gebhart/patrepeval huggingface dataset:
Low-Complexity Transform and Quantization in H.264/AVC (2003)

This paper presents an overview of the transform and quantization designs in H.264. Unlike the popular 8×8 discrete cosine transform used in previous standards, the 4×4 transforms in H.264 can be computed exactly in integer arithmetic, thus avoiding inverse transform mismatch problems. The new transforms can also be computed without multiplications, just additions and shifts, in 16-bit arithmetic, thus minimizing computational complexity, especially for low-end processors. By using short tables, the new quantization formulas use multiplications but avoid divisions.
Exploring the transcriptome ofluxI−andΔainSmutants and the impact of N-3-oxo-hexanoyl-L- and N-3-hydroxy-decanoyl-L-homoserine lactones on biofilm formation inAliivibrio salmonicida (2019)

These findings imply that the LuxI and AinS autoinducer synthases play a critical role in the regulation of biofilm formation, EPS production, and motility.
Total Synthesis of Fellutamide B and Deoxy-Fellutamides B, C, and D (2013)

The total syntheses of the marine-derived lipopeptide natural product fellutamide B and deoxy-fellutamides B, C, and D are reported. These compounds were accessed through a novel solid-phase synthetic strategy using Weinreb amide-derived resin. As part of the synthesis, a new enantioselective route to (3R)-hydroxy lauric acid was developed utilizing a Brown allylation reaction followed by an oxidative cleavage-oxidation sequence as the key steps. The activity of these natural products, and natural product analogues was also assessed against Mycobacterium tuberculosis in vitro.
Physics of self-aligned assembly at room temperature (2018)

Self-aligned assembly, making use of capillary forces, is considered as an alternative to active alignment during thermo-compression bonding of Si chips in the 3D heterogeneous integration process. Various process parameters affect the alignment accuracy of the chip over the patterned binding site on a substrate/carrier wafer. This paper discusses the chip motion due to wetting and capillary force using a transient coupled physics model for the two regimes (that is, wetting regime and damped oscillatory regime) in the temporal domain. Using the transient model, the effect of the volume of the liquid and the placement accuracy of the chip on the alignment force is studied. The capillary time (that is, the time it takes for the chip to reach its mean position) for the chip is directly proportional to the placement offset and inversely proportional to the viscosity. The time constant of the harmonic oscillations is directly proportional to the gap between the chips due to the volume of the fluid. The predicted behavior from transient simulations is next experimentally validated and it is confirmed that the liquid volume and the initial placement affect the final alignment accuracy of the top chip on the bottom substrate. With statistical experimental data, we demonstrate an alignment accuracy reaching &amp;lt;1 μm.
Gold–Palladium Bimetallic Catalyst Stability: Consequences for Hydrogen Peroxide Selectivity (2017)

During application, electrocatalysts are exposed to harsh electrochemical conditions, which can induce degradation. This work addresses the degradation of AuPd bimetallic catalysts used for the electrocatalytic production of hydrogen peroxide (H2O2) by the oxygen reduction reaction (ORR). Potential-dependent changes in the AuPd surface composition occur because the two metals have different dissolution onset potentials, resulting in catalyst dealloying. Using a scanning flow cell (SFC) with an inductively coupled plasma mass spectrometer (ICP-MS), simultaneous Pd and/or Au dissolution can be observed. Thereafter, three accelerated degradation protocols (ADPs), simulating different dissolution regimes, are employed to study the catalyst structure degradation on the nanoscale with identical location (IL) TEM. When only Pd or both Au and Pd dissolve, the composition changes rapidly and the surface becomes enriched with Au, as observed by cyclic voltammetry and elemental mapping. Such changes are mirrored by the evolution of electrocatalytic performances toward H2O2 production. Our experimental findings are finally summarized in a dissolution/structure/selectivity mechanism, providing a clear picture of the degradation of bimetallic catalyst used for H2O2 synthesis.
Cisplatin, bleomycin, and vinblastine combination therapy of testicular tumors: An analysis (1979)

A combination regimen consisting of cisplatin, bleomycin, and vinblastine was evaluated in 86 patients with metastatic testicular tumors. Prior therapy included surgical resection of primary tumor (84 patients), radiotheapy (21 patients), chemotherapy (33 patients). Thirteen patients received prior bleomycin and vincristine or vinblastine. Of 80 evaluable patients 51 achieved complete response (CR) and 26 achieved partial response (PR), for an overall response rate 96.5%. There was no significant difference in response rates or survival with respect to prior therapy, sites of metastatic lesions, and tumor histology. The median survival time was not reached in an observation period of 44+ months. Sixty patients were alive 11+--44+ months, and 57 of these were free of disease. Thirty-two of the 60 patients (53%) had a survival time greater than 20 months. Toxicities included nephrotoxicity (18 patients) leukopenia, (69 patients), thrombocytopenia (nine patients), and anemia (56 patients). Bleomycin-induced pulmonary toxicity was fatal in one patient. Other toxicities included nausea and vomiting, stomatitis, fever, alopecia, and neurological effects.
Microbial transformation of precocene II: oxidative reactions by Streptomyces griseus (1987)

