gebhart/patrepeval huggingface dataset:
WRPN: Wide Reduced-Precision Networks (2018)

For computer vision applications, prior works have shown the efficacy of reducing numeric precision of model parameters (network weights) in deep neural networks. Activation maps, however, occupy a large memory footprint during both the training and inference step when using mini-batches of inputs. One way to reduce this large memory footprint is to reduce the precision of activations. However, past works have shown that reducing the precision of activations hurts model accuracy. We study schemes to train networks from scratch using reduced-precision activations without hurting accuracy. We reduce the precision of activation maps (along with model parameters) and increase the number of filter maps in a layer, and find that this scheme matches or surpasses the accuracy of the baseline full-precision network. As a result, one can significantly improve the execution efficiency (e.g. reduce dynamic memory footprint, memory bandwidth and computational energy) and speed up the training and inference process with appropriate hardware support. We call our scheme WRPN - wide reduced-precision networks. We report results and show that WRPN scheme is better than previously reported accuracies on ILSVRC-12 dataset while being computationally less expensive compared to previously reported reduced-precision networks.
Designing and Slicing Heterogeneous Components for Rapid Prototyping 428 (2000)

Many rapid prototyping techniques have the potential for fabricating components whose composition is non-uniform and varies in a desired fashion. A shape and composition modeling technique was developed to enable the representation and design of such heterogeneous components. Techniques for interactively and automatically designing such components are presented. Automatic design is made possible using optimization techniques where the optimal composition distribution is computed based on specified design objective and constraints. Software was also developed to slice 3D heterogeneous solids to generate cross-sectional images as well as composition distribution for each cross-section. Slicing and generation of cross-sectional data are essential to enable rapid prototyping of these components.
Structure, Function and Dynamics in Adenovirus Maturation (2014)

Here we review the current knowledge on maturation of adenovirus, a non-enveloped icosahedral eukaryotic virus. The adenovirus dsDNA genome fills the capsid in complex with a large amount of histone-like viral proteins, forming the core. Maturation involves proteolytic cleavage of several capsid and core precursor proteins by the viral protease (AVP). AVP uses a peptide cleaved from one of its targets as a "molecular sled" to slide on the viral genome and reach its substrates, in a remarkable example of one-dimensional chemistry. Immature adenovirus containing the precursor proteins lacks infectivity because of its inability to uncoat. The immature core is more compact and stable than the mature one, due to the condensing action of unprocessed core polypeptides; shell precursors underpin the vertex region and the connections between capsid and core. Maturation makes the virion metastable, priming it for stepwise uncoating by facilitating vertex release and loosening the condensed genome and its attachment to the icosahedral shell. The packaging scaffold protein L1 52/55k is also a substrate for AVP. Proteolytic processing of L1 52/55k disrupts its interactions with other virion components, providing a mechanism for its removal during maturation. Finally, possible roles for maturation of the terminal protein are discussed.
Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory (2017)

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.
Vitronectin Regulation of Vascular Endothelial Growth Factor-Mediated Angiogenesis (2014)

These results underscore the importance of VN in the regulation of angiogenesis induced by VEGF.
Trafficking and Subcellular Localization of Multiwalled Carbon Nanotubes in Plant Cells (2010)

Major barriers to delivery of biomolecules are crossing the cellular membranes and achieving a high cytoplasmic concentration by circumventing entrapment into endosomes and other lytic organelles. Motivated by such aim, we have investigated the capability of multiwalled carbon nanotubes (MWCNTs) to penetrate the cell membrane of plant protoplasts (plant cells made devoid of their cell walls via enzymatic treatment) and studied their internalization mechanism via confocal imaging and TEM techniques. Our results indentified an endosome-escaping uptake mode of MWCNTs by plant protoplasts. Moreover, short MWCNTs (<100 nm) were observed to target specific cellular substructures including the nucleus, plastids, and vacuoles. These findings are expected to have a significant impact on plant cell biology and transformation technologies.
FDQM: Fast Quality Metric for Depth Maps Without View Synthesis (2014)

We propose a fast quality metric for depth maps, called fast depth quality metric (FDQM), which efficiently evaluates the impacts of depth map errors on the qualities of synthesized intermediate views in multiview video plus depth applications. In other words, the proposed FDQM assesses view synthesis distortions in the depth map domain, without performing the actual view synthesis. First, we estimate the distortions at pixel positions, which are specified by reference disparities and distorted disparities, respectively. Then, we integrate those pixel-wise distortions into an FDQM score by employing a spatial pooling scheme, which considers occlusion effects and the characteristics of human visual attention. As a benchmark of depth map quality assessment, we perform a subjective evaluation test for intermediate views, which are synthesized from compressed depth maps at various bitrates. We compare the subjective results with objective metric scores. Experimental results demonstrate that the proposed FDQM yields highly correlated scores to the subjective ones. Moreover, FDQM requires at least 10 times less computations than conventional quality metrics, since it does not perform the actual view synthesis.
The World’s Technological Capacity to Store, Communicate, and Compute Information (2011)

