gebhart/patrepeval huggingface dataset:
A standardised static<i>in vitro</i>digestion method suitable for food – an international consensus (2014)

Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.
Electric Field Servoing for robotic manipulation (2008)

This paper presents two experiments with electric field servoing for robotic manipulation. In the first, a robot hand pre-shapes to the geometry and pose of objects to be grasped, by servoing each finger according to the values on EF sensors built in to each finger. In the second, a 7 degree of freedom arm aligns itself in 2 dimensions with a target object using electric field measurements as the error signal. This system also allows the end effector to dynamically track the target object as it is moved.
Hot Water Dipping of Olives (<i>Olea europaea</i>) for Virgin Oil Debittering (2005)

Olives (Olea europaea L.) of the Manzanilla, Picual, and Verdial varieties harvested at the green mature stage of ripening were dipped in hot water at a range of temperatures between 60 and 72 degrees C for 3 min. Immediately after treatment, oils were physically extracted from the olives. Olive heating promotes a reduction of oil bitterness in direct relationship to the temperature used. Fruit heating at > or =60 degrees C for 3 min did not cause significant changes in acidity, UV absorption, peroxide index, and panel test score of the oils obtained but decreased its oxidative stability. Oils extracted from heated fruit showed higher concentrations of chlorophylls and carotenes and lower total phenol content.
Catalytic Enantioselective Diethylzinc Addition to N‐Phosphinoylimine Using Thiophosphoramide of Homologated Binaphthyl N,O‐Ligand. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Scalable malware classification with multifaceted content features and threat intelligence (2016)

Recent years have witnessed the very rapid increase in both the volume and sophistication of malware programs. Malware authors invest heavily in technologies and capabilities to streamline the process of building and mutating existing malware programs to evade traditional protection. One major challenge currently faced by the antivirus industry is to efficiently process the vast amount of incoming suspicious samples. Since most new malware is a variation of an existing malware family with the same forms of malicious behavior, automatic clustering and classification of malware programs into families have become valuable tools for malware analysts. Such grouping criteria not only allow analysts to prioritize the allocation of their investigation efforts but may also be applied to detect new malware samples based on their association with existing families. In this paper, we address the multi-class malware classification challenge from a scalability perspective. We present the design, development, and evaluation of a novel machine learning classifier trained on multifaceted content features (e.g., instruction sequences, strings, section information, and other malware features) as well as threat intelligence gathered from external sources (e.g., antivirus output). Our experiments on a dataset of 21,741 malware samples demonstrate the efficacy and precision of the proposed algorithm and also provide insights into the utility of various features.
Chemistry of Seawater Neutralization of Bauxite Refinery Residues (Red Mud) (2004)

Bayer process red muds are highly alkaline, and their disposal and potential for reuse are complicated by high concentrations of sodium, high pH, and high alkalinity. Several methods of neutralization of red muds have been reported including: infiltration of rainwater and atmospheric CO2, treatment with strong acids, gypsum addition, and seawater neutralization. Using seawater to neutralize red mud at the Queensland Alumina Ltd. (QAL) refinery at Gladstone, QLD, began as a fresh water conservation measure but led to many benefits, including reduced freshwater use at the refinery, increased settling rates at the pond and reduced alkalinity and sodicity in the solid wastes and entrained liquor. The study reported here describes and quantifies the geochemical consequences of seawater neutralization of bauxite refinery residues. Methods and results presented allow description of the chemical, mineralogical, and physical characteristics of seawater-neutralized red mud. Experiments then identify and quantify the chemical consequences of seawater neutralization. Scanning electron micrographs show how the analytically characterized chemical changes are manifested physically. Seawater neutralization of bauxite refinery residues causes chemical changes and improves physical characteristics of the material. At the refinery, faster settling due to agglomerate consolidation and increased ease of handling after neutralization are positive impacts for management. In postdisposal reuse, seawater neutralization results in an increased acid neutralization capacity, improved soil properties, and increased phosphate adsorption capacity.
A Classroom Note on: The Average Distance in an Ellipse. (2011)