Various species of "Streptomyces," "Aspergillus," "Rhodotorula," "Brevilegnia," "Syncephalastrum," and "Stysanus" were found to transform precocene II to three major metabolites. These major biotransformation products were isolated from a preparative-scale incubation of precocene II with Streptomyces griseus and were conclusively identified as (-)cis- and (+)trans-precocene II-3,4-dihydrodiols and (+)-3-chromenol. 18O2 incorporation studies indicated the involvement of a monooxygenase enzyme system in precocene II transformation by S. griseus. A mechanism is proposed for the formation of (+)-3-chromenol.
An All-Dielectric Polaritonic Metasurface with a Giant Nonlinear Optical Response (2022)

Enhancing the efficiency of second-harmonic generation using all-dielectric metasurfaces to date has mostly focused on electromagnetic engineering of optical modes in the meta-atom. Further advances in nonlinear conversion efficiencies can be gained by engineering the material nonlinearities at the nanoscale, however this cannot be achieved using conventional materials. Semiconductor heterostructures that support resonant nonlinearities using quantum engineered intersubband transitions can provide this new degree of freedom. By simultaneously optimizing the heterostructures and meta-atoms, we experimentally realize an all-dielectric polaritonic metasurface with a maximum second-harmonic generation power conversion factor of 0.5 mW/W<sup>2</sup> and power conversion efficiencies of 0.015% at nominal pump intensities of 11 kW/cm<sup>2</sup>. These conversion efficiencies are higher than the record values reported to date in all-dielectric nonlinear metasurfaces but with 3 orders of magnitude lower pump power. Our results therefore open a new direction for designing efficient nonlinear all-dielectric metasurfaces for new classical and quantum light sources.
Finite element analysis of the seismic shake‐table response of a rocking podium structure (2020)

Abstract Rocking podium structures consist of rocking columns supporting a platform to achieve kinematic seismic isolation of the superstructure above. This article presents detailed finite element (FE) analysis modeling and results of the benchmark rocking podium structure that was tested as part of a blind prediction contest organized by the Pacific Earthquake Engineering Research center (PEER) at UC Berkeley, the University of Bristol, and ETH Zurich in 2019. Details of the FE modeling approach, as well as a discussion on key results and findings of this study are outlined herein. It was found that the FE model of the rocking podium structure was not sensitive to the element type, mesh layout or maximum time step, while the choice of contact algorithm influences the stability of the predicted rocking behavior. Modeling of the friction interactions between the rocking interfaces also had a nontrivial influence on the dynamic rocking response as it represented the main source of energy dissipation in the system. Further, instead of assuming an arbitrary value for inherent damping which was deemed to be very low for such a structure, explicit modeling of the frictional dissipation mechanism at the column‐to‐podium interface was preferred in this study.
Exploring and Enhancing Conductivity in Semiconductor Nanoparticle Films (2007)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2007.
Multimodal Flow Visualization and Optimization of Pneumatic Blood Pump for Sorbent Hemodialysis System (2009)

Renal Solutions Allient Sorbent Hemodialysis System utilizes a two-chambered pneumatic pump (Pulsar Blood Pump, Renal Solutions, Inc., Warrendale, PA, USA) to avoid limitations associated with peristaltic pumping systems. Single-needle access is enabled by counter-pulsing the two pump chambers, thereby obviating compliance chambers or blood reservoirs. Each chamber propels 20 cc per pulse of 3 s (dual access) or 6 s (single access) duration, corresponding to a peak Reynolds number of approximately 8000 (based on inlet velocity and chamber diameter). A multimodal series of flow visualization studies (tracer particle, dye washout, and dye erosion) was conducted on a sequence of pump designs with varying port locations and diaphragms to improve the geometry with respect to risk of thrombogenesis. Experiments were conducted in a simplified flow loop using occluders to simulate flow resistance induced by tubing and dialyzer. Tracer visualization revealed flow patterns and qualitatively indicated turbulence intensity. Dye washout identified dwell volume and areas of flow stagnation for each design. Dye erosion results indicated the effectiveness and homogeneity of surface washing. Compared to a centered inlet which resulted in a fluid jet that produced two counter-rotating vortices, a tangential inlet introduced a single vortex, and kept the flow laminar. It also provided better surface washing on the pump inner surface. However, a tangential outlet did not present as much benefit as expected. On the contrary, it created a sharp defection to the flow when transiting from filling to ejection.
Evaluation of sFLT1 protein levels in human eyes with the FLT1 rs9943922 polymorphism (2017)

