gebhart/patrepeval huggingface dataset:
A hierarchical decomposition methodology for multistage clock circuits (1997)

This paper describes a novel methodology to automate the design of the interconnect distribution for multistage clock circuits. We introduce two key ideas. First, a hierarchical decomposition of the layout divides the problem into a set of local Steiner-wired latch clusters (to minimize and balance local capacitance) fed globally by a balanced binary tree (to maximize performance). Second, we recast the global clock distribution problem as a simultaneous optimization of clock topology, clock segment routing, wiresizing, and buffering. The hierarchical decomposition reduces the problem complexity and allows use of more aggressive optimization techniques. Integration of the geometric and electrical optimizations likewise allows more aggressive performance goals. Experiments with an industrial design comprising over 16,000 latches demonstrate the efficiency of the approach: a complete clock distribution solution met a 200MHz cycle time specification with only 310ps of skew, met strict current density constraints, exhibited good delay matching across uniform wire width and device variations, and was completed in under 10 CPU hours.
Speed of Sound Imaging with Curvilinear Probes from Full-Synthetic Aperture Data (2022)

Speed-of-sound (SoS) estimation is important in abdominal ultrasound for both aberration compensation and liver tissue quantification, and there is need to develop SoS reconstruction methods for curvilinear array geometries. In this work, we directly reconstruct SoS from full-synthetic aperture (FSA) datasets. We first introduce scatterer triangulation from Common-Mid-Point (CMP) gathers acquired with curvilinear probe geometries, where a spatio-temporally filter allows selection of scattering signals from a single azimuth direction. Next we develop a ray-tracing interpolation approach and regularized inversion for ultrasound computed tomography reconstruction in polar geometries. Our method allows direct estimation of both scattering locations and absolute time delays for SoS estimation. Experimental SoS estimation in attenuating phantoms is feasible at depths> 120 mm. Experimental SoS reconstruction is demon-strated in layered abdominal phantoms simulating fatty liver disease stages through aberrating subcutaneous tissue layers.
Electronic structures and optical properties of CuMgVO<sub>4</sub> and AgMgVO<sub>4</sub>: a first-principles study (2018)

Electronic structures and optical properties of CuMgVO4 and AgMgVO4 with optimized structures were investigated using the generalized gradient approximation proposed by Perdew-Burke-Ernzerhof and the Heyd-Scuseria-Ernzerhof hybrid functional. From the energy band calculation, we found that CuMgVO4 and AgMgVO4 have indirect band gaps. The upper valence band is mainly composed of fully occupied Cu 3d (Ag 4d) states, and the lower is mainly comprises O 2p states. The conduction band can be divided into two regions because of the crystal-field splitting by the interaction between the V 3d and the O 2p states. The optical properties of CuMgVO4 and AgMgVO4 were predicted from the complex dielectric function, ε(ω) = ε1(ω) + iε2(ω). The static dielectric constants were estimated from the real part of the dielectric functions, ε1(ω). The imaginary part of the dielectric functions, ε2(ω), demonstrated optical anisotropy, with the component along the z (y) direction being larger than the others for CuMgVO4 (AgMgVO4) in the wavelength range of visible light. The absorption coefficient I(ω) was also calculated from the dielectric function.
High Spectral Irradiance White Light Continuum Z-scan (2006)

We generate high-energy, high-quality supercontinua in Krypton gas for Z-scan measurements of nonlinear absorption and refraction spectra in optical materials throughout the visible. This eliminates the need for tunable sources (OPA’s) for nonlinear measurements.
Temporal associations of the COVID-19 related border restrictions and respiratory viral infections in New Zealand (2022)

Abstract New Zealand (NZ)’s elimination of community transmission of influenza and respiratory syncytial virus (RSV) infections in May 2020, due to stringent COVID-19 countermeasures, provided a rare opportunity to assess the impact of border restrictions and relaxations on common respiratory viral infections over the subsequent two-years. Using multiple surveillance systems, we observed that border closure to most non-residents, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Partial border relaxations through quarantine free travel with Australia and other countries were associated, within weeks, with importation of RSV and influenza into NZ in 2021 and 2022. Border restrictions did not have effect on community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type 1. These data can inform future pandemic influenza preparedness as well as provide insights into effective strategies to plan and model the impact of seasonal influenza, RSV, and other respiratory viral infections.
Exploring the involvement of FGFR4 in hepatocellular carcinoma (2007)

