gebhart/patrepeval huggingface dataset:
Prodrugs as therapeutics (2004)

Prodrugs are bioreversible derivatives of drug molecules used to overcome some barriers to the utility of the parent drug molecule. These barriers include, but are not limited to, solubility, permeability, stability, presystemic metabolism and targeting limitations. The patent literature shows a dramatic increase in numbers of prodrug patents (> 2000% increase in 2002 compared to 1993), with claims for cancer treatment comprising 37% of these. This increase is largely due to the rise from North American-based multinationals and some smaller drug delivery companies mirroring the overall trend. In 2001 and 2002, 14% of all new approved chemical drugs were prodrugs. It appears that prodrugs to overcome barriers to the delivery of problematic drug candidates are becoming an integral part of the drug discovery paradigm.
Ursa minor: versatile cluster-based storage (2005)

No single encoding scheme or fault model is optimal for data. A versatile storage system allows them to be matched to access patterns, reliability requirements, and cost goals on a per-data item basis. Ursa Minor is a cluster-based storage system that allows data-specific selection of, and on-line changes to, encoding schemes and fault models. Thus, different data types can share a scalable storage infrastructure and still enjoy specialized choices, rather than suffering from one size fits all. Experiments with Ursa Minor show performance benefits of 2-3× when using specialized choices as opposed to a single, more general, configuration. Experiments also show that a single cluster supporting multiple workloads simultaneously is much more efficient when the choices are specialized for each distribution rather than forced to use a one size fits all configuration. When using the specialized distributions, aggregate cluster throughput nearly doubled.
Effects of 12-O-tetradecanoylphorbol-13-acetate and mezerein on epidermal ornithine decarboxylase activity, isoproterenol-stimulated levels of cyclic adenosine 3':5'-monophosphate, and induction of mouse skin tumors in vivo. (1979)

The tumor promoter 12-O-tetradecanoylphorbol-13-acetate and the antileukemic agent mezerein are diterpene esters of plant origin with certain structural similarities. Both compounds, when applied topically to mouse skin, were equipotent on a molar basis in inducing hyperplasia, inflammation, and ornithine decarboxylase activity, as well as in reducing cyclic adenosine 3':5'-monophosphate accumulation in response to beta-adrenergic stimulation. In contrast, mezerein was much less effective as a tumor promoter; the phorbol ester at 8.5 nmol/application yielded 78-fold more tumors than did 8.5 nmol mezerein per application to similarly initiated SENCAR mice. The superiority of the phorbol ester was nearly as great in CD-1 mice.
Upscaling Ambisonic sound scenes using compressed sensing techniques (2011)

This paper considers the application of compressed sensing to spherical acoustics in order to improve spatial sound field reconstruction. More specifically, we apply compressed sensing techniques to a set of Ambisonic sound signals to obtain a super-resolution plane-wave decomposition of the original sound field. That is to say, we investigate using the plane-wave decomposition to increase the spherical harmonic order of the Ambisonic sound scene. We refer to this as upscaling the Ambisonic sound scene. A focus of the paper is using sub-band analysis to make the plane-wave decomposition more robust. Results show that the sub-band analysis does indeed improve the robustness of the plane-wave decomposition when dominant overlapping sources are present or in noisy or diffuse sound conditions. Upscaling Ambisonic sound scenes allows more loudspeakers to be used for spatial sound field reconstruction, resulting in a larger sweet spot and improved sound quality.
Comparison of Flat and Hollow‐Fiber Mixed‐Matrix Composite Membranes for CO2 Separation with Temperature (2017)

Abstract Zeolite A/poly (1‐trimethylsilyl‐1‐propyne) (zeoliteA/PTMSP) and [emim][Ac]/chitosan (IL/CS) are mixed‐matrix membrane (MMM) materials with enhanced CO 2 /N 2 permselectivity even at higher temperature. The scalability to asymmetric flat and hollow‐fiber geometry by a simple dip‐coating method was analyzed. The CO 2 /N 2 separation performance was evaluated at different temperatures. The resulting composite membranes exhibit a significantly enhanced CO 2 permeation flux because the MMM layer thickness is reduced by 97 % from flat to hollow‐fiber geometries in IL‐CS composite membranes, while the selectivity is maintained similar to the self‐standing membranes, thus proving that compatibility between the membrane component materials leads to a defect‐free composite membrane, regardless the geometry and temperature.
AutoGluon-Tabular: Robust and Accurate AutoML for Structured Data (2020)

