gebhart/patrepeval huggingface dataset:
Coherent beam combining with multilevel optical phase-locked loops (2007)

Coherent beam combining (CBC) technology holds the promise of enabling laser systems with very high power and near-ideal beam quality. We propose and demonstrate a novel servo system composed of multilevel optical phase lock loops. This servo system is based on entirely electronic components and consequently can be considerably more compact and less expensive compared to servo systems made of optical phase/frequency shifters. We have also characterized the noise of a 1064 nm Yb-doped fiber amplifier to determine its effect on the CBC and studied theoretically the efficiency of combining a large array of beams with the filled-aperture implementation. In a proof-of-concept experiment we have combined two 100 mW 1064 nm semiconductor lasers with an efficiency of 94%.
Single crystal and polycrystalline CVD diamond for demanding optical applications (2011)

Diamond's extremely wide transparency, combined with its other exceptional properties including hardness, strength and thermal conductivity make it a desirable material for optical windows. Polycrystalline diamond grown by chemical vapour deposition (CVD) has become the preferred window material for high power CO2 laser systems since its development in the 1990s. The range and availability of diamond materials is expanding, and in recent years has been extended to include CVD single crystal diamond. This paper reviews the quality of these materials, looking at optical scatter and absorption around 1 and 10 microns, along with their thermal and mechanical properties. We also discuss selection of appropriate grades and how they may best be integrated into demanding optical applications.
Optimizing task layout on the Blue Gene/L supercomputer (2005)

A general method for optimizing problem layout on the Blue Gene®/L (BG/L) supercomputer is described. The method takes as input the communication matrix of an arbitrary problem as an array with entries C(i, j), which represents the data communicated from domain i to domain j. Given C(i, j), we implement a heuristic map that attempts to sequentially map a domain and its communication neighbors either to the same BG/L node or to near-neighbor nodes on the BG/L torus, while keeping the number of domains mapped to a BG/L node constant. We then generate a Markov chain of maps using Monte Carlo simulation with free energy F = ∑ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i,j</inf> C(i, j)H(i, j), where H(i, j) is the smallest number of hops on the BG/L torus between domain i and domain j. For two large parallel applications, SAGE and UMT2000, the method was tested against the default Message Passing Interface rank order layout on up to 2,048 BG/L nodes. It produced maps that improved communication efficiency by up to 45%.
Communicating over nonstationary nonflat wireless channels (2005)

We develop the concept of joint time-frequency estimation of wireless channels. The motivation is to optimize channel usage by increasing the signal-to-noise ratio (SNR) after demodulation while keeping training overhead at a moderate level. This issue is important for single-input single-output (SISO) and multiple-input multiple-output (MIMO) systems but particularly so for the latter. Linear operators offer a general mathematical framework for symbol modulation in channels that vary both temporally and spectrally within the duration and bandwidth of one symbol. In particular, we present a channel model that assumes first-order temporal and spectral fluctuations within one symbol or symbol block. Discrete prolate spheroidal sequences (Slepian sequences) are used as pulse-shaping functions. The channel operator in the Slepian basis is almost tridiagonal, and the simple intersymbol interference pattern can be exploited for efficient and fast decoding using Viterbi's algorithm. To prove the concept, we use the acoustic channel as a meaningful physical analogy to the radio channel. In acoustic 2 /spl times/ 2 MIMO experiments, our method produced estimation results that are superior to first-order time-only, frequency-only, and zeroth-order models by 7.0, 9.4, and 11.6 db. In computer simulations of cellular wireless channels with realistic temporal and spectral fluctuations, time-frequency estimation gains us 12 to 18 db over constant-only estimation in terms of received SNR when signal-to-receiver-noise is 10 to 20 db. The bit error rate (BER) decreases by a factor of two for a binary constellation.
High‐Performance M<sub><i>x</i></sub>Sb–Al<sub>2</sub>O<sub>3</sub>–C (M=Fe, Ni, and Cu) Nanocomposite‐Alloy Anodes for Sodium‐Ion Batteries (2013)

