gebhart/patrepeval huggingface dataset:
Degradation of the Pesticide Fenitrothion as Mediated by Cationic Surfactants and α-Nucleophilic Reagents (2006)

The reaction of fenitrothion with a series of alpha-nucleophile oximates having pK(a) values in the range of 7.7-11.8 was studied both in the absence and presence of cetyltrimethylammonium (CTA(+)) surfactants. Reaction with CTA-oximates was found to proceed through two pathways: S(N)2(P) and S(N)2(C); an S(N)Ar pathway was not observed. Accordingly, the observed rate constants were dissected into the two corresponding S(N)2(P) and S(N)2(C) pathways. Use of the pseudophase ion exchange (PPIE) model for micellar catalysis in the CTA(+) system allowed evaluation of micellar second-order rate constant (k(2m)) parameters and binding constants, (K(S)). K(S) values for CTA-oximates were found to vary with the counterion, and the rate enhancement depended on a combination of K(S) and k(2m) values. k(2m)/k(2w) values ranged from 0.0025 to 0.64, suggesting that a concentration effect is mainly responsible for the rate enhancement. In the absence of surfactant, an alpha-effect (i.e., k(alpha)/k(normal)) varying from 8 to 450 was observed for the oximate reaction, decreasing with increasing pK(a). It is proposed that differential solvation (transition-state imbalance) is a cause of the alpha-effect in this system.
A secure cookie protocol (2006)

Cookies are the primary means for Web applications to authenticate HTTP requests and to maintain client states. Many Web applications (such as electronic commerce) demand a secure cookie protocol. Such a protocol needs to provide the following four services: authentication, confidentiality, integrity and antireplay. Several secure cookie protocols have been proposed in previous literature; however, none of them are completely satisfactory. In this paper, we propose a secure cookie protocol that is effective, efficient, and easy to deploy. In terms of effectiveness, our protocol provides all of the above four security services. In terms of efficiency, our protocol does not involve any database lookup or public key cryptography. In terms of deployability, our protocol can be easily deployed on an existing Web server, and it does not require any change to the Internet cookie specification. We implemented our secure cookie protocol using PHP, and the experimental results show that our protocol is very efficient.
Nef-Induced CD4 Downregulation: a Diacidic Sequence in Human Immunodeficiency Virus Type 1 Nef Does Not Function as a Protein Sorting Motif through Direct Binding to β-COP (2001)

The Nef protein from the human immunodeficiency virus (HIV) induces CD4 cell surface downregulation by interfering with the endocytic machinery. It has been recently proposed that binding of HIV type 1 Nef to the beta subunit of COPI coatomers participated in the Nef-induced CD4 downregulation through recognition of a novel diacidic motif found in the C-terminal disordered loop of Nef (V. Piguet, F. Gu, M. Foti, N. Demaurex, J. Gruenberg, J. L. Carpentier, and D. Trono, Cell 97:63-73, 1999). We have mutated the glutamate residues which formed this motif in order to document this observation. Surprisingly, mutation of the diacidic sequence of Nef did not significantly affect its ability (i) to interact with beta-COP, (ii) to downregulate CD4 cell surface expression, and (iii) to address an integral resident membrane protein containing Nef as the cytoplasmic domain to the endocytic pathway. Our results indicate that these acidic residues are not involved in the connection of Nef with the endocytic machinery through binding to beta-COP. Additional studies are thus required to characterize the residues of Nef involved in the binding to beta-COP and to evaluate the contribution of this interaction to the Nef-induced perturbations of membrane trafficking.
Baclofen in Parkinson's disease. (1978)

In a controlled trial, baclofen (mean dose 45 mg daily) signficantly increased disability from Parkinsonism in 12 patients with the long-term levodopa syndrome. Peak dose choreoathetosis was not improved but benefit was observed in all four patients with "off period dystonia." Adverse side effects were common and severe, and included visual hallucinations, vomiting, and dizziness.
Autosomal Admixture Levels Are Informative About Sex Bias in Admixed Populations (2014)

Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.
Easy-to-use object-oriented parallel processing with Mentat (1993)

Mentat, an object-oriented parallel processing system designed to directly address the difficulty of developing architecture-independent parallel programs, is discussed. The Mentat system consists of two components: the Mentat programming language and the Mentat runtime system. The Mentat programming language, which is based on C++, is described. Performance results from implementing the Mentat runtime system on a network of Sun 3 and 4 workstations, the Silicon Graphics Iris, the Intel iPSC/2, and the Intel iPSC/860 are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Parallel algorithms for automatic target recognition using laser radar imagery</title> (1990)

This paper describes two techniques for automatic recognition of surface targets from an airborne platform using an imaging laser radar sensor. The first technique rotates a three-dimensional model of the target in real time to enable a generalized Hough transform to match the ladar image to the target''s key discriminating features as a basis for target identification. The second technique uses a variation on minimum average correlation energy filters to perform robust target identification. Examples illustrating the application of these algorithms are presented along with a description of a real-time implementation of the critical parts of the algorithms on a 40 systolic array based on the Geometric Arithmetic Parallel Processor (GAPP) chip.
The effects of insertion of nitrogen atoms on the aromatic nitrogen‐containing compounds: a potential approach for designing stable radical molecular materials (2011)

The effects of insertion of nitrogen atoms on the N―H bond strength of azaphenalene and on the stability of the corresponding radicals were comprehensively investigated using density functional theory. The N―H bond dissociation enthalpy of azaphenalene is found to be strengthened in all cases, but the magnitudes are various with the replaced sites and are additive. It is correlated with the coefficient of frontier molecular orbital; that is, it is correlated with the electron density distribution of the outer electrons. The computational results explain why the product substituted with two CH groups by N atoms in the phenalenyl skeleton yielded radical easily, whereas the product replaced with six nitrogen atoms failed. In addition, the effects of insertion of nitrogen atoms in other aromatic nitrogen‐containing compounds, including carbazole, indole, and pyrrole, were also studied. All the understanding about the insertion effects of nitrogen atoms would be helpful in designing novel molecules for specific applications, such as functional materials and antioxidants. Copyright © 2011 John Wiley & Sons, Ltd.
In Situ Chemical Aminoacylation with Amino Acid Thioesters Linked to a Peptide Nucleic Acid (2004)

tRNA-specific chemical aminoacylation was achieved with nonnatural amino acids. A nonnatural amino acid was activated as a thioester derivative, and the latter was linked through a spacer to the N-terminal of a 9-mer peptide nucleic acid that is complementary to the 3'-terminal region of yeast phenylalanine tRNA. Efficient aminoacylation was observed when the amino acid thioester-spacer-PNA conjugate was mixed with the tRNA. The PNA-assisted aminoacylation was also successful in an Escherichia coli in vitro protein synthesizing system that contained an orthogonalized tRNA. The in situ aminoacylation/in vitro translation gave a mutant protein in which the nonnatural amino acid was incorporated into the position directed by a CGGG 4-base codon/anticodon pair.
Deficits in gastrointestinal responses controlling food intake and body weight (2010)

The gastrointestinal tract serves as a portal sensing incoming nutrients and relays mechanical and chemosensory signals of a meal to higher brain centers. Prolonged consumption of dietary fat causes adaptive changes within the alimentary, metabolic, and humoral systems that promote a more efficient process for energy metabolism from this rich source, leading to storage of energy in the form of adipose tissue. Furthermore, prolonged ingestion of dietary fats exerts profound effects on responses to signals involved in termination of a meal. This article reviews the effects of ingested fat on gastrointestinal motility, hormone release, and neuronal substrates. It focuses on changes in sensitivity to satiation signals resulting from chronic ingestion of high-fat diet, which may lead to disordered appetite and dysregulation of body weight.
A Low Protein Diet Alters the Balance of Islet Cell Replication and Apoptosis in the Fetal and Neonatal Rat and Is Associated with a Reduced Pancreatic Expression of Insulin-Like Growth Factor-II1 (1999)

