gebhart/patrepeval huggingface dataset:
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2009)

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.
Machine Learning versus Deep Learning for Malware Detection (2019)

It is often claimed that the primary advantage of deep learning is that such models can continue to learn as more data is available, provided that sufficient computing power is available for training. In contrast, for other forms of machine learning it is claimed that models ‘‘saturate,’’ in the sense that no additional learning can occur beyond some point, regardless of the amount of data or computing power available. In this research, we compare the accuracy of deep learning to other forms of machine learning for malware detection, as a function of the training dataset size. We experiment with a wide variety of hyperparameters for our deep learning models, and we compare these models to results obtained using �-nearest neighbors. In these experiments, we use a subset of a large and diverse malware dataset that was collected as part of a recent research project.
Architecture and design of AlphaServer GS320 (2000)

This paper describes the architecture and implementation of the AlphaServer GS320, a cache-coherent non-uniform memory access multiprocessor developed at Compaq. The AlphaServer GS320 architecture is specifically targeted at medium-scale multiprocessing with 32 to 64 processors. Each node in the design consists of four Alpha 21264 processors, up to 32GB of coherent memory, and an aggressive IO subsystem. The current implementation supports up to 8 such nodes for a total of 32 processors. While snoopy-based designs have been stretched to medium-scale multiprocessors by some vendors, providing sufficient snoop bandwidth remains a major challenge especially in systems with aggressive processors. At the same time, directory protocols targeted at larger scale designs lead to a number of inherent inefficiencies relative to snoopy designs. A key goal of the AlphaServer GS320 architecture has been to achieve the best-of-both-worlds, partly by exploiting the bounded scale of the target systems.This paper focuses on the unique design features used in the AlphaServer GS320 to efficiently implement coherence and consistency. The guiding principle for our directory-based protocol is to address correctness issues related to rare protocol races without burdening the common transaction flows. Our protocol exhibits lower occupancy and lower message counts compared to previous designs, and provides more efficient handling of 3-hop transactions. Furthermore, our design naturally lends itself to elegant solutions for deadlock, livelock, starvation, and fairness. The AlphaServer GS320 architecture also incorporates a couple of innovative techniques that extend previous approaches for efficiently implementing memory consistency models. These techniques allow us to generate commit events (which are used for ordering purposes) well in advance of formulating the reply to a transaction. Furthermore, the separation of the commit event allows time-critical replies to by-pass inbound requests without violating ordering properties. Even though our design specifically targets medium-scale servers, many of the same techniques can be applied to larger-scale directory-based and smaller-scale snoopy-based designs. Finally, we evaluate the performance impact of some of the above optimizations and present a few competitive benchmark results.
BET Bromodomain Proteins as Cancer Therapeutic Targets (2016)

Epigenetic regulators are emerging therapeutic targets in a wide variety of human cancers. BET bromodomain proteins have been identified as key regulators of oncogenic transcription factors including MYC; therefore, their inhibition might provide a way to block these "undruggable" targets. Several BET bromodomain inhibitors are in clinical development with promising preliminary findings. However, tumors acquire resistance to these agents in several different ways. In this review, we summarize the role that BET bromodomain proteins play in tumorigenesis as well as the molecular mechanisms underlying therapeutic responses and resistance to their inhibition with emphasis on BRD4 and breast cancer.
Encouraging LSTMs to Anticipate Actions Very Early (2017)

In contrast to the widely studied problem of recognizing an action given a complete sequence, action anticipation aims to identify the action from only partially available videos. As such, it is therefore key to the success of computer vision applications requiring to react as early as possible, such as autonomous navigation. In this paper, we propose a new action anticipation method that achieves high prediction accuracy even in the presence of a very small percentage of a video sequence. To this end, we develop a multi-stage LSTM architecture that leverages context-aware and action-aware features, and introduce a novel loss function that encourages the model to predict the correct class as early as possible. Our experiments on standard benchmark datasets evidence the benefits of our approach; We outperform the state-of-the-art action anticipation methods for early prediction by a relative increase in accuracy of 22.0% on JHMDB-21, 14.0% on UT-Interaction and 49.9% on UCF-101.
ChemInform Abstract: Chemotherapeutic Agents. Part 18. Synthesis of π‐Deficient Pyrimidines and Fused Pyrimidines as Leishmanicidal Agents. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Polyaniline‐modified cellulose nanofibrils as reinforcement of a smart polyurethane (2010)

