gebhart/patrepeval huggingface dataset:
Synergistic Effect of Bone Marrow Mobilization and Vascular Endothelial Growth Factor-2 Gene Therapy in Myocardial Ischemia (2004)

Mobilization of endothelial progenitor cells with cytokines potentiates VEGF-2 gene therapy for myocardial ischemia and enhances bone marrow cell incorporation into ischemic myocardium.
Validating a Nonhuman Primate Model of Super-Selective Intraophthalmic Artery Chemotherapy: Comparing Ophthalmic Artery Diameters (2012)

Measurements of the OA luminal diameter at its origin were similar between our NHP and pediatric cohort, validating our NHP model for testing both the hemodynamic consequences and toxicities of SSIOAC.
Enhancing solubilization in microemulsions—State of the art and current trends (2005)

Abstract Along a formulation scan, solubilization is maximal when a bicontinuous microemulsion is in equilibrium with both oil and water excess phases in a so‐called Winsor III system. The logical way to enhance solubilization is to increase the interaction of the surfactant for both the oil and water phases, which can be easily attained by increasing the size of both the head and tail groups. However, this approach is limited by solubility constraints. Additional solubilization enhancement can be attained by introducing a molecule(s) that bridge the bulk phase and the adsorbed surfactant layer; this can be accomplished by using the so‐called lipophilic and hydrophilic “linker effect” or by using block copolymer additives. In either case, the goal is to modify an extended zone in the oil and water domains close to their boundary. The intramolecular grafting of a linker group between the hydrophilic and lipophilic moieties in a surfactant results in a so‐called “extended” surfactant structure, which produces enhanced solubilization, as does the surfactant/linker combination, but with the added benefit that the self‐contained extended surfactant structure does not undergo selective partitioning. We conclude that an improvement in solubilization is directly related to the presence of a smooth, blurred, and expanded transition across the interfacial region from polar to apolar bulk phases.
A Survey of Deep Learning for Scientific Discovery (2020)

Over the past few years, we have seen fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. At the same time, the amount of data collected in a wide array of scientific domains is dramatically increasing in both size and complexity. Taken together, this suggests many exciting opportunities for deep learning applications in scientific settings. But a significant challenge to this is simply knowing where to start. The sheer breadth and diversity of different deep learning techniques makes it difficult to determine what scientific problems might be most amenable to these methods, or which specific combination of methods might offer the most promising first approach. In this survey, we focus on addressing this central issue, providing an overview of many widely used deep learning models, spanning visual, sequential and graph structured data, associated tasks and different training methods, along with techniques to use deep learning with less data and better interpret these complex models --- two central considerations for many scientific use cases. We also include overviews of the full design process, implementation tips, and links to a plethora of tutorials, research summaries and open-sourced deep learning pipelines and pretrained models, developed by the community. We hope that this survey will help accelerate the use of deep learning across different scientific domains.
Neural network model for discharge and water-level prediction for Ramganga River catchment of Ganga Basin, India (2015)

Discharges and water levels are essential components of river hydrodynamics. In unreachable terrains and ungauged locations, it is quite difficult to measure these parameters due to rugged topography. In the present study an artificial neural network model has been developed for the Ramganga River catchment of the Ganga Basin. The modelled network is trained, validated and tested using daily water flow and level data pertaining to 4 years (2010–2013). The network has been optimized using an enumeration technique and a network topology of 4-10-2 with a learning rate set at 0.06, which was found optimum for predicting discharge and water-level values for the considered river. The mean square error values obtained for discharge and water level for the tested data were found to be 0.046 and 0.012, respectively. Thus, monsoon flow patterns can be estimated with an accuracy of about 93.42%.Editor M.C. Acreman; Associate editor E. Gargouri
beta-Hydroxyasparagine in domains homologous to the epidermal growth factor precursor in vitamin K-dependent protein S. (1987)

Vitamin K-dependent protein S is involved in the regulation of blood coagulation. It is a 75-kDa single chain protein with an NH2-terminal gamma-carboxyglutamic acid-containing domain followed by a thrombin-sensitive region and four domains arranged in tandem, each of which is homologous to the epidermal growth factor (EGF) precursor. The NH2-terminal EGF-like domain contains beta-hydroxyaspartic acid, which has been identified in vitamin K-dependent proteins. The following EGF-like repeat has a very pronounced sequence homology (10 consecutive residues identical) to one of the EGF-like units in the EGF precursor. We now show that, in protein S, this EGF-like repeat has one beta-hydroxyasparagine residue formed by hydroxylation of asparagine. The two COOH-terminal EGF-like repeats also contain beta-hydroxyasparagine, an amino acid not previously found in proteins. Sequence comparisons have enabled us to identify a consensus sequence that seems to be required by the hydroxylase(s).
Data Security (1979)

