gebhart/patrepeval huggingface dataset:
Characterizing isolated attosecond pulses from hollow-core waveguides using multi-cycle driving pulses (2009)

The generation of attosecond-duration light pulses using the high-order harmonic generation process is a rapidly evolving area of research. In this work, we combine experimental measurements with careful numerical analysis, to demonstrate that even relatively long-duration, 15 fs, carrier-envelope-phase (CEP) unstabilized near-infrared (NIR) pulses can generate isolated attosecond extreme-ultraviolet (EUV) pulses by the dynamically-changing phase matching conditions in a hollow-core waveguide geometry. The measurements are made using the laser-assisted photoelectric effect to cross-correlate the EUV pulse with the NIR pulse. A FROG CRAB analysis of the resulting traces (photoelectron signal versus photoelectron energy and EUV-NIR delay) is performed using a generalized projections (GP) algorithm, adapted for a wide-angle photoelectron detection geometry and non-CEP stabilized driving laser pulses. In addition, we performed direct FROG CRAB simulations under the same conditions. Such direct simulations allow more freedom to explore the effect of specific pulse parameters on FROG CRAB traces than is possible using the automated GP retrieval algorithm. Our analysis shows that an isolated pulse with duration of approximately 200 attoseconds can result from CEP unstabilized, high intensity approximately 15 fs multi-cycle driving pulses coupled into a hollow-core waveguide filled with low-pressure Argon gas. These are significantly longer driving pulses than used in other experimental implementations of isolated attosecond pulses.
Molecular Aspects of Ligand Interaction with Somatic and Immune Receptors: Insights from Studies of the Mammalian Reoviruses (Part 2 of 2) (1989)

Several characteristics of the reoviruses have facilitated the molecular analysis of virus-host interaction in this experimental system. These studies have benefited from the practical application of the idiotypic network paradigm. Studies of the mammalian reoviruses have helped elucidate the nature of the interaction of idiotype with anti-idiotype, the immune mechanisms which regulate the production of anti-idiotypic antibodies, and the functional consequences idiotypic mechanisms
cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R (2021)

Covariance matrices play fundamental roles in myriad statistical procedures. When the observations in a dataset far outnumber the features, asymptotic theory and empirical evidence have demonstrated the sample covariance matrix to be the optimal estimator of this parameter. This assertion does not hold when the number of observations is commensurate with or smaller than the number of features. Consequently, statisticians have derived many novel covariance matrix estimators for the high-dimensional regime, often relying on additional assumptions about the parameter's structural characteristics (e.g., sparsity). While these estimators have greatly improved the ability to estimate covariance matrices in high-dimensional settings, objectively selecting the best estimator from among the many possible candidates remains a largely unaddressed challenge. The cvCovEst package addresses this methodological gap through its implementation of a cross-validated framework for covariance matrix estimator selection. This data-adaptive procedure's selections are asymptotically optimal under minimal assumptions -in fact, they are equivalent to the selections that would be made if given full knowledge of the true data-generating processes (i.e.
Predictors of Failure of Endovascular Therapy for Peripheral Arterial Disease (2006)

The objective of this study was to assess the usefulness of a comparison of clinical failure and restenosis rates of endovascular procedures at 1 year in patients with peripheral arterial disease. The resulting comparison is presented as "clinical failure/restenosis coordinate." The authors screened 171 papers describing the outcome of lower extremity angioplasty or stent placement. In 20 of them, authors reported detailed outcomes of interest, including baseline demographic measurements, location of arterial occlusive lesions, a measure of restenosis (measured by ankle-brachial indices, ultrasonography, or angiography), and clinical outcomes (mortality, repeat percutaneous transluminal angioplasty, or amputation). An overview of these 20 angioplasty papers was performed. Besides the usual meta-analyses of each end point separately, data were also plotted as coordinates of clinical failure versus restenosis. The clinical failure-to-restenosis coordinate was calculated and reported for percutaneous transluminal angioplasty of the aortoiliac and femoropopliteal distributions. Clinically reported outcomes in the literature were used to calculate the clinical failure/restenosis coordinate. This value was significantly different for various locations of the angioplasty and various baseline angiographic characteristics. A numeric coordinate pair of clinical failure and restenosis is identifiable in patients undergoing endovascular treatment of peripheral arterial disease. The varying coordinates may be important in elucidating the incidence and mechanisms of clinical failure after endovascular treatment. The coordinate reported in this article is hypothesis-generating about mechanisms of endovascular treatment failure. This coordinate is important in determining the role of restenosis in the clinical failure of endovascular therapy of peripheral arterial disease.
Advanced Thermal Study of Very High Power TSV Interposer and Interconnects for 28nm Technology FPGA (2011)