Abstract Segmented polyurethanes exhibiting shape memory properties were modified by the addition of polyaniline (PANI)‐coated cellulose nanofibrils (CNFs). The two‐phase structure of the polymer is responsible for the material's ability to ‘remember’ and autonomously recover its original shape after being deformed in response to an external thermal stimulus. PANI was grown on the surface of the CNFs via in situ polymerization. Modified nanocrystals were added to the segmented polyurethane in concentrations ranging from 0 to 15 wt%. The changes in the material properties associated with the percolation of the coated fibrils appear at higher concentrations than previously observed for non‐modified CNFs, which suggests that fibril agglomeration is occurring due to the PANI coating. The shape memory behavior of the composites is maintained at about the same level as that of the unfilled polyurethane only up to 4 wt% of fibrils. At higher concentrations, the rigidity of the nanofibrils as well as their interaction with the hard‐segment phase and the increasing difficulty of dispersing them in the polymer collaborate to produce early breakage of the specimens when stretched at temperatures above the melting point of the soft segments. Copyright © 2010 Society of Chemical Industry
The value of synovial biopsy, joint aspiration and C-reactive protein in the diagnosis of late peri-prosthetic infection of total knee replacements (2008)

We analysed the serum C-reactive protein level, synovial fluid obtained by joint aspiration and five synovial biopsies from 145 knee replacements prior to revision to assess the value of these parameters in diagnosing late peri-prosthetic infection. Five further synovial biopsies were used for histological analysis. Samples were also obtained during the revision and incubated and analysed in an identical manner for 14 days. A total of 40 total knee replacements were found to be infected (prevalence 27.6%). The aspiration technique had a sensitivity of 72.5% (95% confidence interval (CI) 58.7 to 86.3), a specificity of 95.2% (95% CI 91.2 to 99.2), a positive predictive value of 85.3% (95% CI 73.4 to 100), a negative predictive value of 90.1% (95% CI 84.5 to 95.7) and an accuracy of 89%. The biopsy technique had a sensitivity of 100%, a specificity of 98.1% (95% CI 95.5 to 100), a positive predictive value of 95.2% (95% CI 88.8 to 100), a negative predictive value of 100% and an accuracy of 98.6%. C-reactive protein with a cut-off-point of 13.5 mg/l had a sensitivity of 72.5% (95% CI 58.7 to 86.3), a specificity of 80.9% (95% CI 73.4 to 88.4), a positive predictive value of 59.2% (95% CI 45.4 to 73.0), a negative predictive value of 88.5% (95% 81.0 to 96.0 CI) and an accuracy of 78.1%. We found that biopsy was superior to joint aspiration and C-reactive protein in the diagnosis of late peri-prosthetic infection of total knee replacements.
Origin and heterogeneity of pore sizes in the Mount Simon Sandstone and Eau Claire Formation: Implications for multiphase fluid flow (2016)

The Mount Simon Sandstone and Eau Claire Formation represent a principal reservoir - caprock system for wastewater disposal, geologic CO<sub>2</sub> storage, and compressed air energy storage (CAES) in the Midwestern United States. Of primary concern to site performance is heterogeneity in flow properties that could lead to non-ideal injectivity and distribution of injected fluids (e.g., poor sweep efficiency). Using core samples from the Dallas Center Structure, Iowa, we investigate pore structure that governs flow properties of major lithofacies of these formations. Methods include gas porosimetry and permeametry, mercury intrusion porosimetry, thin section petrography, and X-ray diffraction. The lithofacies exhibit highly variable intra- and inter-informational distributions of pore throat and body sizes. Based on pore-throat size, samples fall into four distinct groups. Micropore-throat dominated samples are from the Eau Claire Formation, whereas the macropore-, mesopore-, and uniform-dominated samples are from the Mount Simon Sandstone. Complex paragenesis governs the high degree of pore and pore-throat size heterogeneity, due to an interplay of precipitation, non-uniform compaction, and later dissolution of cements. Furthermore, the cement dissolution event probably accounts for much of the current porosity in the unit. The unusually heterogeneous nature of the pore networks in the Mount Simon Sandstone indicates that there is a greater-than-normal opportunity for reservoir capillary trapping of non-wetting fluids — as quantified by CO<sub>2</sub> and air column heights — which should be taken into account when assessing the potential of the reservoir-caprock system for CO<sub>2</sub> storage and CAES.
Preheating and Incubation of Cane Juice Prior to Liming:  A Comparison of Intermediate and Cold Lime Clarification (2001)