The rising abuse of computers and increasing threat to personal privacy through data banks have stimulated much interest in the technical safeguards for data. There are four kinds of safeguards, each related to but distinct from the others. Access controls regulate which users may enter the system and subsequently which data sets an active user may read or write. Flow controls regulate the dissemination of values among the data sets accessible to a user. Inference controls protect statistical databases by preventing questioners from deducing confidential information by posing carefully designed sequences of statistical queries and correlating the responses. Statistical data banks are much less secure than most people believe. Data encryption attempts to prevent unauthorized disclosure of confidential information in transit or in storage. This paper describes the general nature of controls of each type, the kinds of problems they can and cannot solve, and their inherent limitations and weaknesses. The paper is intended for a general audience with little background in the area.
Toward antisense oligonucleotide therapy for cancer: ISIS compounds in clinical development. (1999)

Antisense oligonucleotides offer the promise of therapeutic effect with few toxic effects, by virtue of their high selectivity. Preclinical studies have provided evidence of antisense effects in vitro and in vivo, and phase I clinical trials have demonstrated safety, feasibility and activity of antisense oligonucleotides for the treatment of cancer. This review summarizes the status of development of three anticancer antisense oligonucleotides from ISIS Pharmaceuticals.
Detection of transient signals by the Gabor representation (1989)

Gabor representation is used for the detection of transient signals with unknown arrival times. A one-sided exponential window function is used which seems to be most appropriate for transient modelling. Explicit expressions for the Gabor coefficients are given for this window function. When the given signal is random, so are the coefficients. The second-order moments of the Gabor coefficients are computed for a white noise signal. These are then used to introduce a detection statistic based on the Gabor coefficients. The proposed detector is capable of separating transients having different arrival times, even in this case where their waveforms partially overlap.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Resource-Oriented Petri Net for Deadlock Avoidance in Flexible Assembly Systems (2007)

In many flexible assembly systems, base components are transported with pallets; parts to be mounted onto the base ones are transported by trays with no pallets. When an assembly operation is performed by using some parts in a tray but not all, the tray with the remaining parts still occupies a buffer space. In this way, an assembly/disassembly material flow is formed. In such a material flow, deadlock can occur both in the base component and part flow. Furthermore, the assembly operations can also result in a deadlock. Thus, it is a great challenge to tackle deadlocks in such processes. This paper models them using resource-oriented Petri nets. Based on the models, a deadlock control policy is proposed and proved to be computationally efficient and less conservative than the existing policies in the literature. An industrial case study is used to show the results.
Human Serum Binding Capacity and Affinity for 25-Hydroxyergocalciferol and 25-Hydroxycholecalciferol (1976)

25-Hydroxyvitamin D-binding capacity and affinity were studied in human cord, adult, and maternal sera, and in sera from women receiving oral contraceptives, by in vitro satuaration analyses employing dextran-coated charcoal to adsorb unbound sterol. 25-Hydroxyergocalciferol and 25-hydroxycholecalciferol were equipotent in their ability to displace 3H 25-hydroxycholecalciferol from human serum binding sites. At 0C, the apparent dissociation constant for the serum binding of 25-hydroxycholecalciferol was low (Kd=8x 10-10M). Cord and adult sera had a similar 25-hydroxycholecalciferol binding capacity (1.8 x 10-6M), but the binding capacity of maternal sera and the sera from women receiving oral contraceptives was significantly higher. At physiological serum concentrations of 25-hydroxyvitamin D (5 x 10-8M), only 2-3% of human serum 25-hydroxyvitamin D-bindig sites are occupied.
Attenuation of Simian Immunodeficiency Virus SIVmac239 Infection by Prophylactic Immunization with DNA and Recombinant Adenoviral Vaccine Vectors Expressing Gag (2005)

