gebhart/patrepeval huggingface dataset:
A System for Coordinated Network-wide Redundancy Elimination (2008)

Motivation: Today, an increasing number of end-networks are deploying redundancy elimination (RE) solutions to improve their WAN performance. The success of such deploymentshasmotivatedresearchers,equipmentvendors(e.g.,Cisco, Riverbed) and ISPs to explore the potential of network-wide RE. Recent work [1] has shown the benefits of supporting RE as a primitive IP-layer service on network routers. In similar vein, network equipment vendors have highlighted the network-wide support for content caching as a key focus area. Supporting RE at the network-level socializes the benefits of RE to all end-to-end flows and also allows ISPs to better handle bandwidth-intensive workloads. While the problemof RE has been well studied in the context of point deployments(e.g. over a single WAN link of an enterprise network), there has been relatively little work on how to best design network-wide RE deployments. Extending such single vantage point solutions to the network-wide case, as proposed by Anand et. al [1], does not take into account the resource constraints on RE devices. This severely constrainsthe benefits that end applicationsand ISPs can derive from network-wide RE. In this work, we explore how to build effective and practical network-wide RE systems. We present Decor, a coordinated system-wide architecture for in-network RE. Decor allows packets to be decoded at routers multiple hops away from the routerwhere packet was encoded. This allows us to utilize resources from different routers for decoding. Decor takes into account the ISP’s objectives (e.g., network-wide footprint reduction) and the resource constraints of different RE devices, to optimally allocate caching and decoding responsiblities. While our current focus has primarily been on RE in ISPs, our design can be more broadly applied to data-center and multi-hop wireless networks. Design and Implementation: We focus our design on three key elements: ingress, interior nodes and a central configuration model (Figure 1). Ingress nodes encode packets with respect to earlier seen packets in the cache. Interior routers lookup their cache to decode the encoded packet. We leverage ideas from cSamp [2] to split the caching responsibilities for interior routers in terms of hash-range per path per router. Each interior router is responsible for caching those packets whose header’s hash falls in the assigned range for the path. This information is specified by a caching manifest produced by the central configuration module. The central
Direct Pharmacological Inhibition of β-Catenin by RNA Interference in Tumors of Diverse Origin (2016)

The Wnt/β-catenin pathway is among the most frequently altered signaling networks in human cancers. Despite decades of preclinical and clinical research, efficient therapeutic targeting of Wnt/β-catenin has been elusive. RNA interference (RNAi) technology silences genes at the mRNA level and therefore can be applied to previously undruggable targets. Lipid nanoparticles (LNP) represent an elegant solution for the delivery of RNAi-triggering oligonucleotides to disease-relevant tissues, but have been mostly restricted to applications in the liver. In this study, we systematically tuned the composition of a prototype LNP to enable tumor-selective delivery of a Dicer-substrate siRNA (DsiRNA) targeting CTNNB1, the gene encoding β-catenin. This formulation, termed EnCore-R, demonstrated pharmacodynamic activity in subcutaneous human tumor xenografts, orthotopic patient-derived xenograft (PDX) tumors, disseminated hematopoietic tumors, genetically induced primary liver tumors, metastatic colorectal tumors, and murine metastatic melanoma. DsiRNA delivery was homogeneous in tumor sections, selective over normal liver and independent of apolipoprotein-E binding. Significant tumor growth inhibition was achieved in Wnt-dependent colorectal and hepatocellular carcinoma models, but not in Wnt-independent tumors. Finally, no evidence of accelerated blood clearance or sustained liver transaminase elevation was observed after repeated dosing in nonhuman primates. These data support further investigation to gain mechanistic insight, optimize dose regimens, and identify efficacious combinations with standard-of-care therapeutics. Mol Cancer Ther; 15(9); 2143-54. ©2016 AACR.
Notch3<sup>ECD</sup> immunotherapy improves cerebrovascular responses in CADASIL mice (2018)

This study establishes immunotherapy targeting Notch3<sup>ECD</sup> as a new avenue for disease-modifying treatment in CADASIL that warrants further development. Ann Neurol 2018;84:246-259.
<title>Silicon nitride membranes for filtration and separation</title> (1999)