In the U.S., cold lime clarification remains the clarification process of choice in raw sugar manufacturing. A comparative study of cold vs intermediate lime clarification was undertaken at a factory that operated intermediate liming (∼30% mixed juice (MJ) of pH 5.2 ± 0.3 was preheated to 87−93 °C to help maintain clean limed juice heaters, incubated at ∼54 °C, and then limed) but still had the pipes to revert to cold liming (MJ incubated and limed at ∼40 °C) for this study. Hourly samples were collected over a 6 h sampling period across cold and intermediate clarification processes on two consecutive days, respectively, and this was repeated three times across the 1999 grinding season. A total of 1.57% less sucrose was lost to inversion reactions across intermediate rather than cold liming. In intermediate liming, which required ∼4.6% less lime, preheating of only 30% of the MJ markedly removed color (−29%), dextran (−10%), and starch (−24%) and caused large flocs to form that settled faster in the clarifiers. Faster settling led to an impressive 4.6% (season average) more turbidity removal across the clarifiers in intermediate rather than cold liming. Intermediate clarified juice (CJ) turbidity (season average 2028 ICU ± 675) was approximately half of cold CJ turbidity (average 3952 ICU ± 1450) with over 2-fold more CJ turbidity control. Subsequent turbidity values and control were significantly improved in the final evaporator syrup samples too. For both processes, juice incubation caused ∼10% color removal, but this was offset by color formation on liming, because of the alkaline degradation of invert; however, overall, more color was removed than formed in intermediate liming. Starch was reduced in the incubator tank, for both processes, because added filtrate reduced the acidity enabling natural diastase from the cane to degrade starch. Some dextran occasionally formed in the incubator tank, in both processes. Summed across measured parameters, intermediate liming appears to offer several advantages over cold liming. Keywords: Cane juice incubation; cold lime clarification; dextran; intermediate lime clarification; heated cane juice; raw sugar manufacture; starch
The Research on Expression and Purification of a Chimeric Anti-p185 Antibody (2006)

The Her-2 proto-oncogene encodes a 185kDa transmenbrane glycoprotein p185 which has intrinsic tyrosine kinase activity. It is overexpressed in several malignant human tumors like breast cancer. A chimeric antibody by assembling a single-chain Fv antibody and a human IgG1 Fc fragment was constructed. This chimeric antibody reacts with tumor surface antigen p185c-erbB-2 specifically. In order to put the antibody into clinical application, two steps purification method was used to attain the antibody’s purity more than 95%. Both the lyophilized pharmaceutical formulations of the antibody were found. The formulations can keep the stability and activity of the antibody for at least one year. These results were the foundation of the chimeric antibody for cancer therapy.
Iron monitoring and supplementation: how do we achieve the best results? (1998)

A number of factors have been shown to limit the response to recombinant human erythropoietin (r-HuEPO). One major factor appears to be an inadequate iron supply to the bone marrow. Erythropoiesis is dependent upon a continuous supply of iron to the bone marrow. The rate at which iron can be drawn from existing stores may easily limit the rate of delivery for haemoglobin synthesis. This results in 'functional iron deficiency' which is distinct from 'absolute iron deficiency' caused by depletion of iron stores. At present there are three main parameters available to clinicians wishing to monitor iron status in their patients: serum ferritin and transferrin saturation (TFS), which are indirect measurements, and the percentage of hypochromic red cells, which directly reflects marrow iron status. Ferritin levels should be measured before starting r-HuEPO therapy to ensure adequate iron stores (>200 microg/l), and when patients move from the correction phase to the maintenance phase of therapy (have stores become depleted during the correction phase?). In addition, ferritin levels can give an indication of iron overload following excess parenteral iron administration. The TFS represents a balance between iron supply by stores and demand by bone marrow. A saturation below 20% probably indicates iron-deficient erythropoiesis. However, this is an indirect measure of marrow iron supply and wide fluctuations have been observed when determined at different time points. The percentage of hypochromic red blood cells is measured by flow cytometry and a hypochromic subpopulation of more than 10% (normal percentage <2.5%) indicates iron-deficient erythropoiesis. However, not all departments may have access to the required equipment. The aim of iron supplementation is to provide sufficient iron for the correction phase and to replace iron losses (1500-2000 mg/year in haemodialysis patients) during the maintenance phase of r-HuEPO therapy. This amounts to a daily iron need in the range of 5 7 mg, which is well above the normal dietary intake and absorptive capacity of the human intestine. Therefore, there is a need for intravenous iron, in particular when the patient has absolute or functional iron deficiency, is intolerant of oral iron, or is not complying well with the oral regimen.
Optical digital fragmentation measuring systems – inherent sources of error (1998)

Abstract Automated optical imaging systems of measuring fragmentation are increasingly being used in the mining, comminution, and materials handling industries. These methods have been well received in many of the industries involved. Considering that in many of these applications there are no alternative ways of sizing material, having even a rudimentary measurement of size distributions allows evaluations of explosive, blast design, detonator performance, crusher and milling performance, and material degradation due to transport. Optical methods have inherent limitations, which reflect on accuracy, precision, and reproducibility of measurement results. This stems from the fact that there are myriads of variables, which affect the outcome of the measurements. Errors start with the imaging process, which may distort the reality because of the scale of observation, may induce sampling bias, and may simply not return a good representation of the reality. More errors are introduced in the digital processing stage, where blocks may be miss-identified. The reconstruction of three-dimensional distributions from measured two-dimensional distributions of partially-overlapped, fines-censured images can introduce further errors. Understanding of these limitations provides the key to the successful use of optical image systems. Understanding of what can and cannot be measured and the relative accuracy's makes these systems useful. Defining realistic acceptable levels of error is also necessary. This paper seeks to clarify these issues, and to quantify them from laboratory studies wherever possible. Key Words: Fragmentationopticalimage analysismeasurementerrors
<i>Corynebacterium</i>sp. U-96 Contains a Cluster of Genes of Enzymes for the Catabolism of Sarcosine to Pyruvate (2005)