We estimated the world's technological capacity to store, communicate, and compute information, tracking 60 analog and digital technologies during the period from 1986 to 2007. In 2007, humankind was able to store 2.9 × 10(20) optimally compressed bytes, communicate almost 2 × 10(21) bytes, and carry out 6.4 × 10(18) instructions per second on general-purpose computers. General-purpose computing capacity grew at an annual rate of 58%. The world's capacity for bidirectional telecommunication grew at 28% per year, closely followed by the increase in globally stored information (23%). Humankind's capacity for unidirectional information diffusion through broadcasting channels has experienced comparatively modest annual growth (6%). Telecommunication has been dominated by digital technologies since 1990 (99.9% in digital format in 2007), and the majority of our technological memory has been in digital format since the early 2000s (94% digital in 2007).
Biotransformation of tolterodine, a new muscarinic receptor antagonist, in mice, rats, and dogs. (1998)

Tolterodine is a new muscarinic receptor antagonist intended for the treatment of urinary urge incontinence and other symptoms associated with an overactive bladder. The in vivo metabolism of 14C-labeled tolterodine was investigated in rats, mice, and dogs by analysis of blood and urine samples, whereas in vitro metabolism studies were performed by incubation of [14C]tolterodine with mouse, rat, dog, and human liver microsomes in the presence of NADPH. Tolterodine was extensively metabolized in vivo. Mice and dogs showed similar metabolite patterns, which correlated well with that observed in humans. In these species, tolterodine was metabolized along two different pathways, with the more important being the stepwise oxidation of the 5-methyl group to yield the 5-hydroxymethyl metabolite of tolterodine and then, via the aldehyde, the 5-carboxylic acid metabolite. The other pathway involved dealkylation of the nitrogen. In the subsequent phase II metabolism, tolterodine and the metabolites were conjugated with glucuronic acid to various degrees. Rats exhibited more extensive metabolism and a markedly different metabolite pattern, with metabolites also being formed by hydroxylation of the unsubstituted benzene ring. In addition, a gender difference was observed, with male rats showing more extensive metabolism than females. Incubation of [14C]tolterodine with liver microsomes yielded a total of five metabolites with rat liver microsomes and three with mouse, dog, and human liver microsomes. The 5-hydroxymethyl metabolite of tolterodine and N-dealkylated tolterodine were major metabolites in all incubations, representing 83-99% of total metabolism. Although the extent of metabolism varied among species, the metabolic profiles were similar. However, rat liver microsomes also formed metabolites hydroxylated in the unsubstituted benzene ring. These results show that the metabolism of tolterodine in mice and dogs corresponds to that observed in humans, whereas rats exhibit a different metabolite pattern.
Construction and Preliminary Characterization of a Series of Mouse and Rat Testis cDNA Libraries (1999)

We have constructed a series of 23 cDNA libraries from mouse and rat testicular cells. These include libraries made from whole, intact adult testes; seminiferous tubule cells from adult testes; combined populations of primary spermatocytes from 18-day-old mouse testes; and isolated populations of primitive type A spermatogonia, type A spermatogonia, type B spermatogonia, preleptotene spermatocytes, leptotene plus zygotene spermatocytes, juvenile pachytene spermatocytes, adult pachytene spermatocytes, round spermatids, Sertoli cells from 6-, 8-, 17-, and 18-20-day-old mice, and peritubular cells from 18-20 day old mice, all recovered from outbred white Swiss (CD-1) mice. We also constructed libraries from whole adult testes from five other lines of mice: C57 Bl6/J, C3 HEB, BDF-1, Balb/c, and 129 Sv. Finally, there are two libraries made from populations of Sertoli cells and peritubular cells isolated from testes of 20-day-old Sprague-Dawley rats. Enzymatic dissociation, followed by gradient separation or plating/lysing techniques, was used to prepare populations of specific cell types in purities of 85-98%. cDNAs were synthesized from poly A+ mRNA primed with oligo dT and unidirectionally cloned into the lambda Uni-Zap XR expression vector from Stratagene. Primary titers ranged from 2.1 x 10(5) to 2.9 x 10(8) plaque-forming units, and insert sizes averaged 1.0-1.2 kb. These libraries have been amplified once and submitted to the American Type Culture Collection (ATCC) for distribution to interested investigators. ATCC accession numbers are provided.
Advanced charged membranes with highly symmetric spongy structures for vanadium flow battery application (2013)