C73 Hepatocellular carcinoma (HCC) is a major malignancy inflicting most ethnicities with close to half a million fatalities annually. While the etiology of the disease is relatively well-established (mostly due to viral hepatitis and chronic liver injuries), the progression and the treatment of the disease is still poorly understood and under-explored. Hence, we investigated the contributory role of FGFR4 to HCC, a member of the fibroblast growth factor receptor family that has been recently associated with progression of melanoma, breast and head and neck carcinoma. FGFR4 also presents a unique interest to HCC because liver is the tissue type with the highest mRNA expression of FGFR4. We performed a comprehensive resequencing of the entire coding region of FGFR4 in 62 tumor-normal HCC tissue pairs, and also quantified their respective transcript expression by real-time PCR. We found 4 novel genetic alterations (D126N, T179A, G426D, D709G) as well as a dominant representation of two known polymorphisms among the patients (V10I and G338R). Increased FGFR4 mRNA expression was observed in the tumor tissues as compared to the adjacent normal tissue in 31.6% of the patients. Correlation studies with available clinical follow-ups revealed an increased α-fetoprotein (AFP) production in patients bearing the homozygous Arg388 allele, an observation suggestive of the role of FGFR4 in disease progression. Hence, in vitro studies were subsequently performed to confirm the role of FGFR4 in HCC progression. FGFR4 siRNA administration significantly reduced the production of AFP in HuH7, a high AFP-producing cell line. Stimulation of HepG2 cells (low AFP-producing) with FGF19, a specific FGFR4 ligand, also increased the production of AFP. These effects were independent from the impact of FGFR4 activities on cell proliferation. In summary, our data (both in vivo and in vitro) demonstrated that FGFR4 may represent a drug target against the progression of HCC. The specific role of FGFR4 in HCC and the signal transduction pathways implicated will require further investigation.
Induction of Primary Human CD8+ T Lymphocyte Responses In Vitro Using Dendritic Cells (1999)

The ability of two different human professional APCs, specifically macrophages (Mphi) and dendritic cells (DC), to stimulate primary responses in human CD8+ T lymphocytes was examined using both allogeneic and Ag-pulsed autologous APCs. CTL responses in CD8+ T lymphocytes isolated from HIV-uninfected donors were evaluated against six different HIV epitopes that are restricted by four different HLA alleles using autologous human PBMC-derived Mphi and DCs for primary stimulation. In a side-by-side experiment, immature DCs, but not Mphi, were able to prime a CTL response against the B14-restricted p24gag 298-306 epitope; mature DCs were also able to prime a response against this epitope. In addition, DCs were capable of priming CD8+ CTL responses against the B8-restricted p24gag 259-267 epitope. In contrast, Mphi were unable to prime strong CTL responses against other epitopes. Since the Ag-specific cytotoxic responses required subsequent rounds of restimulation before they could be detected, the ability of the allogeneic Mphi and DCs to directly prime CD8+ T lymphocyte responses without subsequent restimulation was examined. Similar to the aforementioned peptide-specific results, DCs were more efficient than Mphi in priming both allogeneic proliferative and cytotoxic responses in human CD8+ T lymphocytes. Collectively, these results promote an enhanced status for DCs in the primary stimulation of human CD8+ T lymphocytes.
Encapsulation of Polypyrrole by Internal Domain Modification of Double-Cylinder-Type Copolymer Brushes (2002)