TSV interposer has emerged as a good solution to provide high wiring density interconnections and improved electrical performance due to shorter interconnection from the die to substrate. Furthermore, silicon interposer minimizes CTE mismatch between the chip and copper filled TSV interposer resulting in high reliability micro bumps. This paper presents the thermal study of TSV interposer technology for a high-performance 28nm logic die that is mounted on a large silicon interposer with Cu through silicon via. A representative silicon interposer test chip with thousands of micro-bumps at 45um pitch has been fabricated. The silicon interposer is 100um thick, and is mounted on a 42.5mmx42.5mm substrate through 180um pitch C4 bumps. 3D thermal modeling and simulation for the packaged device with TSV interposer have been performed. Several DOEs have been constructed to optimize thermal interface material selection and to study the effect of high power and hot spots on underfill and solder bump material properties as well as the effect of bump pitch and underfill properties on the die junction temperatures. Furthermore, thermal behavior of 28nm technology monolithic FPGA was compared to the 3D TSV interposer FPGA package. Optimized passive thermal solution was recommended for this high power FPGA in order to cool down up to 100 Watt power.
Epitope Dampening Monotypic Measles Virus Hemagglutinin Glycoprotein Results in Resistance to Cocktail of Monoclonal Antibodies (2013)

The measles virus (MV) is serologically monotypic. Life-long immunity is conferred by a single attack of measles or following vaccination with the MV vaccine. This is contrary to viruses such as influenza, which readily develop resistance to the immune system and recur. A better understanding of factors that restrain MV to one serotype may allow us to predict if MV will remain monotypic in the future and influence the design of novel MV vaccines and therapeutics. MV hemagglutinin (H) glycoprotein, binds to cellular receptors and subsequently triggers the fusion (F) glycoprotein to fuse the virus into the cell. H is also the major target for neutralizing antibodies. To explore if MV remains monotypic due to a lack of plasticity of the H glycoprotein, we used the technology of Immune Dampening to generate viruses with rationally designed N-linked glycosylation sites and mutations in different epitopes and screened for viruses that escaped monoclonal antibodies (mAbs). We then combined rationally designed mutations with naturally selected mutations to generate a virus resistant to a cocktail of neutralizing mAbs targeting four different epitopes simultaneously. Two epitopes were protected by engineered N-linked glycosylations and two epitopes acquired escape mutations via two consecutive rounds of artificial selection in the presence of mAbs. Three of these epitopes were targeted by mAbs known to interfere with receptor binding. Results demonstrate that, within the epitopes analyzed, H can tolerate mutations in different residues and additional N-linked glycosylations to escape mAbs. Understanding the degree of change that H can tolerate is important as we follow its evolution in a host whose immunity is vaccine induced by genotype A strains instead of multiple genetically distinct wild-type MVs.
Isotopic Probe Illuminates the Role of the Electrode Surface in Proton Coupled Hydride Transfer Electrochemical Reduction of Pyridinium on Pt(111) (2015)

