the experimental research, models developments, analyses of results, salient conclusions and the technology transfer efforts. As planned in the original proposal, the project has been conducted in three separate and concurrent tasks: Task 1 involved a physical model study of the new GAGD process, Task 2 was aimed at further developing the vanishing interfacial tension (VIT) technique for gas-oil miscibility determination, and Task 3 was directed at determining multiphase gas-oil drainage and displacement characteristics in reservoir rocks at realistic pressures and temperatures. The project started with the task of recruiting well-qualified graduate research assistants. After collecting and reviewing the literature on different aspects of the project such gas injection EOR, gravity drainage, miscibility characterization, and gas-oil displacement characteristics in porous media, research plans were developed for the experimental work to be conducted under each of the three tasks. Based on the literature review and dimensional analysis, preliminary criteria were developed for the design of the partially-scaled physical model. Additionally, the need for a separate transparent model for visual observation and verification of the displacement and drainage behavior under gas-assisted gravity drainage was identified. Various materials and methods (ceramic porous material, Stucco, Portland cement, sintered glass beads) were attempted in order to fabricate a satisfactory visual model. In addition to proving the effectiveness of the GAGD process (through measured oil recoveries in the range of 65 to 87% IOIP), the visual models demonstrated three possible multiphase mechanisms at work, namely, Darcy-type displacement until gas breakthrough, gravity drainage after breakthrough and film-drainage in gas-invaded zones throughout the duration of the process. The partially-scaled physical model was used in a series of experiments to study the effects of wettability, gas-oil miscibility, secondary versus tertiary mode gas injection, and the presence of fractures on GAGD oil recovery. In addition to yielding recoveries of up to 80% IOIP, even in the immiscible gas injection mode, the partially-scaled physical model confirmed the positive influence of fractures and oil-wet characteristics in enhancing oil recoveries over those measured in the homogeneous (unfractured) water-wet models. An interesting observation was that a single logarithmic relationship between the oil recovery and the gravity number was obeyed by the physical model, the high-pressure corefloods and the field data.