Double-cylinder-type copolymer brushes were synthesized by free-radical polymerization of vinylbenzyl-terminated poly(α-methylstyrene)-block-poly(2-vinylpyridine) (PMS-block-P2VP) diblock macromonomers. These copolymer brushes formed a single macromolecule even in good solvent due to crowded side chains. To design the encapsulation of conducting polymers, Cu2+ ions (oxidant) were introduced internal P2VP cylindrical domains by complexation based on the pyridine nitrogen interacting with metal ions. Encapsulation of conducting polymers was performed by the oxidation polymerization of double-cylinder-type copolymer brushes complexed with such an oxidizing agent being added to a mixture of pyrrole and water vapor. It was found from light scattering data that the encapsulation materials of polypyrrole (P2VP block 8 mol %) obtained after chemical modifications formed a single macromolecule in good solvent such as benzene.
Optimization of transmitter and receiver design for optoelectronic computing (2002)

Optoelectronic computing systems that combine electronic circuits with optical interconnect elements have been considered for many applications where the cost of communication is higher than that of computation. We have previously developed a method of evaluating the performance of the optoelectronic interface, referred to as a photonics layer, and examined various transmitter and receiver technologies separately. In this paper, we report our recent results in the design optimization of the overall photonics layer. We examine the total electrical power dissipated in both the transmitter and the receiver modules, and optimize the receiver configurations to achieve a minimum electrical power dissipation at a given bit rate.
First demonstration of long-haul transmission using silicon microring modulators (2010)

We report error-free long-haul transmission of optical data modulated using a silicon microring resonator electro-optic modulator with modulation rates up to 12.5 Gb/s. Using bit-error-rate and power penalty characterizations, we evaluate the performance of this device with varying modulation rates, and perform a comparative analysis using a commercial electro-optic modulator. We then experimentally measure the signal integrity degradation of the high-speed optical data with increasing propagation distances, induced chromatic dispersions, and bandwidth-distance products, showing error-free transmission for propagation distances up to 80 km. These results confirm the functional ubiquity of this silicon modulator, establishing the potential role of silicon photonic interconnects for chip-scale high-performance computing systems and memory access networks, optically-interconnected data centers, as well as high-performance telecommunication networks spanning large distances.
Supplementary Table 2 from The miR-17/92 Polycistron Is Up-regulated in Sonic Hedgehog–Driven Medulloblastomas and Induced by N-myc in Sonic Hedgehog–Treated Cerebellar Neural Precursors (2023)

Supplementary Table 2 from The miR-17/92 Polycistron Is Up-regulated in Sonic Hedgehog–Driven Medulloblastomas and Induced by N-myc in Sonic Hedgehog–Treated Cerebellar Neural Precursors
Autonomic Nervous System Tone Measured by Baroreflex Sensitivity Is Depressed in Patients With End-Stage Liver Disease (1999)

OBJECTIVES: Chronic liver disease is often associated with impairment of autonomic nervous system (ANS) reflexes. Baroreflex sensitivity (BRS) testing is an inexpensive, relatively noninvasive test that can be used to assess ANS tone. The aims of the present study were to determine the prevalence of ANS dysfunction in cirrhotics who are being considered for liver transplantation and to explore the potential use of BRS as a prognostic tool in identifying patients awaiting transplantation who are at increased risk for death. METHODS: We studied nine cirrhotics who were awaiting liver transplantation and seven controls without liver disease. BRS (ms/mm Hg) was measured using the phenylephrine method. RESULTS: BRS (mean ± SEM) (ms/mm Hg) was significantly lower in cirrhotics compared with controls (4.2 ± 0.9 vs 21.1 ± 3.8 ms/mm Hg; p < 0.05). Furthermore, BRS was lower in cirrhotics with hepatic encephalopathy compared with those without (2.6 ± 0.9 vs 6.1 ± 1.0 ms/mm Hg; p < 0.05) and there was a trend toward lower BRS values in Child-Pugh class C patients as compared with class B (3.8 ± 1.3 vs 5.3 ± 1.2 ms/mm Hg; p= 0.3). At follow-up (9 months), one patient had died and one underwent liver transplantation. These two patients also had the most severely impaired vagal tone (BRS = 0 and 1.2 ms/mm Hg, respectively). CONCLUSIONS: Vagal tone, as assessed by BRS, is markedly depressed in cirrhotic patients awaiting liver transplantation.
Abstract SY17-02: A systems approach to understanding tumor specific drug response (2011)