We introduce AutoGluon-Tabular, an open-source AutoML framework that requires only a single line of Python to train highly accurate machine learning models on an unprocessed tabular dataset such as a CSV file. Unlike existing AutoML frameworks that primarily focus on model/hyperparameter selection, AutoGluon-Tabular succeeds by ensembling multiple models and stacking them in multiple layers. Experiments reveal that our multi-layer combination of many models offers better use of allocated training time than seeking out the best. A second contribution is an extensive evaluation of public and commercial AutoML platforms including TPOT, H2O, AutoWEKA, auto-sklearn, AutoGluon, and Google AutoML Tables. Tests on a suite of 50 classification and regression tasks from Kaggle and the OpenML AutoML Benchmark reveal that AutoGluon is faster, more robust, and much more accurate. We find that AutoGluon often even outperforms the best-in-hindsight combination of all of its competitors. In two popular Kaggle competitions, AutoGluon beat 99% of the participating data scientists after merely 4h of training on the raw data.
Software reuse (1992)

Software reuse is the process of creating software systems from existing software rather than building software systems from scratch. This simple yet powerful vision was introduced in 1968. Software reuse has, however, failed to become a standard software engineering practice. In an attempt to understand why, researchers have renewed their interest in software reuse and in the obstacles to implementing it. This paper surveys the different approaches to software reuse found in the research literature. It uses a taxonomy to describe and compare the different approaches and make generalizations about the field of software reuse. The taxonomy characterizes each reuse approach in terms of its reusable artifacts and the way these artifacts are abstracted, selected, specialized, and integrated . Abstraction plays a central role in software reuse. Concise and expressive abstractions are essential if software artifacts are to be effectively reused. The effectiveness of a reuse technique can be evaluated in terms of cognitive distance —an intuitive gauge of the intellectual effort required to use the technique. Cognitive distance is reduced in two ways: (1) Higher level abstractions in a reuse technique reduce the effort required to go from the initial concept of a software system to representations in the reuse technique, and (2) automation reduces the effort required to go from abstractions in a reuse technique to an executable implementation. This survey will help answer the following questions: What is software reuse? Why reuse software? What are the different approaches to reusing software? How effective are the different approaches? What is required to implement a software reuse technology? Why is software reuse difficult? What are the open areas for research in software reuse?
Identification and suppression of the p‐coumaroyl CoA:hydroxycinnamyl alcohol transferase in Zea mays L. (2014)

Grasses, such as Zea mays L. (maize), contain relatively high levels of p-coumarates (pCA) within their cell walls. Incorporation of pCA into cell walls is believed to be due to a hydroxycinnamyl transferase that couples pCA to monolignols. To understand the role of pCA in maize development, the p-coumaroyl CoA:hydroxycinnamyl alcohol transferase (pCAT) was isolated and purified from maize stems. Purified pCAT was subjected to partial trypsin digestion, and peptides were sequenced by tandem mass spectrometry. TBLASTN analysis of the acquired peptide sequences identified a single full-length maize cDNA clone encoding all the peptide sequences obtained from the purified enzyme. The cDNA clone was obtained and used to generate an RNAi construct for suppressing pCAT expression in maize. Here we describe the effects of suppression of pCAT in maize. Primary screening of transgenic maize seedling leaves using a new rapid analytical platform was used to identify plants with decreased amounts of pCA. Using this screening method, mature leaves from fully developed plants were analyzed, confirming reduced pCA levels throughout plant development. Complete analysis of isolated cell walls from mature transgenic stems and leaves revealed that lignin levels did not change, but pCA levels decreased and the lignin composition was altered. Transgenic plants with the lowest levels of pCA had decreased levels of syringyl units in the lignin. Thus, altering the levels of pCAT expression in maize leads to altered lignin composition, but does not appear to alter the total amount of lignin present in the cell walls.
Neurotrophic activity of interphotoreceptor matrix on human Y79 retinoblastoma cells (1992)