A recently proposed mechanism for electrochemical CO<sub>2</sub> reduction on Pt (111) catalyzed by aqueous acidic pyridine solutions suggests that the observed redox potential of ca. -600 mV vs. SCE is due to the one-electron reduction of pyridinium through proton coupled electron transfer (PCET) to form H atoms adsorbed on the Pt surface (H<sub>ads</sub>). The initial pyridinium reduction was probed isotopically via deuterium substitution. A combined experimental and theoretical analysis found equilibrium isotope effects (EIE) due to deuterium substitution at the acidic pyridinium site. A shift in the cathodic cyclic voltammetric half wave potential of -25 mV was observed, consistent with the theoretical prediction of -40 mV based on the recently proposed reaction mechanism where pyridinium is essential to establish a high concentration of Bronsted acid in contact with the substrate CO<sub>2</sub> and with the Pt surface. A prefeature in the cyclic voltammogram was examined under isotopic substitution and indicated an H-ads intermediate in pyridinium reduction. In conclusion, the theoretical prediction and observation of an BM supported the assignment of the cathodic wave to the proposed reduction of pyridinium through PCET forming H<sub>ads</sub> and eventually H<sub>2</sub> on the Pt surface.
Investigation of AlGaAs/GaAs V-grooved Quantum Wire Infrared Photodetector Structures (2000)

An Al 0.5 Ga 0.5 As/GaAs quantum wires infrared photo-detectors (QWRIP) based on V-grooved substrate is fabricated. The inter-band transition in the quantum wires is characterized by spatially resolved micro-photoluminescence (micro-PL) measurement. The theoretical calculation of electronic structures is accomplished based on the Green function. The inter-subband transition is measured by photocurrent at 80 K, and the origin of the infrared response at 9 µm is from the inter-subband transition in quantum wire region, which is confirmed by the theoretical calculation results.
Optimal Therapy for the Distal Ureteral Stone: Extracorporeal Shock Wave Lithotripsy Versus Ureteroscopy (1994)

Extracorporeal shock wave lithotripsy (ESWL not equal to) is the optimal therapy for renal calculi less than 2 cm. in diameter and for proximal ureteral calculi. Controversy continues over the initial approach to distal ureteral calculi (that is below the bony pelvis): in situ ESWL versus ureteroscopy. Since February 1990, 76 distal ureteral calculi were treated at our institution using either in situ ESWL (Dornier HM3 ESWL with a Stryker frame modification in 27 patients or Siemen's Lithostar electromagnetic ESWL in 22) or ureteroscopy (27 patients). Patient age and stone size were similar among the groups. All ESWL treatments were performed with the patient under intravenous sedation and on an outpatient basis. Stone-free rates were 96% for the HM3 device, 84% for the Lithostar and 100% for ureteroscopy. Retreatment was required in 3 Lithostar cases (14%) and 1 HM3 case (4%). When compared to ESWL ureteroscopy for distal ureteral stones was more time-consuming, entailed routine placement of a ureteral stent, often required general anesthesia, more often led to hospitalization and doubled the convalescence period. From a cost standpoint, ESWL on an HM3 unit was a few hundred dollars more expensive than ureteroscopy. In summary, we believe that in situ ESWL provides optimal first line therapy for distal ureteral calculi, while ureteroscopy is better reserved as a salvage procedure should ESWL fail.
Optimization of Substrate‐Analogue Furin Inhibitors (2017)

The proprotein convertase furin is a potential target for drug design, especially for the inhibition of furin-dependent virus replication. All effective synthetic furin inhibitors identified thus far are multibasic compounds; the highest potency was found for our previously developed inhibitor 4-(guanidinomethyl)phenylacetyl-Arg-Tle-Arg-4-amidinobenzylamide (MI-1148). An initial study in mice revealed a narrow therapeutic range for this tetrabasic compound, while significantly reduced toxicity was observed for some tribasic analogues. This suggests that the toxicity depends at least to some extent on the overall multibasic character of this inhibitor. Therefore, in a first approach, the C-terminal benzamidine of MI-1148 was replaced by less basic P1 residues. Despite decreased potency, a few compounds still inhibit furin in the low nanomolar range, but display negligible efficacy in cells. In a second approach, the P2 arginine was replaced by lysine; compared to MI-1148, this furin inhibitor has slightly decreased potency, but exhibits similar antiviral activity against West Nile and Dengue virus in cell culture and decreased toxicity in mice. These results provide a promising starting point for the development of efficacious and well-tolerated furin inhibitors.
Comparison of Lipid Amphotericin B Preparations in Treating Murine Zygomycosis (2008)