The prophylactic efficacy of DNA and replication-incompetent adenovirus serotype 5 (Ad5) vaccine vectors expressing simian immunodeficiency virus (SIV) Gag was examined in rhesus macaques using an SIVmac239 challenge. Cohorts of either Mamu-A*01(+) or Mamu-A*01(-) macaques were immunized with a DNA prime-Ad5 boost regimen; for comparison, a third cohort consisting of Mamu-A*01(+) monkeys was immunized using the Ad5 vector alone for both prime and boost. All animals, along with unvaccinated control cohorts of Mamu-A*01(+) and Mamu-A*01(-) macaques, were challenged intrarectally with SIVmac239. Viral loads were measured in both peripheral and lymphoid compartments. Only the DNA prime-Ad5-boosted Mamu-A*01(+) cohort exhibited a notable reduction in peak plasma viral load (sevenfold) as well as in early set-point viral burdens in both plasma and lymphoid tissues (10-fold) relative to those observed in the control monkeys sharing the same Mamu-A*01 allele. The degree of control in each animal correlated with the levels of Gag-specific immunity before virus challenge. However, virus control was short-lived, and indications of viral escape were evident as early as 6 months postinfection. The implications of these results in vaccine design and clinical testing are discussed.
Quality of Acute Psychedelic Experience Predicts Therapeutic Efficacy of Psilocybin for Treatment-Resistant Depression (2018)

<b>Introduction:</b> It is a basic principle of the "psychedelic" treatment model that the quality of the acute experience mediates long-term improvements in mental health. In the present paper we sought to test this using data from a clinical trial assessing psilocybin for treatment-resistant depression (TRD). In line with previous reports, we hypothesized that the occurrence and magnitude of Oceanic Boundlessness (OBN) (sharing features with mystical-type experience) and Dread of Ego Dissolution (DED) (similar to anxiety) would predict long-term positive outcomes, whereas sensory perceptual effects would have negligible predictive value. <b>Materials and Methods:</b> Twenty patients with treatment resistant depression underwent treatment with psilocybin (two separate sessions: 10 and 25 mg psilocybin). The Altered States of Consciousness (ASC) questionnaire was used to assess the quality of experiences in the 25 mg psilocybin session. From the ASC, the dimensions OBN and DED were used to measure the mystical-type and challenging experiences, respectively. The Self-Reported Quick Inventory of Depressive Symptoms (QIDS-SR) at 5 weeks served as the endpoint clinical outcome measure, as in later time points some of the subjects had gone on to receive new treatments, thus confounding inferences. In a repeated measure ANOVA, Time was the within-subject factor (independent variable), with QIDS-SR as the within-subject dependent variable in baseline, 1-day, 1-week, 5-weeks. OBN and DED were independent variables. OBN-by-Time and DED-by-Time interactions were the primary outcomes of interest. <b>Results:</b> For the interaction of OBN and DED with Time (QIDS-SR as dependent variable), the main effect and the effects at each time point compared to baseline were all significant (<i>p</i> = 0.002 and <i>p</i> = 0.003, respectively, for main effects), confirming our main hypothesis. Furthermore, Pearson's correlation of OBN with QIDS-SR (5 weeks) was specific compared to perceptual dimensions of the ASC (<i>p</i> < 0.05). <b>Discussion:</b> This report further bolsters the view that the quality of the acute psychedelic experience is a key mediator of long-term changes in mental health. Future therapeutic work with psychedelics should recognize the essential importance of <i>quality of experience</i> in determining treatment efficacy and consider ways of enhancing mystical-type experiences and reducing anxiety. <b>Trial Registration:</b> ISRCTN, number ISRCTN14426797, http://www.isrctn.com/ISRCTN14426797.
Cation−π Interactions in Ligand Recognition by Serotonergic (5-HT3A) and Nicotinic Acetylcholine Receptors:  The Anomalous Binding Properties of Nicotine (2002)

A series of tryptophan analogues has been introduced into the binding site regions of two ion channels, the ligand-gated nicotinic acetylcholine and serotonin 5-HT(3A) receptors, using unnatural amino acid mutagenesis and heterologous expression in Xenopus oocytes. A cation-pi interaction between serotonin and Trp183 of the serotonin channel 5-HT(3A)R is identified for the first time, precisely locating the ligand-binding site of this receptor. The energetic contribution of the observed cation-pi interaction between a tryptophan and the primary ammonium ion of serotonin is estimated to be approximately 4 kcal/mol, while the comparable interaction with the quaternary ammonium of acetylcholine is approximately 2 kcal/mol. The binding mode of nicotine to the nicotinic receptor of mouse muscle is examined by the same technique and found to differ significantly from that of the natural agonist, acetylcholine.
Big data exploration requires collaboration between visualization and data infrastructures (2016)