A neurotrophic activity of adult monkey and bovine interphotoreceptor matrix (IPM) was examined by using cultured human Y79 retinoblastoma cells as a model system. The cells were stimulated for 7 days in suspension culture with soluble IPM components and then attached to poly-D-lysine substratum. IPMs from both species induced greater than 80% neuronal differentiation of Y79 cell aggregates after 11 days of attachment as adjudged morphologically by the extension of lengthy, neurite-like processes. Immunocytochemical studies indicate that differentiated Y79 cells had an increased level of expression of neuron-specific enolase and a concomitant decreased expression of glial fibrillary acidic protein. This neurotrophic activity cannot be ascribed to nerve growth factor, platelet-derived growth factor, fibroblast growth factor, epidermal growth factor, or transforming growth factor beta. Although the nature of the factor and its cellular source have yet to be characterized, it may be related to a recently described neurotrophic protein secreted by human fetal retinal pigment epithelial cells in culture. Our findings provide evidence supporting the neuroblastic potential of the Y79 cell line and indicate that the IPM contains a potent neurotrophic activity. Such factors may be important to normal differentiation and maintenance of function of the neural retina.
Antagonising the expression of VEGF in pathological angiogenesis (1998)

Vascular endothelial growth factor (VEGF) is the prototype of a subfamily of five growth factors sharing structural homologies with the platelet-derived growth factor (PDGF) protein superfamily. The VEGFs are potent mitogens specific for endothelial cells of the blood or lymphatic vasculature and are effective modulators of vessel permeability in the normal physiological processes of angiogenesis and vasculogenesis. VEGF appears to be a significant promoter of the inappropriate angiogenesis that sustains tumour growth and metastasis, inflammatory joint disease and diabetic retinopathy. Understanding the cell biology and control of VEGF expression has led to the development of several strategies for antagonising the pathological angiogenesis associated with these common diseases. This review describes these promising approaches in the context of current understanding of VEGF biology.
Effect of acute and chronic administration of the GABA B agonist baclofen on 24 hour pH metry and symptoms in control subjects and in patients with gastro-oesophageal reflux disease (2003)

The GABA(B) agonist baclofen reduces 24 hour gastro-oesophageal reflux and increases gastric pH in GORD patients and controls. When given for one month to GORD patients, baclofen reduces oesophageal acid refluxes and significantly improves symptoms. Baclofen may be useful in the therapy of GORD.
Risk of Thromboembolic Events in Controlled Trials of rFVIIa in Spontaneous Intracerebral Hemorrhage (2008)

There appears to be a increased risk of arterial TEs associated with higher doses of rFVIIa in ICH patients as compared with placebo. Further studies are underway to identify specific factors associated with these events and to define the dose that maximizes benefit and minimizes risk.
Uniform High-Current Cathodes Using Massive Arrays of Si Field Emitters Individually Controlled by Vertical Si Ungated FETs—Part 1: Device Design and Simulation (2011)

In this paper, we report the design and simulation of electron sources composed of arrays of Si field emitters (FEs) that are individually ballasted by a current source. Each FE is fabricated on top of a vertical ungated field-effect transistor (FET), a two-terminal device based on a very-high-aspect-ratio Si column. The ungated FET takes advantage of the velocity saturation of electrons in silicon, the high aspect ratio of the ungated FET, and the doping concentration of the semiconductor to achieve current-source-like behavior. The proposed technology can be used to implement cathodes capable of reliable uniform and high current emission.
No User Left Behind (2012)

Usability and accessibility have become increasingly important in computing curricula. This article briefly reviews how these concepts may be included in existing courses. The authors conducted a survey of student attitudes toward these issues at the start and end of a usability engineering course that included a group project with an accessibility component. Results of the survey indicate that students’ awareness of issues related to usability and accessibility are increased after taking the course and completing the project. Our work and results are potentially valuable to CS educators in three ways: (1) They validate the usefulness of the survey instrument in assessing pedagogies in usability engineering, (2) They provide useful insights into the attitudes of CS majors relative to the important topics of usability and accessibility, and (3) They point to possible benefits of including usability and accessibility topics into CS curricula.
Transmission of Avian Influenza Virus (H3N2) to Dogs (2008)