We compared the efficacies of liposomal amphotericin B (LAmB) and an amphotericin B lipid complex (ABLC) in diabetic ketoacidotic (DKA) or neutropenic mice with disseminated zygomycosis. ABLC was as effective as LAmB in neutropenic but not DKA mice. Low-dose ABLC was less effective than LAmB at reducing brain fungal burdens in both models.
Chemical targeting of voltage sensitive dyes to specific cells and molecules in the brain (2018)

Voltage sensitive fluorescent dyes (VSDs) are important tools for probing signal transduction in neurons and other excitable cells. These sensors, rendered highly lipophilic to anchor the conjugated pi-wire molecular framework in the membrane, offer several favorable functional parameters including fast response kinetics and high sensitivity to membrane potential changes. The impact of VSDs has, however, been limited due to the lack of cell-specific targeting methods in brain tissue or living animals. We address this key challenge by introducing a non-genetic molecular platform for cell- and molecule-specific targeting of synthetic voltage sensitive dyes in the brain. We employ a dextran polymer particle to overcome the inherent lipophilicity of voltage sensitive dyes by dynamic encapsulation, and high-affinity ligands to target the construct to specific neuronal cells utilizing only native components of the neurotransmission machinery at physiological expression levels. Dichloropane, a monoamine transporter ligand, enables targeting of dense dopaminergic axons in the mouse striatum and sparse noradrenergic axons in the mouse cortex in acute brain slices. PFQX in conjunction with ligand-directed acyl imidazole chemistry enables covalent labeling of AMPA-type glutamate receptors in the same brain regions. Probe variants bearing either a classical electrochromic ANEP dye or state-of-the-art VoltageFluor-type dye respond to membrane potential changes in a similar manner to the parent dyes, as shown by whole-cell patch recording. We demonstrate the feasibility of optical voltage recording with our probes in brain tissue with one-photon and two-photon fluorescence microscopy and define the signal limits of optical voltage imaging with synthetic sensors under a low photon budget determined by the native expression levels of the target proteins. We envision that modularity of our platform will enable its application to a variety of molecular targets and sensors, as well as lipophilic drugs and signaling modulators. This work demonstrates the feasibility of a chemical targeting approach and expands the possibilities of cell-specific imaging and pharmacology.
Thiazolidine‐2‐thione Directed Diastereoselective Addition of Chlorotitanium Enolates to Aldimines. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Fully Metallic Crooked Wire Antenna for UHF RFID Tags (2019)

In this paper, a 3 dimensions (3D) fully metallic antenna for an RFID tag is presented. It is a crooked wire monopole antenna. Close to the frequencies of the European UHF RFID band, it exhibits an input impedance that is the conjugate of the one of the Monza R6 chip. The latter with the proposed antenna presents a reading range of 11.87 meters and occupies a volume of 23 mm x 23.4 mm x 23.8 mm. This 3D tag structure could be useful for applications in metallic environments or applications in very severe environments where nonmetallic materials are useless such as in some aerospatiale applications. With a simple meander antenna, the proposed antenna, the reading range is approximately 6m.
Step edge influence on barrier height and contact area in vertical heterojunctions between epitaxial graphene and n-type 4H-SiC (2014)

Vertical rectifying contacts of epitaxial graphene grown by Si sublimation on the Si-face of 4H-SiC epilayers were investigated. Forward bias preferential conduction through the step edges was correlated by linear current density normalization. This phenomenon was observed on samples with 2.7–5.8 monolayers of epitaxial graphene as determined by X-ray photoelectron spectroscopy. A modified Richardson plot was implemented to extract the barrier height (0.81 eV at 290 K, 0.99 eV at 30 K) and the electrically dominant SiC step length of a Ti/Al contact overlapping a known region of approximately 0.52 μm wide SiC terraces.
STX140 Is Efficacious In vitro and In vivo in Taxane-Resistant Breast Carcinoma Cells (2008)

STX140 shows excellent efficacy in both MCF-7(WT) and MCF-7(DOX) breast cancer xenograft models, in contrast to Taxol and 2-MeOE2. The clinical potential of STX140 was further highlighted by the efficacy seen in xenografts recently derived from patients who had failed on taxane therapy.
Distal axonopathy in an alsin-deficient mouse model (2007)