Based on these data, we conclude that the rs9943922 SNP in the FLT1 gene does not result in a large difference in FLT1 protein levels, regardless of whether it is the soluble or the membrane bound form.
Control of Alq3 Wetting Layer Thickness via Substrate Surface Functionalization (2007)

The effects of substrate surface energy and vapor deposition rate on the initial growth of porous columnar tris(8-hydroxyquinoline)aluminum (Alq3) nanostructures were investigated. Alq3 nanostructures thermally evaporated onto as-supplied Si substrates bearing an oxide were observed to form a solid wetting layer, likely caused by an interfacial energy mismatch between the substrate and Alq3. Wetting layer thickness control is important for potential optoelectronic applications. A dramatic decrease in wetting layer thickness was achieved by depositing Alq3 onto alkyltrichlorosilane-derivatized Si/oxide substrates. Similar effects were noted with increasing deposition rates. These two effects enable tailoring of the wetting layer thickness.
The KEGG resource for deciphering the genome (2003)

A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.
An analytical model of the induction machine for the development of diagnostic techniques (2011)

In the technical literature many models capable of representing the behavior of the induction machine have been presented. The traditional Park model is very easy to be implemented but it does not take into account the flux density space harmonics. It is well known that it can be modified in order to consider stator and rotor asymmetries. However for some applications such as the study and the development of diagnostic techniques the results are not accurate enough. More detailed models have been presented; many of them are based on the winding function approach. They are suitable to represent the behavior of the machine under faulty conditions, since they take into account the effect of the eccentricity, the bar skewing, the magnetic saturation and the electrical asymmetries. All of them are very complex and their employment implies a huge computational burden. In this paper the authors propose a new accurate model based on the winding functions which is capable of representing any kind of stator and rotor asymmetry; air gap eccentricity and magnetic saturation have been neglected. Under these hypotheses it will be shown how all of the inductances can be calculated analytically: this dramatically reduces the requirements in terms of computational power. Some numerical results obtained with the presented model will be shown.
Displacement monitoring system based on a quadrature self-injection-locked radar technology (2017)

This paper presents a quadrature self-injection-locked (SIL) radar to detect the displacement of a moving target. Owing to the quadrature phase-switching architecture and corresponding digital signal processing techniques, this proposed system is capable of achieving excellent detection sensitivity and determining the target's Doppler phase shift without being affected by nonlinear distortion caused by the SIL phenomenon. In the experiment, a metal plate is driven by a laptop-controlled linear stage, and a 2.4-GHz ISM-band prototype is placed 1.25 m away from the target to detect its motion. As a result, the measured error is less than 3 mm for the moving plate with a peak-to-peak displacement up to 5 cm.
Effect of Film Thickness on the Annealing Texture in Sputtered and Electroplated Cu Films (2006)

For optimum fabrication and usage of Cu films, an understanding of the relationship between processing and microstructure is required. The existence of twins is another significant factor for texture development in Cu films. Texture character and strength in the Cu film is dependent on the twin boundary development that is a function of processing conditions and film thickness. In this study, determination of grain growth and texture in the sputtered and electroplated Cu films during annealing was performed for films of 100, 480 and 850 nm in thickness deposited on a Ta(25 nm)/Si wafer. The texture was measured by X-ray pole figure. The effect of film thickness on the annealing texture in the sputtered and electroplated Cu films is examined and discussed.
Abstract 1703: Discovery and validation of 20 novel breast cancer methylation biomarkers: A new workflow for methylation biomarker development (2012)