In South Korea, where avian influenza virus subtypes H3N2, H5N1, H6N1, and H9N2 circulate or have been detected, 3 genetically similar canine influenza virus (H3N2) strains of avian origin (A/canine/Korea/01/2007, A/canine/Korea/02/2007, and A/canine/Korea/03/2007) were isolated from dogs exhibiting severe respiratory disease. To determine whether the novel canine influenza virus of avian origin was transmitted among dogs, we experimentally infected beagles with this influenza virus (H3N2) isolate. The beagles shed virus through nasal excretion, seroconverted, and became ill with severe necrotizing tracheobronchitis and bronchioalveolitis with accompanying clinical signs (e.g., high fever). Consistent with histologic observation of lung lesions, large amounts of avian influenza virus binding receptor (SAalpha 2,3-gal) were identified in canine tracheal, bronchial, and bronchiolar epithelial cells, which suggests potential for direct transmission of avian influenza virus (H3N2) from poultry to dogs. Our data provide evidence that dogs may play a role in interspecies transmission and spread of influenza virus.
Treatment of wide-necked intracranial aneurysms with a self-expanding stent system: initial clinical experience. (2003)

Preliminary data demonstrate that this extremely flexible stent is technically easy to deploy and can be easily and safely maneuvered through severely tortuous vessels, enabling the treatment of intracranial wide-necked aneurysms. The combination of endovascular reconstruction of the parent vessel with use of a self-expanding stent followed by coil embolization offers a promising therapeutic alternative for wide-necked aneurysms not amenable to coil embolization alone. Although immediate angiographic results are promising, long-term angiographic and clinical follow-up is essential to determine permanent vessel patency and aneurysm occlusion rate.
Improvement of Biocompatibility of Chitosan Fiber Modified by Ca-Phosphate Deposition through an Alternate Soaking Process (2009)

A tube consisted of chitin/chitosan nanofibers is one of the candidates to support nerve regeneration. However, chitin/chitosan would cause inflammation when implanted in human body. This study indicates that chitosan nanofibers (degree of deacetylation; 78% and 93%) could be modified by alternate soaking in calcium and phosphate solutions, resulting in the improvement of their biocompatibility in terms of both in vitro cell culture experiment and in vivo animal test. Deacetylation of the chitosan nanofibers appeared to have little effect on in vitro and in vivo behaviors after 3 days. However, the alternate soaking process clearly improved in vitro and in vivo responses against the chitosan nanofibers. During the process, the surface morphology of the chitosan nanofiber was not changed, i.e. no hydroxyapatite was deposited due to the limited number of soaking. Thus, the surface chemical and physical states of the modified chitosan nanofiber such as surface charge, surface free-energy, and wettability was found to influence both the cell attachment and inflammation.
The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology (2016)

Recent advances in deep learning and specifically in generative adversarial networks have demonstrated surprising results in generating new images and videos upon request even using natural language as input. In this paper we present the first application of generative adversarial autoencoders (AAE) for generating novel molecular fingerprints with a defined set of parameters. We developed a 7-layer AAE architecture with the latent middle layer serving as a discriminator. As an input and output the AAE uses a vector of binary fingerprints and concentration of the molecule. In the latent layer we also introduced a neuron responsible for growth inhibition percentage, which when negative indicates the reduction in the number of tumor cells after the treatment. To train the AAE we used the NCI-60 cell line assay data for 6252 compounds profiled on MCF-7 cell line. The output of the AAE was used to screen 72 million compounds in PubChem and select candidate molecules with potential anti-cancer properties. This approach is a proof of concept of an artificially-intelligent drug discovery engine, where AAEs are used to generate new molecular fingerprints with the desired molecular properties.
Peptide-based coatings for flexible implantable neural interfaces (2018)