Abstract Systematic characterization of cancer genomes has revealed a staggering complexity of aberrations among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remains poorly defined. A major challenge involves the development of analysis methods to uncover biological insights from the data, including the identification of the key mutations that drive cancer and how these events alter cellular regulation. We have developed Conexic, a novel Bayesian Network-based framework to integrate chromosomal copy number and gene expression data to detect to detect driver genes located in regions that are aberrant in tumors. The underlying assumption is that a driving mutation might be associated with a characteristic gene expression signature representing genes whose expression is modulated by the driver. Thus our score guided approach searches for genes that are both recurrently aberrant and associated with variance of expression patterns across tumor samples. This method not only pinpoints specific regulators within a large aberrant region, but also by associating drivers with gene modules whose expression vary with the driver, provides insight into the physiological roles of drivers and associated genes. We demonstrated the utility of the CONEXIC framework using a melanoma dataset, our analysis correctly identified known drivers in melanoma (such as MITF) and connected these to many of their known targets, as well as the biological processes they regulate. In addition, it predicted multiple tumor dependencies TBC1D16 and RAB27A in melanoma and showed that tumors highly expressing these genes are dependent on the same gene for growth. Additionally, gene expression in the associated modules is altered following knockdown as predicted by our model. The identity of these drivers suggests that abnormal regulation of protein trafficking is important for cell survival in melanoma and highlights the importance of protein trafficking in this malignancy. We also present more recent results of applying CONEXIC to additional cancers, including glioblastoma and ovarian cancers, as well as additional phenotypes including invasion and drug resistance. Together, these results demonstrate the ability of integrative Bayesian approaches to identify novel drivers with biological, and possibly therapeutic, importance in cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr SY17-02. doi:10.1158/1538-7445.AM2011-SY17-02
Bandwidth allocation and call admission control in high-speed networks (1997)

The authors discuss the broad issue of bandwidth allocation and call admission control (CAC) in high-speed networks, focusing on asynchronous transfer mode technology. It is maintained that despite the considerable amount of high-quality work carried out in this area, the debate surrounding these issues is not yet resolved. The complexity of dealing with a wide variety of as yet unknown user traffic types, as well as the evolving architecture of networks, means that currently proposed solutions are only an intermediate step of the design process. The authors discuss the nature of user traffic and illustrate how it can impact the debate on the quality of service, concentrating on some "equivalent bandwidth" type CAC strategies. Also discussed is a method which uses diffusion approximations. Finally, the authors discuss the novel issue of evaluating the overload created by the CAC procedure itself on network nodes. The article is complemented by several numerical and simulation results which illustrate the discussion.
Figure S4 from Intratumoral G100, a TLR4 Agonist, Induces Antitumor Immune Responses and Tumor Regression in Patients with Merkel Cell Carcinoma (2023)

&lt;p&gt;Figure S4 shows MCPyV-reactive T cells detected post-G100 treatment&lt;/p&gt;
An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation (2019)

Mutations in <i>CTNNB1</i>, the gene encoding β-catenin, are common in colon and liver cancers, the most frequent mutation affecting Ser-45 in β-catenin. Peptides derived from WT β-catenin have previously been shown to be presented on the cell surface as part of major histocompatibility complex (MHC) class I, suggesting an opportunity for targeting this common driver gene mutation with antibody-based therapies. Here, crystal structures of both the WT and S45F mutant peptide bound to HLA-A*03:01 at 2.20 and 2.45 Å resolutions, respectively, confirmed the accessibility of the phenylalanine residue for antibody recognition. Phage display was then used to identify single-chain variable fragment clones that selectively bind the S45F mutant peptide presented in HLA-A*03:01 and have minimal WT or other off-target binding. Following the initial characterization of five clones, we selected a single clone, E10, for further investigation. We developed a computational model of the binding of E10 to the mutant peptide-bound HLA-A3, incorporating data from affinity maturation as initial validation. In the future, our model may be used to design clones with maintained specificity and higher affinity. Such derivatives could be adapted into either cell-based (CAR-T) or protein-based (bispecific T-cell engagers) therapies to target cancer cells harboring the S45F mutation in <i>CTNNB1</i>.
Micro‐Resonator Soliton Generated Directly with a Diode Laser (2018)