Abstract Methylation is a process of regulation of gene expression. Methylation pattern changes are implicated in the pathology of cancer and other disorders but at the same time they can be used as biomarkers for clinical disease management. There are four primary fields of use for biomarkers in clinical disease management: diagnosis, prognosis/prediction, prevention, pharmacoepigenomics. Methylation biomarkers have already been shown to fulfill the requirements of each of the above categories. Therefore, a lot of research in the field is currently focused on discovery and validation of methylation biomarkers for clinical use. The process of biomarker development can be subdivided into five steps workflow: discovery of the biomarker, initial clinical biomarker validation, retrospective biomarker validation, prospective validation and the use of the marker in clinical practice. Following the above workflow, we have combined the Roche/NimbleGen Methylation arrays and Methylation Sensitive High Resolution Melting (MS-HRM) (ref: 1, 2), into one platform for methylation biomarker development and validation. Our approach allowed us, firstly to discover 20 novel loci undergoing aberrant methylation during breast cancer development. Subsequently the biomarkers were subjected to initial clinical validation. This procedure aimed to evaluate to what extent the biomarkers can distinguish 274 breast tumor samples (disease) from 78 breast normal tissue samples (healthy). Our results show that the specificity of almost all of the novel biomarkers except for one was above 80%, with four of these showing hypermethylation only in tumor tissue, which corresponds to 100% specificity. The odds ratio (OR, interpreted as the probability with which our new biomarker can distinguish a tumor sample from a non-malignant sample) for our novel biomarkers was in the extraordinary range from 4(2; 7) to 563(166; 1902), Overall our results clearly illustrate the exceptional accuracy of the chosen approach for methylation biomarker discovery and development. All the biomarkers that successfully completed initial clinical validation are now undergoing retrospective validation (see above) based on almost 1200 archival breast cancer samples with detailed clinical follow up. This procedure will allow investigating the clinical management field of use for each of the novel biomarkers. References: 1. Wojdacz, T.K., Dobrovic, A. &amp; Hansen, L.L. Methylation-sensitive high-resolution melting. Nature Protocols 3 (2008). 2. Wojdacz, T.K. &amp; Dobrovic, A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 35, e41 (2007). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1703. doi:1538-7445.AM2012-1703
Query portals (2010)

Many web queries seek information about named entities (such as products or people). Web search engines federate such entity-oriented queries to relevant structured databases; the results of those searches are then returned to the user along with web search results. Current federated approaches have two limitations: (i) they often fail to return important results for a broad class of such entity-oriented queries and (ii) the information they return per entity is often inadequate. In this paper, we present the Query Portals system that addresses these limitations. The Query Portals system dynamically generates a portal for an entity-oriented query. It first provides an overview of the relevant entities and further allows users to drill down to gather additional information on these entities. Our architecture uses a judicious combination of pre-processing and query time techniques so that the query portal can be generated efficiently.
Side-Chain Effects on the Conductivity, Morphology, and Thermoelectric Properties of Self-Doped Narrow-Band-Gap Conjugated Polyelectrolytes (2014)

This contribution reports a series of anionic narrow-band-gap self-doped conjugated polyelectrolytes (CPEs) with π-conjugated cyclopenta-[2,1-b;3,4-b']-dithiophene-alt-4,7-(2,1,3-benzothiadiazole) backbones, but with different counterions (Na(+), K(+), vs tetrabutylammonium) and lengths of alkyl chains (C4 vs C3). These materials were doped to provide air-stable, water-soluble conductive materials. Solid-state electrical conductivity, thermopower, and thermal conductivity were measured and compared. CPEs with smaller counterions and shorter side chains exhibit higher doping levels and form more ordered films. The smallest countercation (Na(+)) provides thin films with higher electrical conductivity, but a comparable thermopower, compared to those with larger counterions, thereby leading to a higher power factor. Chemical modifications of the pendant side chains do not influence out of plane thermal conductivity. These studies introduce a novel approach to understand thermoelectric performance by structural modifications.
Highly Ordered Mesostructured Vanadium Phosphonate toward Electrode Materials for Lithium‐Ion Batteries (2017)

Highly ordered mesostructured vanadium phosphonates (VP) have been synthesized in the presence of cetyltrimethylammonium bromide (CTAB) as a structure-directing agent. Nitrilotris(methylene)triphosphonic acid (NMPA) and (ammonium/sodium) metavanadate (NH<sub>4</sub> VO<sub>3</sub> /NaVO<sub>3</sub> ) have been used for the construction of pore walls. The CTAB templates are removed from the materials by an extraction process without destroying the parent mesostructure. The formation mechanism for the ordered mesoporous structure and its impact on electrochemical application in lithium ion batteries (LIBs) are explained by considering the structural and electrochemical stability of the framework. The results demonstrate that the counter cations (NH<sub>4</sub><sup>+</sup> /Na<sup>+</sup> ) of the metavanadate precursors have a crucial role in stabilizing the mesoporous structure of the mesoporous VP materials. Mesoporous VP materials with highly ordered structure have great applicability as high-performance electrode materials in LIBs due to the advantages of their large contact area with electrolyte and short transport paths for lithium ions. Mesoporous VP electrodes exhibit high reversible specific capacity with superb cycling stability (100 cycles) and excellent retention of capacity (92 %).