This article presents an applied calculus exercise that can be easily shared with students. One of Kepler's greatest discoveries was the fact that the planets move in elliptic orbits with the sun at one focus [1, 2]. Astronomers characterize the orbits of particular planets by their minimum and maximum distances to the sun, known respectively as the perihelion and aphelion. Mathematically, for the ellipse with foci at (±c, 0), where c^sup 2^ = a^sup 2^ -b^sup 2^, as shown in Figure 1, the perihelion is a -c and the aphelion is a+c. For the earth, the perihelion and aphelion distances are 93.1 and 94.4 million miles, respectively. Typically, the distance from the earth to the sun is taken as approximately 93.75 million miles, which is just the mean of the perihelion and aphelion values. Since the orbits of most planets (with the exception of Pluto, which is no longer officially classified as a planet), are quite circular, it seems reasonable to use the average. In the present article, we raise the more sophisticated mathematical question: What is the true average distance of a planet from the sun? More generally, we ask: For any ellipse, what is the true average distance from all points P(x, y) on the ellipse to a particular focus, (c, 0)? IfP(x, v) is any point on the ellipse (1), then the distance D to the focus (c, 0), as shown in Figure 2, is given by After some routine algebraic manipulation, including the fact that c^sup 2^ = a^sup 2^ - b^sup 2^ , this expression reduces to the surprisingly simple Furthermore, for any point on the ellipse, x ≤ a and so, because c The average value for this distance over the entire upper half of the ellipse is then given by the definite integral When we evaluate this integral using the Fundamental Theorem, we get a. That is, the average distance from a focus to all points in the upper half of an ellipse is precisely equal to a, the length of the semi-major axis. The identical average will, of course, apply to all of the points in the lower half of the ellipse, and so the average distance to the focus for all the points on the ellipse will be a. We note that this rather surprising and simple result is not particularly well known, at least in mathematics, in an era when there has been a diminished emphasis on analytic geometry in the curriculum. …
RiceGAAS: an automated annotation system and database for rice genome sequence (2002)

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.
A Molecular Model for Self-Assembly of Amyloid Fibrils: Immunoglobulin Light Chains (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Molecular Model for Self-Assembly of Amyloid Fibrils: Immunoglobulin Light ChainsFred J. Stevens, Elizabeth A. Myatt, Chong-Hwan Chang, Florence A. Westholm, Manfred Eulitz, Deborah T. Weiss, Charles Murphy, Alan Solomon, and Marianne SchifferCite this: Biochemistry 1995, 34, 34, 10697–10702Publication Date (Print):August 29, 1995Publication History Published online1 May 2002Published inissue 29 August 1995https://pubs.acs.org/doi/10.1021/bi00034a001https://doi.org/10.1021/bi00034a001research-articleACS PublicationsRequest reuse permissionsArticle Views332Altmetric-Citations75LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
XmdvTool: integrating multiple methods for visualizing multivariate data (1994)

Much of the attention in visualization research has focussed on data rooted in physical phenomena, which is generally limited to three or four dimensions. However, many sources of data do not share this dimensional restriction. A critical problem in the analysis of such data is providing researchers with tools to gain insights into characteristics of the data, such as anomalies and patterns. Several visualization methods have been developed to address this problem, and each has its strengths and weaknesses. This paper describes a system named XmdvTool which integrates several of the most common methods for projecting multivariate data onto a two-dimensional screen. This integration allows users to explore their data in a variety of formats with ease. A view enhancement mechanism called an N-dimensional brush is also described. The brush allows users to gain insights into spatial relationships over N dimensions by highlighting data which falls within a user-specified subspace. >
Thiols and Disulfides on the Au(111) Surface:  The Headgroup−Gold Interaction (2000)