Abstract M x Sb–Al 2 O 3 –C (M=Fe, Ni, and Cu) nanocomposites were synthesized by mechanochemical reduction of Sb 2 O 3 with Al and other metals (Fe, Ni, and Cu) in the presence of carbon and they were subsequently assessed as potential anode materials for sodium‐ion batteries. Various characterization methods, including XRD and transmission electron microscopy (TEM), reveal that the as‐prepared nanocomposites consist of nanostructured M x Sb particles in a matrix of amorphous Al 2 O 3 and conductive carbon. The incorporation of Al 2 O 3 and a conductive metal‐support into the Sb–C composite leads to an improved cycle life. The Cu 2 Sb–Al 2 O 3 –C and NiSb–Al 2 O 3 –C electrodes show, respectively, 80 and 90 % capacity retention after 70 cycles at a current rate of 100 mA g −1 , and the M x Sb–Al 2 O 3 –C composite anodes display >70 % retention at high current densities of 10 000 mA g −1 . These characteristics are attributed to the presence of both a metal framework to support the electrochemically active Sb, which results in a low electrode impedance, and a ceramic oxide and conductive carbon matrix, which reduce the agglomeration of nanoparticles as well as buffer the volume expansion/contraction during alloying/dealloying. Ex situ XRD analysis of the sodium‐storage mechanism in M x Sb–Al 2 O 3 –C composite anodes confirms the formation of a Na 3 Sb phase during sodiation.
Self-aligned Silicon Fins in Metallic Slits as a Platform for Planar Tunable Nanoscale Resonant Photodetectors (2012)

We demonstrate self-aligned fabrication of etched silicon fins in metallic slits and show that this structure supports both dielectric and plasmonic resonances and photodetection that can be tuned by varying the width of the fin
Design of a Multi-Color Plenoptic Camera for Snapshot Hyperspectral Imaging (2018)

The design of a custom camera lens including: a two-lens optical system, filter array, and iris has been developed enabling a greyscale plenoptic camera to acquire full field-of-view, 2D, instantaneous hyperspectral measurements. This work focuses on the use of 7 discrete color filters and their effect on the image quality. It was determined that the placement of the filters inside the aperture plane of the camera was paramount to mitigating image artifacts. In addition, design rules were developed such that the optimal optical parameters (image distance, working distance, and focal length) can be easily determined from a few charts.
Measurement of Trabecular Bone Thickness in the Limited Resolution Regime of In Vivo MRI by Fuzzy Distance Transform (2004)

Trabecular or cancellous bone, the type of bone found in the vertebrae and near the joints of long bones, consists of a network of plates and struts. Accurate measurement of trabecular thickness is of significant interest, for example, to assess the effectiveness of anabolic (bone forming) agents of patients with osteoporosis. Here, we introduce a new fuzzy distance transform (FDT)-based thickness computation method that obviates binary segmentation and that can effectively deal with images acquired at a voxel size comparable to the typical trabecular bone thickness. The method's robustness is shown on the basis of micro-CT images of human trabecular bone, resampled at progressively coarser resolution and after application of rotation and addition of noise as a means to simulate the in vivo situation. Reproducibility of the method is demonstrated with micro-CT images by comparing histograms of thickness within and between data sets and with micro-MRI volume data sets of human volunteers imaged repeatedly. Finally, with in vivo micro-MR images from a prior study in rabbits subjected to corticosteroid exposure, it is demonstrated that short-term treatment resulting in trabecular thinning can be quantified with the new method.
Development of Potent μ and δ Opioid Agonists with High Lipophilicity (2010)

An SAR study on the Dmt-substituted enkephalin-like tetrapeptide with a N-phenyl-N-piperidin-4-ylpropionamide moiety at the C-terminal was performed and has resulted in highly potent ligands at μ and δ opioid receptors. In general, ligands with the substitution of D-Nle(2) and halogenation of the aromatic ring of Phe(4) showed highly increased opioid activities. Ligand 6 with good biological activities in vitro demonstrated potent in vivo antihyperalgesic and antiallodynic effects in the tail-flick assay.
Anion Activation Site of Insulin-degrading Enzyme (2011)