Advanced charged membranes with highly symmetric spongy structures were specially designed for vanadium flow batteries (VFBs). These membranes are formed with a unique stack of closed cells consisting of positively charged ultrathin walls and combine excellent V ion rejection with high proton conductivity. They achieve impressive VFB performance in a wide operation current density range, further promoting the development of much needed energy storage.
[The role of the kidneys in vitamin metabolism]. (2001)

It is well established that the kidney plays an essential role in regulating the homeostasis of body fluids. Recent studies provided evidence for the kidney to be an important organ for the regulation in the metabolism of both fat (vitamin A, D) and water soluble vitamins (e.g. vitamin B12). This regulation is mediated by glomerular filtration as well as reabsorption and secretion processes of protein-bound vitamins. Vitamin transport proteins such as retinol-binding protein, vitamin D-binding protein and transcobalamin II are filtered in renal glomeruli and subsequently reabsorbed in the proximal tubules by endocytosis from the tubular fluid. Megalin, a scavenger receptor belonging to the LDL receptor family, is probably the most important receptor in this process in the proximal tubule cells. The carrier proteins are degraded in lysosomes whereas the vitamins are probably stored, may become coupled to newly synthesized carriers and secreted at the basolateral plasma membrane. A renal vitamin excretion is observed in dogs and other species of the family Canidae, in form of fat soluble retinol and retinyl esters bound to Tamm-Horsfall protein. This and the high vitamin A concentrations in renal tissue of canines suggest an important role of the kidneys in vitamin A metabolism of these species.
<i>The Cellulase/Hemicellulase System of the Anaerobic Fungus</i><scp>Orpinomyces</scp><i>PC‐2 and Aspects of Its Applied Use</i> (2008)

Anaerobic fungi, first described in 1975 by Orpin, live in close contact with bacteria and other microorganisms in the rumen and caecum of herbivorous animals, where they digest ingested plant food. Seventeen distinct anaerobic fungi belonging to five different genera have been described. They have been found in at least 50 different herbivorous animals. Anaerobic fungi do not possess mitochondria, but instead have hydrogenosomes, which form hydrogen and carbon dioxide from pyruvate and malate during fermentation of carbohydrates. In addition, they are very oxygen- and temperature-sensitive, and their DNA has an unusually high AT content of from 72 to 87 mol%. My initial reason for studying anaerobic fungi was because they solubilize lignocellulose and produce all enzymes needed to efficiently hydrolyze cellulose and hemicelluloses. Although some of these enzymes are found free in the medium, most of them are associated with cellulosomal and polycellulosomal complexes, in which the enzymes are attached through fungal dockerins to scaffolding proteins; this is similar to what has been found for cellulosomes from anaerobic bacteria. Although cellulosomes from anaerobic fungi share many properties with cellulosomes of anaerobic cellulolytic bacteria and have comparable structures, their structures differ in their amino acid sequences. I discuss some features of the cellulosome of the anaerobic fungus Orpinomyces sp. PC-2 and some possible uses of its enzymes in industrial settings.
Anomaly Detection Using Persistent Homology (2016)

Many aspects of our daily lives now rely on computers, including communications, transportation, government, finance, medicine, and education. However, with increased dependence comes increased vulnerability. Therefore recognizing attacks quickly is critical. In this paper, we introduce a new anomaly detection algorithm based on persistent homology, a tool which computes summary statistics of a manifold. The idea is to represent a cyber network with a dynamic point cloud and compare the statistics over time. The robustness of persistent homology makes for a very strong comparison invariant.
Determination of pore-size distribution in low-dielectric thin films (2000)

Positronium annihilation lifetime spectroscopy is used to determine the pore-size distribution in low-dielectric thin films of mesoporous methylsilsesquioxane. A physical model of positronium trapping and annihilating in isolated pores is presented. The systematic dependence of the deduced pore-size distribution on pore shape/dimensionality and sample temperature is predicted using a simple quantum mechanical calculation of positronium annihilation in a rectangular pore. A comparison with an electron microscope image is presented.
Novel Gram-Scale Production of Enantiopure R-Sulforaphane from Tuscan Black Kale Seeds (2014)