How thiols and disulfides bind to gold surfaces to form self-assembled monolayers is a long-standing open question. In particular, determining the nature itself of the anchor groups and of their interaction with the metal is a priority issue, which has so far been approached only with oversimplified models. We present ab initio calculations of the adsorption configurations (dissociative and not) of methanethiol and dimethyl disulfide on Au(111) at low coverage, which are based on density functional theory using gradient-corrected exchange-correlation functionals. A complete characterization of their structure, binding energies, and type of bonding is obtained. It is established that dissociation is clearly favored for the disulfide with subsequent formation of strongly bound thiolates, in agreement with experimental evidence, whereas thiolates resulting from S−H bond cleavage in thiols can coexist with the adsorbed “intact” species and become favored if accompanied by the formation of molecular hydrogen.
Identification of Modular Chiral Bisphosphines Effective for Cu(I)-Catalyzed Asymmetric Allylation and Propargylation of Ketones (2010)

New modular chiral phosphines effective for two distinct Cu(I)-catalyzed asymmetric tetrasubstituted-carbon-forming reactions, namely, allylation and propargylation of ketones, were identified. The optimized phosphine 8 was readily synthesized on a gram scale in high yield via three facile transformations (O-alkylation, bisaminal formation, and phosphination) from commercially available materials. In both reactions, excellent enantioselectivity (up to 98% ee) was produced from a range of substrates, including aromatic and aliphatic ketones, using 0.1-5 mol % catalyst loading. Specifically, catalytic enantioselective propargylation was the first example, affording synthetically useful chiral building blocks that have not been easily accessed to date. In addition to the enantioselectivity, the high catalytic activity of the CuOAc-8 complex is noteworthy. Preliminary studies to elucidate the structure-catalyst activity relationship suggested that the high catalytic activity of the Cu-8 complex is due to the extraordinarily wide bite angle ( angleP-Cu-P = 137.8 degrees ), leading to the stabilization of the active monomeric catalytically active species. Furthermore, mechanistically intriguing nonconventional hydrogen bonds existed between the acetate ligand of Cu and the bisaminal hydrogen atoms, stabilizing the distorted tetrahedral coordination state of the Cu atom.
Condensation of hydrogen isotopes in laser fusion targets (1977)

In the development of laser fusion targets, glass microballoons (∼100 μm diam) containing D2, T2, or DT were cooled through four types of heat transfer: radiation, solid conduction, exchange gas, and a cold He stream. Observations of condensate temperature of formation, volume, and distribution roughly agreed with calculations. A thermal gradient set up by the cold He stream from above was useful in counteracting gravity, and the resulting condensate formed a fairly uniform spherical shell, the desired form for the fuel.
Vapor deposition of platinum using cw laser energy (1972)

The fabrication of beam lead silicon integrated-circuit devices involves the vapor deposition of platinum, which is generally accomplished by electron-beam bombardment or by low-voltage sputtering. In an effort to develop alternative platinum-deposition techniques, we have evaluated the feasibility of using a cw laser as the energy source for a thermal-evaporation process. Using a 20-W-output YAG laser, uniform platinum films were successfully deposited in a stable easily controlled process. Films deposited on oxidized silicon slices evidenced no space-charge buildup in the oxide, the change in flat-band voltage following platinum deposition being negligible. Although the evaporation rate that was obtained is but 0.2 Å/min at a 6-cm source-to-substrate distance, it is concluded that this is entirely a result of the limited power output of the particular laser that was used. No theoretical limitation to the utilization of a laser in vapor-deposition processes was encountered in this study.
Structural similarities of Na,K-ATPase and SERCA, the Ca2+-ATPase of the sarcoplasmic reticulum (2001)