Insulin-degrading enzyme (IDE) (insulysin) is a zinc metallopeptidase that metabolizes several bioactive peptides, including insulin and the amyloid β peptide. IDE is an unusual metallopeptidase in that it is allosterically activated by both small peptides and anions, such as ATP. Here, we report that the ATP-binding site is located on a portion of the substrate binding chamber wall arising largely from domain 4 of the four-domain IDE. Two variants having residues in this site mutated, IDEK898A,K899A,S901A and IDER429S, both show greatly decreased activation by the polyphosphate anions ATP and PPPi. IDEK898A,K899A,S901A is also deficient in activation by small peptides, suggesting a possible mechanistic link between the two types of allosteric activation. Sodium chloride at high concentrations can also activate IDE. There are no observable differences in average conformation between the IDE-ATP complex and unliganded IDE, but regions of the active site and C-terminal domain do show increased crystallographic thermal factors in the complex, suggesting an effect on dynamics. Activation by ATP is shown to be independent of the ATP hydrolysis activity reported for the enzyme. We also report that IDEK898A,K899A,S901A has reduced intracellular function relative to unmodified IDE, consistent with a possible role for anion activation of IDE activity in vivo. Together, the data suggest a model in which the binding of anions activates by reducing the electrostatic attraction between the two halves of the enzyme, shifting the partitioning between open and closed conformations of IDE toward the open form.
Development of a prototype superconducting radio-frequency cavity for conduction-cooled accelerators (2023)

The higher efficiency of superconducting radio-frequency (SRF) cavities compared to normal-conducting ones enables the development of high-energy continuous-wave linear accelerators (linacs). Recent progress in the development of high-quality ${\mathrm{Nb}}_{3}\mathrm{Sn}$ film coatings along with the availability of cryocoolers with high cooling capacity at 4 K makes it feasible to operate SRF cavities cooled by thermal conduction at relevant accelerating gradients for use in accelerators. A possible use of conduction-cooled SRF linacs is for environmental applications, requiring electron beams with energy of 1--10 MeV and 1 MW of power. We have designed a 915 MHz SRF linac for such an application and developed a prototype single-cell cavity to prove the proposed design by operating it with cryocoolers at the accelerating gradient required for 1 MeV energy gain. The cavity has a $\ensuremath{\sim}3\text{ }\text{ }\mathrm{\ensuremath{\mu}}\mathrm{m}$ thick ${\mathrm{Nb}}_{3}\mathrm{Sn}$ film on the inner surface, deposited on a $\ensuremath{\sim}4\text{ }\text{ }\mathrm{mm}$ thick bulk Nb substrate and a bulk $\ensuremath{\sim}7\text{ }\text{ }\mathrm{mm}$ thick Cu outer shell with three Cu attachment tabs. The cavity was tested up to a peak surface magnetic field of 53 mT in liquid He at 4.3 K. A horizontal test cryostat was designed and built to test the cavity cooled with three Gifford-McMahon cryocoolers. The rf tests of the conduction-cooled cavity, performed at General Atomics, achieved a peak surface magnetic field of 50 mT and stable operation was possible with up to 18.5 W of rf heat load. The peak frequency shift due to microphonics was 23 Hz. These results represent the highest peak surface magnetic field achieved in a conduction-cooled SRF cavity to date and meet the requirements for a 1 MeV energy gain.
A farnesyltransferase inhibitor activates lysosomes and reduces tau pathology in mice with tauopathy (2019)

Tau inclusions are a shared feature of many neurodegenerative diseases, among them frontotemporal dementia caused by tau mutations. Treatment approaches for these conditions include targeting posttranslational modifications of tau proteins, maintaining a steady-state amount of tau, and preventing its tendency to aggregate. We discovered a new regulatory pathway for tau degradation that operates through the farnesylated protein, Rhes, a GTPase in the Ras family. Here, we show that treatment with the farnesyltransferase inhibitor lonafarnib reduced Rhes and decreased brain atrophy, tau inclusions, tau sumoylation, and tau ubiquitination in the rTg4510 mouse model of tauopathy. In addition, lonafarnib treatment attenuated behavioral abnormalities in rTg4510 mice and reduced microgliosis in mouse brain. Direct reduction of Rhes in the rTg4510 mouse by siRNA reproduced the results observed with lonafarnib treatment. The mechanism of lonafarnib action mediated by Rhes to reduce tau pathology was shown to operate through activation of lysosomes. We finally showed in mouse brain and in human induced pluripotent stem cell-derived neurons a normal developmental increase in Rhes that was initially suppressed by tau mutations. The known safety of lonafarnib revealed in human clinical trials for cancer suggests that this drug could be repurposed for treating tauopathies.
Short-pulse intracavity Raman laser (1988)