Dietary R-sulforaphane is a highly potent inducer of the Keap1/Nrf2/ARE pathway. Furthermore, sulforaphane is currently being used in clinical trials to assess its effects against different tumour processes. This study reports an efficient preparation of enantiopure R-sulforaphane based on the enzymatic hydrolysis of its natural precursor glucoraphanin. As an alternative to broccoli seeds, we have exploited Tuscan black kale seeds as a suitable source for gram-scale production of glucoraphanin. The defatted seed meal contained 5.1% (w/w) of glucoraphanin that was first isolated through an anion exchange chromatographic process, and then purified by gel filtration. The availability of glucoraphanin (purity≈95%, weight basis) has allowed us to develop a novel simple hydrolytic process involving myrosinase (EC 3.2.1.147) in a biphasic system to directly produce R-sulforaphane. In a typical experiment, 1.09 g of enantiopure R-sulforaphane was obtained from 150 g of defatted Tuscan black kale seed meal.
Tritium Measurement Technique Using “In-Bed” Calorimetry (1992)

One of the new technologies that has been introduced to the Savannah River Site (SRS) is the production scale use of metal hydride technology to store, pump, and compress hydrogen isotopes. For tritium stored in metal hydride storage beds, a unique relationship does not exist between the amount of tritium in the bed and the pressure-volume-temperature properties of the hydride material. Determining the amount of tritium in a hydride bed after desorbing the contents of the bed to a tank and performing pressure, volume, temperature, and composition (PVTC) measurements is not practical due to long desorption/absorption times and the inability to remove tritium “heels” from the metal hydride materials under normal processing conditions. To eliminate the need to remove tritium from hydride storage beds for measurement purposes, an “in-bed” tritium calorimetric measurement technique has been developed. The steady-state temperature rise of a gas stream flowing through a jacketed metal hydride storage bed is measured and correlated with power input to electric heaters used to simulate the radiolytic power generated by the decay of tritium to 3He. Temperature rise results for prototype metal hydride storage beds and the effects of using different gases in the bed are shown. Linear regression results shows that for 95% confidence intervals, temperature rise measurements can be obtained in 14 hours and have an accuracy of ± 1.6% of a tritium filled hydride storage bed.
REVIEW—Transformation Toughening in Ceramics: Martensitic Transformations in Crack‐Tip Stress Fields (1980)

The toughness of ceramics can be substantially enhanced by inducing a martensitic transformation in the stress field of the dominant crack. The specific characteristics of martensitic transformations pertinent to this toughening process are examined in this paper. A generalized model of the toughening is developed, which indicates the specific roles of the transformation parameters on the expected magnitude of the toughening. Finally, the implications of the analysis for the development of high‐toughness ceramics are discussed.
Resolution of coronavirus disease 2019 (COVID-19) (2020)

The exit strategy for a path back to normal life is required, which should involve a multi-prong effort toward development of new treatment and a successful vaccine to protect public health worldwide and prevent future COVID-19 outbreaks. Therefore, the bench to bedside translational research as well as reverse translational works focusing bedside to bench is very important and would provide the foundation for the development of targeted drugs and vaccines for COVID-19 infections.
A distributed real-time tool for IP-flow measurement (2004)

It is getting more difficult to monitor multiple services as well as to detect and/or to trace denial of service attacks with only tools showing graphs of the whole IP layer traffic like MRTG or by checking counters of router interfaces. In this paper, we discuss the specification of a software-based real-time measurement tool for flow which consists of multiple capture devices, a manager device and user interface devices, enabling flexible flow definition on demand without stopping system and working with IPv4 and/or IPv6, while also enabling high performance. With this discussion, we propose its architecture, bit-pattern-based flow definition method and data structure. Then we report on the performance evaluation of a prototype of proposed real-time flow measurement tools developed on PC-UNIXs and show that the number of bit-pattern composing flow definitions impact on the performance. Lastly we show an example of measuring flows in a real world environment and confirm that the flow extraction is simplified.
Pistis: A Privacy-Preserving Content Recommender System for Online Social Communities (2011)

With the explosive growth of online social communities and massive user-generated content, privacy-preserving recommender systems, which identify information of interest to individual users without disclosing personal interests to other parties, have become increasingly important. Collaborative filtering (CF), a widely used recommendation technique, recommends content that similar users have liked. As a result, CF-based recommender systems may expose sensitive personal interest information. This is demonstrated by a privacy attack model we present that targets online social communities. To solve this problem, we propose an interest group based privacy-preserving recommender system called Pistis. By identifying inherent item-user interest groups and separating users' private interests from their public interests, Pistis can make recommendations based on aggregated judgments of group members and local personalization, thus avoiding the disclosure of personal interest information. Pistis has been deployed and evaluated in an online social community with over 63,000 users, 20,000 daily posts, and 180,000 daily reads. Compared with two representative CF-based methods, our evaluation results demonstrate that Pistis achieves better performance in privacy preservation, recommendation quality, and efficiency.