As datasets grow to tera- and petabyte sizes, exploratory data visualization becomes very difficult: a screen is limited to a few million pixels, and main memory to a few tens of millions of data points. Yet these very large scale analyses are of tremendous interest to industry and academia. This paper discusses some of the major challenges involved in data analytics at scale, including issues of computation, communication, and rendering. It identifies techniques for handling large scale data, grouped into "look at less of it," and "look at it faster." Using these techniques involves a number of difficult design tradeoffs for both the ways that data can be represented, and the ways that users can interact with the visualizations.
Improved brain uptake of peptide-based CNS drugs via alternative routes of administrations of its nanocarrier delivery systems: a promising strategy for CNS targeting delivery of peptides (2014)

Although using nanocarriers or delivery via alternative routes could improve to a certain extent the brain uptake of peptides, the magnitude of changes remains moderate. Alternatively, intranasal administration of nanocarriers loaded with peptide has been demonstrated to be an effective approach for CNS-targeted delivery of peptides.
The syntax augmented MT (SAMT) system for the shared task in the 2007 ACL Workshop on Statistical Machine Translation (2007)

We describe the CMU-UKA Syntax Augmented Machine Translation system 'SAMT' used for the shared task "Machine Translation for European Languages" at the ACL 2007 Workshop on Statistical Machine Translation. Following an overview of syntax augmented machine translation, we describe parameters for components in our open-source SAMT toolkit that were used to generate translation results for the Spanish to English in-domain track of the shared task and discuss relative performance against our phrase-based submission.
Protein Purification Protocols (1996)

General Strategies, Shawn Doonan. Preparation of Extracts from Animal Tissues, Shawn Doonan. Protein Extraction from Plant Tissues, Peter R. Shewry and Roger J. Fido. Extraction of Recombinant Protein from Bacteria, D. Margaret Worrall. Protein Extraction from Fungi, Paul Bridge. Subcellular Fractionation of Animal Tissues, Norma M. Ryan. Subcellular Fractionation of Plant Tissues: Isolation of Chloroplasts and Mitochondria from Leaves, Alyson K. Tobin. The Extraction of Enzymes from Plant Tissues Rich in Phenolic Compounds, William S. Pierpoint. Avoidance of Proteolysis in Extracts, Robert J. Beynon and Simon Oliver. Concentration of Extracts, Shawn Doonan. Making and Changing Buffers, Shawn Doonan. Purification and Concentration by Ultrafiltration, Paul Schratter. Bulk Purification by Fractional Precipitation, Shawn Doonan. Ion-Exchange Chromatography, David Sheehan and Richard FitzGerald. Hydrophobic Interaction Chromatography, Paul O'Farrell. Affinity Chromatography, Paul Cutler. Dye-Ligand Affinity Chromatography, D. Margaret Worrall. Lectin Affinity Chromatography, Iris West and Owen Goldring. Immunoaffinity Chromatography, George W. Jack and David J. Beer. Immobilized Metal Ion Affinity Chromatography, Tai-Tung Yip and T. William Hutchens. Chromatography on Hydroxyapatite, Shawn Doonan. Affinity Precipitation Methods, Jane A. Irwin and Keith F. Tipton. Isoelectric Focusing, Reiner Westermeier. Chromatofocusing, Timothy J. Mantle and Patricia Noone. Size-Exclusion Chromatography, Paul Cutler. Fast Protein Liquid Chromatography (FPLC) Methods, David Sheehan. Reversed-Phase Chromatography of Proteins, Bill Neville. Extraction of Membrane Proteins, Kay Ohlendieck. Removal of Detergent from Protein Fractions, Kay Ohlendieck. Purification of Membrane Proteins, Kay Ohlendieck. Lyophilization of Proteins, Ciaran A Fagain. Storage of Pure Proteins, Ciaran A Fagain. Electroelution of Proteins from Polyacrylamide Gels, Michael J. Dunn. Electroblotting of Proteins from Polyacrylamide Gels, Michael J. Dunn. High-Performance Electrophoresis Chromatography, Serge Desnoyers, Sylvie Bourassa, and Guy G. Poirier. Practical Column Chromatography, Shawn Doonan. Index.
Isolation and Characterization of D‐Threonine Aldolase, A Pyridoxal‐5′‐Phosphate‐Dependentenzyme from Arthrobacter sp. DK‐38 (1997)