In the last decade, the use of flexible biosensors for neuroprosthetic and translational applications has widely increased. Among them, the polyimide (PI)-based thin-film electrodes got a large popularity. However, the usability of these devices is still hampered by a non-optimal tissue-device interface that usually compromises the long-term quality of neural signals. Advanced strategies able to improve the surface properties of these devices have been developed in the recent past. Unfortunately, most of them are not easy to be developed and combined with micro-fabrication processes, and require long-term efforts to be testable with human subjects. Here we show the results of the design and in vitro testing of an easy-to-implement and potentially interesting coating approach for thin-film electrodes. In particular, two biocompatible coatings were obtained via covalent conjugation of a laminin-derived peptide, CAS-IKVAV-S (IKV), with polyimide sheets that we previously functionalized with vinyl- and amino- groups (PI_v and PI_a respectively). Both the engineered coatings (PI_v+IKV and PI_a+IKV) showed morphological and chemical properties able to support neuronal adhesion, neurite sprouting, and peripheral glial cell viability while reducing the fibroblasts contamination of the substrate. In particular, PI_v+IKV showed promising results that encourage further in vivo investigation and pave the way for a new generation of peptide-coated thin-film electrodes.
MicroRNAs: regulators of gene expression and cell differentiation (2006)

The existence and roles of a class of abundant regulatory RNA molecules have recently come into sharp focus. Micro-RNAs (miRNAs) are small (approximately 22 bases), non-protein-coding RNAs that recognize target sequences of imperfect complementarity in cognate mRNAs and either destabilize them or inhibit protein translation. Although mechanisms of miRNA biogenesis have been elucidated in some detail, there is limited appreciation of their biological functions. Reported examples typically focus on miRNA regulation of a single tissue-restricted transcript, often one encoding a transcription factor, that controls a specific aspect of development, cell differentiation, or physiology. However, computational algorithms predict up to hundreds of putative targets for individual miRNAs, single transcripts may be regulated by multiple miRNAs, and miRNAs may either eliminate target gene expression or serve to finetune transcript and protein levels. Theoretical considerations and early experimental results hence suggest diverse roles for miRNAs as a class. One appealing possibility, that miRNAs eliminate low-level expression of unwanted genes and hence refine unilineage gene expression, may be especially amenable to evaluation in models of hematopoiesis. This review summarizes current understanding of miRNA mechanisms, outlines some of the important outstanding questions, and describes studies that attempt to define miRNA functions in hematopoiesis.
Nonencapsulated, intact omeprazole granules effectively suppress intragastric acidity when administered via a gastrostomy. (1997)

Omeprazole effectively suppresses intragastric acidity when given through a gastrostomy tube as nonencapsulated, intact granules.
Fish Allergy: Fish and Products Thereof (2004)

ABSTRACT: Allergy to fish is a common cause of IgE‐mediated food allergic reactions especially in geographic regions where fish is an important dietary component. Fish allergy is estimated to affect 0.4% of the total population in the United States. All species of fish are believed to be allergenic, but allergic reactions to fish reported in the medical literature are most commonly caused by cod and salmon. The major allergen in fish is a naturally occurring muscle protein called parvalbumin. Some evidence exists of allergic reactions to other fish proteins including collagen. This review addresses fish allergy and fish‐derived ingredients, namely gelatin, isinglass, fish maws, ice‐structuring protein, fish oil, and Worcestershire sauce.
Inorganic Phosphate Export by the Retrovirus Receptor XPR1 in Metazoans (2013)

Inorganic phosphate uptake is a universal function accomplished by transporters that are present across the living world. In contrast, no phosphate exporter has ever been identified in metazoans. Here, we show that depletion of XPR1, a multipass membrane molecule initially identified as the cell-surface receptor for xenotropic and polytropic murine leukemia retroviruses (X- and P-MLV), induced a decrease in phosphate export and that reintroduction of various XPR1 proteins, from fruit fly to human, rescued this defect. Inhibition of phosphate export was also obtained with a soluble ligand generated from the envelope-receptor-binding domain of X-MLV in all human cell lines tested, as well as in diverse stem cells and epithelial cells derived from renal proximal tubules, the main site of phosphate homeostasis regulation. These results provide new insights on phosphate export in metazoans and the role of Xpr1 in this function.