Semi-Permeable silicon nitride membranes have been developed using a Bosch etch process followed by a reactive ion etch process. These membranes were observed to allow air but not water to pass through them into surface micromachined, silicon nitride microfluidic channels. Membranes with this property have potential use in microfluidic systems as gas bubble traps and vents, filters to remove particles and gas partitioning membranes. Membrane permeation was measured as 1.6 X 10<SUP>-8</SUP> mol/m<SUP>2</SUP>Pa s of helium for inline membranes at the entrance and exit of the silicon nitride microfluidic channels.
Stereochemical specificity of Alzheimer's disease ?-peptide assembly (1999)

The formation and growth of insoluble amyloid deposits composed primarily of the human beta-amyloid peptide (A beta) in brain is an essentially invariant feature of Alzheimer's disease (AD) and is widely believed to contribute to the progressive neurodegeneration of the disorder. To probe the specificity of amyloid formation and growth, we synthesized and examined the self-assembly of D- and L-stereoisomers of A beta in vitro. While both enantiomers formed insoluble aggregates at similar rates with amyloid-like fibrillar morphology, deposition of soluble A beta peptide onto preexisting A beta aggregates was stereospecific. Although the L-peptide deposited readily onto immobilized L-A beta aggregates with first-order kinetic dependence on soluble peptide concentration, essentially no association between the D-peptide and L-template was observed. Similarly, the D-peptide deposited with first-order kinetics onto a D-A beta aggregate template but did not deposit onto a similar template composed of aggregates of the L-enantiomer. Furthermore, although the L-A beta isomer deposited onto authentic AD amyloid in preparations of unfixed AD brain, no focal association between the D-peptide and brain amyloid was detected. These results establish that deposition of soluble A beta onto preexisting amyloid template is stereospecific, likely involving direct docking interactions between peptide backbone and/or side chains rather than simple hydrophobic association.
Primo: Programmable Real-Time Incoherent Matrix Multiplier For Optical Processing (1987)

An optical matrix processing system based on an edge-addressed electro-optic modulator can perform matrix-matrix multiplications, correlations, convolutions, cross ambiguity functions, and matrix inversions. Architectures have been developed for handling bipolar and complex data, as well as for the compensation of square-law detection nonlinearities.
Ultraviolet micro-Raman spectrograph for the detection of small numbers of bacterial cells (1993)

The construction of a practical UV micro-Raman spectrograph capable of selective excitation of bacterial cells and other microscopic samples has been described. A reflective objective is used to focus cw laser light on a sample and at the same time collect the scattered light at 180°. With the aid of a quartz lens the image produced is focused on the slits of a spectrograph equipped with a single 2400 grooves/mm grating optimized for 250 nm. Spectra were detected by means of a blue-intensified diode array detector. Resonance Raman spectra of Bacillus subtilis and Flavobacterium capsulatum excited by the 257.2 nm output of a cw laser were recorded in the 900–1800 cm−1 region. Bacterial cells were immobilized on a quartz plate by means of polylysine and were counted visually. Cooling was required to retard sample degradation. Sample sizes ranged from 1 to 50 cells with excitation times varying from 15 to 180 s. Excellent spectra have been obtained from 20 cells in 15 s using a spectrograph having only 3% throughput.
Statistical artifacts in diffusion tensor MRI (DT-MRI) caused by background noise (2000)