Abstract An external‐cavity diode laser for 1550‐nm wavelength is reported with ultra‐low noise, high power coupled to a fiber, and fast tunability. These characteristics enable the generation of an optical frequency comb in a silica micro‐resonator with a single‐soliton state. Neither an optical amplifier nor a modulator is used in the experiment. This demonstration greatly simplifies the soliton generation setup and represents a significant step forward to a fully integrated soliton comb system.
Trans-Urethral Ultrasound (TUUS) Imaging for Visualization and Analysis of the Prostate and Associated Tissues (2000)

The incidence of prostate disease is high. However, accurate assessment of pathological conditions is still difficult. Although CT, MRI, and TRUS imaging methods provide useful information, each has specific drawbacks. Our work examines the potential and utility of 3D trans-urethral ultrasound (TUUS) for improved imaging of the prostate. Four normal canines were examined with TUUS. The catheter was placed in the urethra and used to image the prostate, rectum, bladder, ureter, neuro-vascular bundles, arteries, and surrounding tissue. 2D and 3D datasets were acquired and digitized. The 2D data provides useful visualization of the tissue. The clinician was also able to watch urine enter the bladder and perform a digital rectal exam in real-time. 3D data visualization required torodial reconstruction. The algorithm was optimized to provide very fast 3D reconstructions of the prostate. Segmentation of the data proved challenging, but 3D visualization, including volume rendered data and surface rendered data, were well accepted by clinicians. Clinicians and researchers determined a number of potential applications of these new techniques, including: prostate cancer diagnosis and staging, assessment of Benign Nodular Enlargement, assessment of physiologic function of the bladder, evaluation of morphologic properties of the prostate, and image guided biopsy and therapy.
Increase in oxide hole trap density associated with nitrogen incorporation at the SiO2/SiC interface (2008)

Nitrogen incorporation at the SiO2/SiC interface via high temperature nitric oxide annealing leads to the passivation of electrically active interface defects, yielding improved inversion mobility in the semiconductor. However, we find that such nitrided oxides can possess a larger density of hole traps than as-grown oxides, which is detrimental to the reliability of devices (e.g., can lead to large threshold voltage instabilities and to accelerated failure). Three different charge injection techniques are used to characterize this phenomenon in metal–oxide–semiconductor structures: x-ray irradiation, internal photoemission and Fowler–Nordheim tunneling. Some nitrogen-based atomic configurations that could act as hole traps in nitrided SiO2 are discussed based on first-principles density functional calculations.
Two New Devices for Identifying Electrochemical Reaction Intermediates with Desorption Electrospray Ionization Mass Spectrometry (2017)

Desorption electrospray ionization mass spectrometry (DESI-MS) previously has been used to capture and identify transient intermediates in electrochemical redox reactions on a platinum-covered rotating waterwheel. We present here two different setups that use a flat surface with porous carbon tape as the working electrode, where analyte-containing microdroplets from the DESI probe contacted with electrolyte supplied onto the surface. One setup had the conducting carbon tape in the form of a grooved inclined plane; the other one was in the form of a flat plane that had the conducting carbon tape as its front surface. Both these setups, which were relatively robust and easy to operate, overcame interference from the electrospray sheath gas that disturbs and dries the flowing electrolyte. By using the inclined-plane device, we observed radical cations and dimer species generated in the electrochemical oxidation of triphenylamine, diimine and imine alcohol in the electrochemical oxidation of uric acid, and the reductive cleavage of disulfide bonds in glutathione disulfide. By using the device with the flat carbon tape, we detected nitrenium ions generated in the electrochemical oxidation of N,N'-dimethyoxydiphenylamine and di-p-tolylamine. Our experience suggests that the flat porous carbon tape surface might be preferable over the inclined plane because of its ease of setup.