Mutations in Alsin are associated with chronic juvenile amyotrophic lateral sclerosis (ALS2), juvenile primary lateral sclerosis and infantile-onset ascending spastic paralysis. The primary pathology and pathogenic mechanism of the disease remain largely unknown. Here we show that alsin-deficient mice have motor impairment and degenerative pathology in the distal corticospinal tracts without apparent motor neuron pathology. Our data suggest that ALS2 is predominantly a distal axonopathy, rather than a neuronopathy in the central nervous system of the mouse model, implying that alsin plays an important role in maintaining the integrity of the corticospinal axons.
Learning Adaptive Axis Attentions in Fine-tuning: Beyond Fixed Sparse Attention Patterns (2022)

We present a comprehensive study of sparse attention patterns in Transformer models. We first question the need for pre-training with sparse attention and present experiments showing that an efficient fine-tuning only approach yields a slightly worse but still competitive model. Then we compare the widely used local attention pattern and the less-well-studied global attention pattern, demonstrating that global patterns have several unique advantages. We also demonstrate that a flexible approach to attention, with different patterns across different layers of the model, is beneficial for some tasks. Drawing on this insight, we propose a novel Adaptive Axis Attention method, which learns-during fine-tuning-different attention patterns for each Transformer layer depending on the downstream task. Rather than choosing a fixed attention pattern, the adaptive axis attention method identifies important tokens-for each task and model layer-and focuses attention on those. It does not require pre-training to accommodate the sparse patterns and demonstrates competitive and sometimes better performance against fixed sparse attention patterns that require resource-intensive pre-training.
Reasoning About LLVM Code Using Codewalker (2015)

This paper reports on initial experiments using J Moore's Codewalker to reason about programs compiled to the Low-Level Virtual Machine (LLVM) intermediate form. Previously, we reported on a translator from LLVM to the applicative subset of Common Lisp accepted by the ACL2 theorem prover, producing executable ACL2 formal models, and allowing us to both prove theorems about the translated models as well as validate those models by testing. That translator provided many of the benefits of a pure decompilation into logic approach, but had the disadvantage of not being verified. The availability of Codewalker as of ACL2 7.0 has provided an opportunity to revisit this idea, and employ a more trustworthy decompilation into logic tool. Thus, we have employed the Codewalker method to create an interpreter for a subset of the LLVM instruction set, and have used Codewalker to analyze some simple array-based C programs compiled to LLVM form. We discuss advantages and limitations of the Codewalker-based method compared to the previous method, and provide some challenge problems for future Codewalker development.
Making the case for applications of switched reluctance motor technology in automotive products (2006)

Switched reluctance machines (SRM) offer attractive attributes for automotive applications. These include robustness to harsh operational conditions, rugged structure, fault resilient performance, and a wide range of speed. The main debate over the adequacy of switched reluctance drives in automotive applications has often focused on efficiency and position sensorless control over the entire speed range, adaptation of control algorithms in the presence of parameter variations, and high levels of acoustic noise and vibration. The present paper demonstrates three key technologies developed over the past few years that have resulted in tangible improvements in the performance of SRM/generators (SRM/G) as related to the above areas of interest. This paper intends to illustrate the new possibilities and remaining challenges in applications of SRM in automotive industry. The proposed technologies have been validated by simulation and experimental results
RingSTM (2008)

Existing Software Transactional Memory (STM) designs attach metadata to ranges of shared memory; subsequent runtime instructions read and update this metadata in order to ensure that an in-flight transaction's reads and writes remain correct. The overhead of metadata manipulation and inspection is linear in the number of reads and writes performed by a transaction, and involves expensive read-modify-write instructions, resulting in substantial overheads.
Air-Gap Transmission Lines on Organic Substrates for Low-Loss Interconnects (2007)

The fabrication of low-loss transmission line structures with an air dielectric layer is described. The channels are characterized at low frequency (10 and 100 kHz) using capacitance and loss tangent and at high frequency (500 MHz to 10 GHz) using -parameter measurements. The incorporation of an air gap resulted in structures with effective dielectric constants between 1.5-1.8 and significantly lower loss tangents. The fabrication technique could be used to create more complicated air gap transmission line structures for use in monolithic microwave integrated circuits.