This work helps elucidate how background noise introduces statistical artifacts in the distribution of the sorted eigenvalues and eigenvectors in diffusion tensor MRI (DT-MRI) data. Although it was known that sorting eigenvalues (principal diffusivities) by magnitude introduces a bias in their sample mean within a homogeneous region of interest (ROI), here it is shown that magnitude sorting also introduces a significant bias in the variance of the sample mean eigenvalues. New methods are presented to calculate the mean and variance of the eigenvectors of the diffusion tensor, based on a dyadic tensor representation of eigenvalue-eigenvector pairs. Based on their use it is shown that sorting eigenvalues by magnitude also introduces a bias in the mean and the variance of the sample eigenvectors (principal directions). This required the development of new methods to calculate the mean and variance of the eigenvectors of the diffusion tensor, based on a dyadic tensor representation of eigenvalue-eigenvector pairs. Moreover, a new approach is proposed to order these pairs within an ROI. To do this, a correspondence between each principal axis of the diffusion ellipsoid, an eigenvalue-eigenvector pair, and a dyadic tensor constructed from it is exploited. A measure of overlap between principal axes of diffusion ellipsoids in different voxels is defined that employs projections between these dyadic tensors. The optimal eigenvalue assignment within an ROI maximizes this overlap. Bias in the estimate of the mean and of the variance of the eigenvalues and of their corresponding eigenvectors is reduced in DT-MRI experiments and in Monte Carlo simulations of such experiments. Improvement is most significant in isotropic regions, but some is also observed in anisotropic regions. This statistical framework should enhance our ability to characterize microstructure and architecture of healthy tissue, and help to assess its changes in development, disease, and degeneration. Mitigating these artifacts should also improve the characterization of diffusion anisotropy and the elucidation of fiber-tract trajectories in the brain and in other fibrous tissues. Magn Reson Med 44:41-50, 2000. Published 2000 Wiley-Liss, Inc.
The first committed step reaction of caffeine biosynthesis: 7‐methylxanthosine synthase is closely homologous to caffeine synthases in coffee (<i>Coffea arabica</i> L.)<sup>1</sup> (2003)

In coffee and tea plants, caffeine is synthesized from xanthosine via a pathway that has three methylation steps. We identified and characterized the gene encoding the enzyme for the first methylation step of caffeine biosynthesis. The full-length cDNA of coffee tentative caffeine synthase 1, CtCS1, previously isolated by the rapid amplification of cDNA ends was translated with an Escherichia coli expression system and the resultant recombinant protein was purified using Ni-NTA column. The protein renamed CmXRS1 has 7-methylxanthine synthase (xanthosine:S-adenosyl-L-methionine methyltransferase) activity. CmXRS1 was specific for xanthosine and xanthosine 5'-monophosphate (XMP) could not be used as a substrate. The K(m) value for xanthosine was 73.7 microM. CmXRS1 is homologous to coffee genes encoding enzymes for the second and third methylation steps of caffeine biosynthesis.
A Versatile Chemoenzymatic Synthesis for the Discovery of Potent Cryptophycin Analogs (2020)

The cryptophycins are a family of macrocyclic depsipeptide natural products that display exceptionally potent antiproliferative activity against drug-resistant cancers. Unique challenges facing the synthesis and derivatization of this complex group of molecules motivated us to investigate a chemoenzymatic synthesis designed to access new analogs for biological evaluation. The cryptophycin thioesterase (CrpTE) and the cryptophycin epoxidase (CrpE) are a versatile set of enzymes that catalyze macrocyclization and epoxidation of over 20 natural cryptophycin metabolites. Thus, we envisioned a drug development strategy involving their use as standalone biocatalysts for production of unnatural derivatives. Herein, we developed a scalable synthesis of 12 new unit A-B-C-D linear chain elongation intermediates containing heterocyclic aromatic groups as alternatives to the native unit A benzyl group. <i>N</i>-Acetyl cysteamine activated forms of each intermediate were assessed for conversion to macrocyclic products using wild type CrpTE, which demonstrated the exceptional flexibility of this enzyme. Semipreparative scale reactions were conducted for isolation and structural characterization of new cryptophycins. Each was then evaluated as a substrate for CrpE P450 and its ability to generate the epoxidized products from these substrates that possess altered electronics at the unit A styrenyl double bond position. Finally, biological evaluation of the new cryptophycins revealed a des-β-epoxy analog with low picomolar potency, previously limited to cryptophycins bearing epoxide functionality.
The effects of supplementing growing-finishing pig diets with carnitine and(or) chromium on growth and carcass characteristics (1996)

Eighty crossbred gilts (initially 83 lb) were used to examine the effects of 50 ppm carnitine and(or) 200 ppb chromium from chromium nicotinate on growth performance and carcass characteristics. In this trial, adding carnitine and(or) chromiunm to the diets of high-lean growth finishing gilts did not increase carcass leanness. However, the combination of carnitine and chromium improved the color characteristics of the longissimus muscle.; Swine Day, Manhattan, KS, November 21, 1996
Electrical Switching and Memory Phenomena in Semiconducting Organic Thin Films (1982)