We discuss the physics and design of a new class of tunable variable duration, short-pulse laser. Figure 1 shows a unidirectional ring laser containing a medium with gain at the fundamental frequency and a (nearly) copropagating unidirectional ring laser for the Stokes shifted Raman frequency with intersection of the beams in the Raman gain medium common to both rings. The laser cavity lengths are adjusted to differ by the amount Δ/so that the cavity round trip times differ by the desired output pulse duration (i.e., Δl= cτout). A fundamental pulse and a small Raman seed pulse are injected Into the pump and Stokes cavities, respectively. One pulse Is delayed relative to the other so they overlap during successive trips through the cavities. When the fundamental pulse overlaps the seed Raman pulse in the Raman medium, the fundamental pulse is converted into Stokes light via stimulated Raman scattering. Gain at the Stokes frequency occurs only during the overlap of the fundamental and Stokes pulses; this occurs for a time duration Δl/c. The Stokes pulse is partially outcoupled via the partially reflecting mirror which serves as the output coupler. However, some significant fraction of the pulse remains within its cavity. On successive round trip passes through the cavities, more and more of the fundamental pulse is converted to Stokes light, and the fundamental pulse becomes successively narrower as it is consumed. Consumption of the fundamental takes place from either its leading or trailing edge depending on the initial pulse delay and cavity lengths. For efficient conversion to take place during the overlap of the pump and Stokes pulses inside the Raman medium, it is desirable that the response time of the Raman medium (the T2 time of the polarization at the Stokes frequency) be small compared with the overlap time Δl/c. Otherwise the Raman conversion efficiency may not be sufficient to consume the fundamental during the overlap with the seed Stokes pulse.
Integrating PET and CT information to improve diagnostic accuracy for lung nodules: A semiautomatic computer-aided method. (2006)

Our CAD scheme based on both PET and CT was better able to differentiate benign from malignant pulmonary nodules than were the CAD schemes based on PET alone and CT alone.
Enhancing Mobile App Bug Reporting via Real-time Understanding of Reproduction Steps (2022)

One of the primary mechanisms by which developers receive feedback about in-field failures of software from users is through bug reports. Unfortunately, the quality of manually written bug reports can vary widely due to the effort required to include essential pieces of information, such as detailed reproduction steps (S2Rs). Despite the difficulty faced by reporters, few existing bug reporting systems attempt to offer automated assistance to users in crafting easily readable, and conveniently reproducible bug reports. To address the need for proactive bug reporting systems that actively aid the user in capturing crucial information, we introduce a novel bug reporting approach called EBug. EBug assists reporters in writing S2Rs for mobile applications by analyzing natural language information entered by reporters in real-time, and linking this data to information extracted via a combination of static and dynamic program analyses. As reporters write S2Rs, EBug is capable of automatically suggesting potential future steps using predictive models trained on realistic app usages. To evaluate EBug, we performed two user studies based on 20 failures from $11$ real-world apps. The empirical studies involved ten participants that submitted ten bug reports each and ten developers that reproduced the submitted bug reports. In the studies, we found that reporters were able to construct bug reports 31 faster with EBug as compared to the state-of-the-art bug reporting system used as a baseline. EBug's reports were also more reproducible with respect to the ones generated with the baseline. Furthermore, we compared EBug's prediction models to other predictive modeling approaches and found that, overall, the predictive models of our approach outperformed the baseline approaches. Our results are promising and demonstrate the potential benefits provided by proactively assistive bug reporting systems.
In Vitro and In Vivo Gene Delivery by Recombinant Baculoviruses (2003)