The sarcosine oxidase gene and nearby genes from Corynebacterium sp. U-96 were determined. The genes for serine hydroxymethyltransferase, the beta, delta, alpha, and gamma subunits of sarcosine oxidase, serine dehydratase, and 10-formyltetrahydrofolate hydrolase are arranged in this order. This suggests that the bacteria contain a cluster of genes for the catabolism of sarcosine to pyruvate. The possibility that the gene cluster is a merit for the cellular energy demands of the bacteria is discussed. Functional expression of sarcosine oxidase in Escherichia coli was accomplished, but the beta subunit and the betadelta complex were expressed at a low level as a soluble protein.
The willgerodt‐kindler reactions. 7. The mechanisms (1989)

Abstract The mechanisms involved in various stages of the Kindler Reaction are discussed, with particular attention especially to its most unusual feature: the movement of a carbonyl group from methylene carbon to methylene carbon in an unbranched alkyl chain, or around a cycloalkyl ring. The first step is the reversible formation of an enamine, which is attacked by a catalyst generated from sulfur and the amine solvent to form a highly reactive intermediate with a sulfur‐containing heterocyclic ring. The natures of the catalytically active species and the reactive intermediates are proposed. Other steps involved in the Kindler Reaction are also discussed, as is the relationship of the Willgerodt Reaction to the Kindler Reaction.
Learning Spatiotemporal Features Using 3DCNN and Convolutional LSTM for Gesture Recognition (2017)

Gesture recognition aims at understanding the ongoing human gestures. In this paper, we present a deep architecture to learn spatiotemporal features for gesture recognition. The deep architecture first learns 2D spatiotemporal feature maps using 3D convolutional neural networks (3DCNN) and bidirectional convolutional long-short-term-memory networks (ConvLSTM). The learnt 2D feature maps can encode the global temporal information and local spatial information simultaneously. Then, 2DCNN is utilized further to learn the higher-level spatiotemporal features from the 2D feature maps for the final gesture recognition. The spatiotemporal correlation information is kept through the whole process of feature learning. This makes the deep architecture an effective spatiotemporal feature learner. Experiments on the ChaLearn LAP large-scale isolated gesture dataset (IsoGD) and the Sheffield Kinect Gesture (SKIG) dataset demonstrate the superiority of the proposed deep architecture.
Molecular interactions between serum albumin proteins and Keggin type polyoxometalates studied using luminescence spectroscopy (2013)

The interaction between the plenary Keggin H3PW12O40, lacunary Keggin K7PW11O39 and the Eu(III)-substituted Keggin K4EuPW11O39 (Eu-Keggin) type polyoxometalates (POMs), and the proteins human and bovine serum albumin (HSA and BSA) was studied using steady state and time-resolved Eu(III) luminescence and tryptophan (Trp) fluorescence spectroscopy. The excitation spectrum of the Eu-Keggin POM is dominated by a ligand-to-metal charge transfer band at 291 nm. In the absence of proteins, the number of water molecules coordinated in the first coordination sphere of the Eu(III) center of Eu-Keggin was determined to be 4, indicating that Eu(III) occurs as a 1 : 1 isomer in solution. In the presence of HSA or BSA, the number of coordinated water molecules decreased to 0 and 1, respectively, suggesting interaction between the Eu-Keggin POM and the protein surface. As a result of this interaction, a five-fold increase of the hypersensitive (5)D0 → (7)F2 transition in the luminescence intensity was observed for the Eu-Keggin-HSA complex. The association constants were calculated to be 1.5 × 10(2) M(-1) and 2.0 × 10(3) M(-1) for the Eu-Keggin-HSA and Eu-Keggin-BSA complexes, respectively. Tryptophan fluorescence quenching studies were performed and the quenching constants were calculated using a Stern-Volmer analysis. The obtained values of the quenching constants were 6.1 × 10(4) M(-1) and 2.0 × 10(6) M(-1) for the Eu-Keggin-HSA and Eu-Keggin-BSA complexes, respectively. The surface map of both proteins shows that the cavity containing the tryptophan has a positive surface potential, providing a specific binding site at the surface of albumin proteins for the negatively charged POM.