Switching and Memory Device: Materials and Fabrication This paper is a report on stable and reproducible current-controlled bistable electrical switching and memory phenomena observed in polycrystalline metal-organic semiconducting films. The effects are observed in films of either copper or silver complexed with the electron acceptors tetracyanoethylene (TCNE), tetracyanonapthoquinodimethane (TNAP), tetracyanoquinodimethane (TCNQ), (1) or other TCNQ derivatives shown below. The character of the switching in going from a high- to a low-impedance state in these organic charge-transfer complexes is believed to be comparable in many respects to existing inorganic materials. The basic configuration of the device, shown in Figure 1, consists of a 5-10 µm thick polycrystalline aggregate of a copper or a silver charge-transfer complex sandwiched between two metal electrodes. Electrical connection is made to the two metal electrodes through silver conducting paste or through liquid metals of mercury gallium or gallium-indium eutectic. Fabrication of the device consists of first
Shell texture functions (2004)

We propose a texture function for realistic modeling and efficient rendering of materials that exhibit surface mesostructures, translucency and volumetric texture variations. The appearance of such complex materials for dynamic lighting and viewing directions is expensive to calculate and requires an impractical amount of storage to precompute. To handle this problem, our method models an object as a shell layer, formed by texture synthesis of a volumetric material sample, and a homogeneous inner core. To facilitate computation of surface radiance from the shell layer, we introduce the shell texture function (STF) which describes voxel irradiance fields based on precomputed fine-level light interactions such as shadowing by surface mesostructures and scattering of photons inside the object. Together with a diffusion approximation of homogeneous inner core radiance, the STF leads to fast and detailed raytraced renderings of complex materials.
Postmortem Object Type Identification (2003)

This paper presents a novel technique for the automatic type identification of arbitrary memory objects from a memory dump. Our motivating application is debugging memory corruption problems in optimized, production systems -- a problem domain largely unserved by extant methodologies. We describe our algorithm as applicable to any typed language, and we discuss it with respect to the formidable obstacles posed by C. We describe the heuristics that we have developed to overcome these difficulties and achieve effective type identification on C-based systems. We further describe the implementation of our heuristics on one C-based system -- the Solaris operating system kernel -- and describe the extensions that we have added to the Solaris postmortem debugger to allow for postmortem type identification. We show that our implementation yields a sufficiently high rate of type identification to be useful for debugging memory corruption problems. Finally, we discuss some of the novel automated debugging mechanisms that can be layered upon postmortem type identification.
Robust Visual Person Tracking for Interactive Displays (1998)

We present an approach to real-time person tracking in crowded and/or unknown environments using integration of multiple visual modalities. We combine stereo, color, and face detection modules into a single robust system, and show an initial application in an interactive, face-responsive display. Dense, real-time stereo processing is used to isolate users from other objects and people in the background. Skin-hue classification identifies and tracks likely body parts within the silhouette of a user. Face pattern detection discriminates and localizes the face within the identified body parts. Faces and bodies of users are tracked over several temporal scales: short-term (user stays within the field of view), medium-term (user exits/reenters within minutes), and long term (user returns after hours or days). Short-term tracking is performed using simple region position and size correspondences, while medium and long-term tracking are based on statistics of user appearance.
Continuous flow synthesis of amine oxides by oxidation of tertiary amines (2019)

An efficient, safe and scalable continuous flow process for the synthesis of amine oxides with hydrogen peroxide is described.
The Carver-Greenfield Process{reg_sign}: Resource recovery system for wet, oily wastes (1994)