The crystal structure of SERCA1a (skeletal-muscle sarcoplasmic-reticulum/endoplasmic-reticulum Ca2+-ATPase) has recently been determined at 2.6 Å (note 1 Å = 0.1nm) resolution [Toyoshima, Nakasako, Nomura and Ogawa (2000) Nature (London) 405, 647–655]. Other P-type ATPases are thought to share key features of the ATP hydrolysis site and a central core of transmembrane helices. Outside of these most-conserved segments, structural similarities are less certain, and predicted transmembrane topology differs between subclasses. In the present review the homologous regions of several representative P-type ATPases are aligned with the SERCA sequence and mapped on to the SERCA structure for comparison. Homology between SERCA and the Na,K-ATPase is more extensive than with any other ATPase, even PMCA, the Ca2+-ATPase of plasma membrane. Structural features of the Na,K-ATPase are projected on to the Ca2+-ATPase crystal structure to assess the likelihood that they share the same fold. Homology extends through all ten transmembrane spans, and most insertions and deletions are predicted to be at the surface. The locations of specific residues are examined, such as proteolytic cleavage sites, intramolecular cross-linking sites, and the binding sites of certain other proteins. On the whole, the similarity supports a shared fold, with some particular exceptions.
Artificial Intelligence and Statistics 2001 : proceedings of the eighth international workshop : January 4-7, 2001, Key West, Florida (2001)

Artificial Intelligence and Statistics 2001: Proceedings of the Eighth Internatinoal Workshop.
Thermally sensitive micelles self-assembled from poly( <i>N</i> -isopropylacrylamide- <i>co</i> - <i>N,N</i> -dimethylacrylamide)- <i>b</i> -poly( <scp>d</scp> , <scp>l</scp> -lactide- <i>co</i> -glycolide) for controlled delivery of paclitaxel (2005)

Thermally sensitive micelles self-assembled from poly(N-isopropylacrylamide-co- N,N-dimethylacrylamide)-b-poly(d,l-lactide-co-glycolide)[P(NIPAAm-co-DMAAm)-b-PLGA] are fabricated and used as a carrier for the controlled delivery of paclitaxel. Paclitaxel is efficiently loaded into the micelles by a membrane dialysis method. The lower critical solution temperature (LCST) of the micelles is 39.0 degrees C in PBS. Encapsulation efficiency and loading level of paclitaxel are affected by the initial loading level of paclitaxel, fabrication temperature and polymer composition. The blank and paclitaxel-loaded micelles are characterized by particle size analysis (DLS), morphology (TEM and AFM) and paclitaxel distribution (NMR, DSC and WAXRD). The micelles are spherical in shape, having an average size less than 130 nm. Paclitaxel is molecularly distributed within the core of micelles. Sustained release of paclitaxel is achieved, which is much faster at a temperature above the LCST than at the normal body temperature (37 degrees C). Cytotoxicity of free paclitaxel and paclitaxel-loaded micelles against a human breast carcinoma cell line (MDA-MB-435S) is studied at different temperatures. The cytotoxicity of the paclitaxol-loaded micelles is greater as compared to free paclitaxel. Enhanced cytotoxicity is achieved by the paclitaxol-loaded micelles when the environmental temperature increases slightly above the LCST. Paclitaxel-loaded P(NIPAAm-co-DMAAm)-b-PLGA micelles may provide a good formulation for cancer therapy.
Challenges in Neuroprotective Nanomedicine Development: Progress Towards Noninvasive Gene Therapy of Glaucoma (2012)

Over the past decade the application of gene therapy of retinal diseases such as glaucoma has produced promising results. However, optic nerve regeneration and restoration of vision in patients with glaucoma is still far from reality. Neuroprotective approaches in the form of gene therapy may provide significant advantages, but are still limited by many factors both at the organ and cellular levels. In general, gene delivery systems for eye diseases range from simple eye drops and ointments to more advanced bio- and nanotechnology-based systems such as muco-adhesive systems, polymers, liposomes and ocular inserts. Most of these technologies were developed for front-of-the-eye ophthalmic therapies and are not applicable as back-of-the-eye delivery systems. Currently, only the invasive intravitreal injections are capable of successfully delivering genes to the retina. Here we review the challenges and possible strategies for the noninvasive gene therapy of glaucoma including the barriers in the eye and in neural cells, and present a cross-sectional view of gene delivery as it pertains to the prevention and treatment of glaucoma.