D-Threonine aldolase is an enzyme that catalyzes the cleavage of D-threonine into glycine and acetaldehyde. Its activity was found in several genera of bacteria such as Arthrobacter, Alcaligenes, Xanthomonas, and Pseudomonas, but not in yeasts or fungi. The enzyme was purified to homogeneity from one strain, Arthrobacter sp. DK-38. The enzyme appeared to consist of a single polypeptide chain with an apparent molecular mass of 51 kDa. This enzyme, as well as L-threonine aldolase, requires pyridoxal 5'-phosphate (pyridoxal-P) as a coenzyme. Unlike other pyridoxal-P enzymes, D-threonine aldolase also requires a divalent cation such as Co2+, Ni2+, Mn2+, or Mg2+ for its catalytic activity. The enzyme completely lost its activity in the absence of either pyridoxal-P or a divalent cation. A divalent cation was also essential for the thermal stability of the enzyme. The metal-free enzyme tends to become thermally unstable, resulting in the irreversible loss of its catalytic activity. The enzyme is strictly D-specific for the alpha-position, whereas it cannot distinguish between threo and erythro forms at the beta-position. Thus, D-threonine and D-allothreonine act as substrates of the enzyme, but their kinetic parameters are different; the Km and Vmax values are 3.81 mM and 38.8 micromol x min(-1) x mg(-1) toward D-threonine, and 14.0 mM and 102 micromol x min(-1) x mg(-1) toward D-allothreonine. respectively. The aldolase reaction is reversible, and the enzyme is therefore able to produce nearly equimolar amounts of D-threonine and D-allothreonine through C-C bond formation between glycine and acetaldehyde. The enzyme also acts, in the same manner, on several other D-beta-hydroxy-alpha-amino acids, including D-beta-phenylserine, D-beta-hydroxy-alpha-aminovaleric acid, D-beta-3,4-dihydroxyphenylserine, and D-beta-3,4-methylenedioxyphenylserine.
Matrices, Vector Spaces, and Information Retrieval (1999)

The evolution of digital libraries and the Internet has dramatically transformed the processing, storage, and retrieval of information. Efforts to digitize text, images, video, and audio now consume a substantial portion of both academic and industrial activity. Even when there is no shortage of textual materials on a particular topic, procedures for indexing or extracting the knowledge or conceptual information contained in them can be lacking. Recently developed information retrieval technologies are based on the concept of a vector space. Data are modeled as a matrix, and a user's query of the database is represented as a vector. Relevant documents in the database are then identified via simple vector operations. Orthogonal factorizations of the matrix provide mechanisms for handling uncertainty in the database itself. The purpose of this paper is to show how such fundamental mathematical concepts from linear algebra can be used to manage and index large text collections.
Prognostic and Therapeutic Significance of Carbohydrate Antigen 19-9 as Tumor Marker in Patients with Pancreatic Cancer (2006)

In pancreatic cancer (PC) accurate determination of treatment response by imaging often remains difficult. Various efforts have been undertaken to investigate new factors which may serve as more appropriate surrogate parameters of treatment efficacy. This review focuses on the role of carbohydrate antigen 19-9 (CA 19-9) as a prognostic tumor marker in PC and summarizes its contribution to monitoring treatment efficacy. We undertook a Medline/PubMed literature search to identify relevant trials that had analyzed the prognostic impact of CA 19-9 in patients treated with surgery, chemoradiotherapy and chemotherapy for PC. Additionally, relevant abstract publications from scientific meetings were included. In advanced PC, pretreatment CA 19-9 levels have a prognostic impact regarding overall survival. Also a CA 19-9 decline under chemotherapy can provide prognostic information for median survival. A 20% reduction of CA 19-9 baseline levels within the first 8 weeks of chemotherapy appears to be sufficient to define a prognostic relevant subgroup of patients ('CA 19-9 responder'). It still remains to be defined whether the CA 19-9 response is a more reliable method for evaluating treatment efficacy compared to conventional imaging.