A combination dehydration/solvent extraction treatment technology, the patented Carver-Greenfield (C-G) Process, can be used to separate wet, oily solid-liquid waste materials into three separate product streams convenient for resource recovery or other disposition: (1) clean, dry solids suitable for fixation or non-hazardous landfilling; (2) water virtually free of solids and oils which can be processed in an industrial or public wastewater treatment facility or which can be returned to the land with the solids; and (3) oil indigenous to the feed, a mixture of extracted hydrocarbon-soluble compounds suitable for resource recovery via recycle to an oil refinery or other processing facility. Hazardous contaminants, e.g. PCBs, in the indigenous oil may be isolated in a small, volume reduced stream for more economic disposal. This paper discusses the C-G Process application flexibilities for resource recovery from oil refinery wastes, sites contaminated with residual coal tars, spent drilling fluids (US EPA SITE Program), as well as to various wet and oily hazardous soil and sludge wastes containing PCB`s and similar ``trace component`` hazardous materials.
Data-center, metro and long-haul applications based on advanced photonic integrated circuits (2015)

We present data for long-haul, metro, and data-center applications using large scale Photonic Integrated Circuits (PICs) packaged in high capacity optical modules.
Assessment of non-native speech using vowel space characteristics (2010)

In this paper, we propose the idea of using the characteristics of a speaker's vowel space for automated assessment of second language (L2) pronunciation. Specifically, we adopt features that were shown in previous studies to be good indicators of native speaker intelligibility and clarity and apply them to L2 speech from non-native speakers. The features focus on three peripheral vowels (IY, AA, and OW) and measure a speaker's coverage of the vowel space. A pilot study and a large-scale corpus study involving read speech produced by native and non-native speakers were conducted in which the vowel space features were rank correlated with pronunciation scores provided by human listeners for the non-native speech and an assumed higher score for the native speech. The results of the studies show that several of the features achieve moderately high correlations with the pronunciation scores, supporting their usefulness for automated assessment of non-native speech. The feature with the best performance in the large-scale study was the F2 - F1 distance for IY, which achieved a correlation of 0.78 with pronunciation proficiency scores.
Video And Audio Disk File System (1985)

A new disk format and a new recorder were developed, based on the still picture disk file system which was put on the market a few years ago, whereby a video disk system that permits concurrent continuous recording of video and audio signals has been developed. In order to achieve a prolonged. recording time, the disk track pitch was narrowed from the conventional 2.5 μm to 1.6 μm and a contrivance was also made circuit-wise to eliminate the resulting cross talk interference. Because of these innovations, 13.3 minutes (24,000 frames) of continuous recording is now realized on a disk 20 cm in diameter. For a continuous recording of sound signals, a continuous track is necessary. To solve this problem, a spiral track was developed in lieu of the conventional concentric track. To indicate addresses, this track is locally interrupted. Such interruptions would normally interfere with sound recording but such interferences could be prevented by selecting the optimum relation between, the length of interruptions and the sound carrier frequency.
Chrysophaentins A−H, Antibacterial Bisdiarylbutene Macrocycles That Inhibit the Bacterial Cell Division Protein FtsZ (2010)

Eight new antimicrobial natural products named chrysophaentins A-H belonging to a new structural class have been isolated from the marine chrysophyte alga Chrysophaeum taylori. Their structures were determined by extensive 2D NMR and MS techniques and are characterized by the presence of two polyhalogenated, polyoxygenated omega,omega'-diarylbutene units connected by two ether bonds to form the suite of macrocyclic natural products. Chrysophaentin A, the most potent of these antibiotics, inhibited the growth of clinically relevant Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MIC(50) 1.5 +/- 0.7 microg/mL), multidrug-resistant S. aureus (1.3 +/- 0.4 microg/mL), and vancomycin-resistant Enterococcus faecium (MIC(50) 2.9 +/- 0.8 microg/mL). In vitro enzyme assays and transmission electron microscopy showed chrysophaentin A to inhibit the GTPase activity of the bacterial cytoskeletal protein FtsZ with an IC(50) value of 6.7 +/- 1.7 microg/mL, as well as GTP-induced formation of FtsZ protofilaments. Saturation Transfer Difference (STD) NMR experiments further confirmed chrysophaentin A binds to FtsZ, and NMR competition experiments with GTPgammaS showed chrysophaentin A and GTP to bind competitively to FtsZ. Last, molecular docking simulations provided a low energy model in which chrysophaentin A binds in and occludes a large portion of the GTP binding site of FtsZ in a manner that is consistent with the binding epitope determined by STD NMR.