Although recombinant baculovirus vectors can be an efficient tool for gene transfer into mammalian cells in vitro, gene transduction in vivo has been hampered by the inactivation of baculoviruses by serum complement. Recombinant baculoviruses possessing excess envelope protein gp64 or other viral envelope proteins on the virion surface deliver foreign genes into a variety of mammalian cell lines more efficiently than the unmodified baculovirus. In this study, we examined the efficiency of gene transfer both in vitro and in vivo by recombinant baculoviruses possessing envelope proteins derived from either vesicular stomatitis virus (VSVG) or rabies virus. These recombinant viruses efficiently transferred reporter genes into neural cell lines, primary rat neural cells, and primary mouse osteal cells in vitro. The VSVG-modified baculovirus exhibited greater resistance to inactivation by animal sera than the unmodified baculovirus. A synthetic inhibitor of the complement activation pathway circumvented the serum inactivation of the unmodified baculovirus. Furthermore, the VSVG-modified baculovirus could transduce a reporter gene into the cerebral cortex and testis of mice by direct inoculation in vivo. These results suggest the possible use of the recombinant baculovirus vectors in combination with the administration of complement inhibitors for in vivo gene therapy.
Near-Infrared Dual-Comb Spectroscopy of Gases (2014)

Coherent dual-frequency comb spectroscopy provides a means to probe molecular spectra with the full accuracy and precision of frequency combs. We will discuss our dual comb spectrometer for precision laboratory measurement and recent outdoor measurements.
Handheld and bodyworn graphical displays: presented at the International Symposium on Wearable Computing (ISWC'98) (2002)

This paper describes two display systems developed by Honeywell under a DARPA program called Handheld and Bodyworn Graphical Display. The bodyworn display is worn on the wrist and has a wireless interface to the computer. The transmitter is attached to the standard VGA connector of a wearable computer. It transmits 16 color VGA (640/spl times/480) at 30 frames/sec over a 53 Mbit/sec RF link to the bodyworn display. The display is similar to the ones used in our helmet-mounted displays but is packaged to be worn on the arm or held in your hand. The second display system incorporates a hand held computer with a "see through" display. This computer is intended to be worn around the neck like a pair of binoculars. The optics allow a distant image, which is viewed through the scope, to be superimposed with a VGA display. The development and the applications of these novel display systems will be discussed.
Super high resolution for single molecule‐sequence‐based typing of classical <scp>HLA</scp> loci at the 8‐digit level using next generation sequencers (2012)

Current human leukocyte antigen (HLA) DNA typing methods such as the sequence-based typing (SBT) and sequence-specific oligonucleotide (SSO) methods generally yield ambiguous typing results because of oligonucleotide probe design limitations or phase ambiguity for HLA allele assignment. Here we describe the development and application of the super high-resolution single-molecule sequence-based typing (SS-SBT) of HLA loci at the 8-digit level using next generation sequencing (NGS). NGS which can determine an HLA allele sequence derived from a single DNA molecule is expected to solve the phase ambiguity problem. Eight classical HLA loci-specific polymerase chain reaction (PCR) primers were designed to amplify the entire gene sequences from the enhancer-promoter region to the 3' untranslated region. Phase ambiguities of HLA-A, -B, -C, -DRB1 and -DQB1 were completely resolved and unequivocally assigned without ambiguity to single HLA alleles. Therefore, the SS-SBT method described here is a superior and effective HLA DNA typing method to efficiently detect new HLA alleles and null alleles without ambiguity.
Band-edge photorefractive effect in semiconductors (1990)

We report here for the first time, two-beam coupling energy transfer using the Franz–Keldysh electrorefractive effect in photorefractive semiconductors. A large beam coupling gain coefficient (Γ=2.8 cm−1) exceeding the absorption coefficient (α=2.0 cm−1) is obtained in undoped semi-insulating GaAs using the new photorefractive process. The new photorefractive process differs from conventional photorefractivity in that the direction of energy transfer is dictated by the direction of an externally applied electric field. Using a moving grating technique and combining the electrorefractive grating with the conventional electro-optic grating, a very large gain Γ=16.3 cm−1 (α=3 cm−1, crystal length l=4mm) resulting in net amplification by more than a factor of 200 has been demonstrated.