A programmed turnover of pancreatic beta cells occurs in the neonatal rat involving a loss of beta cells by apoptosis, and their replacement by islet cell replication and neogenesis. The timing of apoptosis is associated with a loss of expression of a survival factor, insulin-like growth factor-II (IGF-II), in the pancreatic islets. Offspring from rats chronically fed a low protein isocalorific diet (LP) exhibit a reduced pancreatic beta cell mass at birth and a reduced insulin secretion in later life. This study therefore investigated the impact of LP on islet cell ontogeny in the late fetal and neonatal rat, and any associated changes in the presence of IGFs and their binding proteins (IGFBPs). Pregnant Wistar rats were fed either LP (8% protein) or normal (C) (20% protein) chow from shortly after conception until the offspring were 21 days postnatal (PN). Bromo-deoxyuridine (BrdU) was administered 1 h before rats were killed and pancreata removed from animals between 19.5 days fetal life and postnatal day 21. Offspring of rats given LP diet had reduced birthweight, pancreatic beta cell mass, and pancreas insulin content, with smaller islets compared with control fed animals, which persisted to weaning. Histological analysis showed that islets from pups given LP diet had a lower nuclear labeling index with BrdU in the beta cells, although, paradoxically, more beta cells showed immunoreactivity for proliferating cell nuclear antigen (PCNA). Because PCNA is present in G1 as well as S phase of the cell cycle, we quantified the number of beta cells immunopositive for cyclin D1, a marker of G1, and NEK2, an indicator of cells in G2 and mitosis. More beta cells in islets from LP-fed animals contained cyclin D1, but less contained NEK2 than did those in controls. This suggests that the beta cell cycle may have a prolonged G1 phase in LP-fed animals in vivo. Offspring of rats given C diet had a low rate of islet cell apoptosis detected by the TUNEL method in fetal and neonatal life (1-2%), with a transient increase to 8% at PN day 14. Offspring of rats receiving LP diet demonstrated a significantly greater level of islet cell apoptosis at every age, rising to 15% at PN 14. IGF-II mRNA was quantified in whole pancreas and was significantly reduced in LP-fed animals at ages up to PN day 10. IGF-II immunoreactivity within the islets of LP-fed rats was also less apparent, but no changes were seen in immunoreactive IGF-I or IGFBPs-2 to -5. These findings show that LP diet changes the balance of beta cell replication and apoptosis in fetal and neonatal neonatal life, which may involve an altered length of beta cell cycle, and contribute to the smaller islet size and impaired insulin release seen in later life. A reduced pancreatic expression of IGF-II may contribute to the lower beta cell proliferation rate and increased apoptosis seen in the fetus and neonate after feeding LP diet.
Oleic Acid enhances all-trans retinoic Acid loading in nano-lipid emulsions. (2016)

The aim of this study was to investigate the enhancement of all-trans retinoic acid (ATRA) loading in nano-lipid emulsions and stability by using oleic acid. The effect of formulation factors including initial ATRA concentration and the type of oil on the physicochemical properties, that is, percentage yield, percentage drug release, and photostability of formulations, was determined. The solubility of ATRA was increased in the order of oleic acid > MCT > soybean oil > water. The physicochemical properties of ATRA-loaded lipid emulsion, including mean particle diameter and zeta potential, were modulated by changing an initial ATRA concentration as well as the type and mixing ratio of oil and oleic acid as an oil phase. The particles of lipid emulsions had average sizes of less than 250 nm and negative zeta potential. The addition of oleic acid in lipid emulsions resulted in high loading capacity. The photodegradation rate was found to be dependent on the initial drug concentration but independent of the type of oily phase used in this study. The release rates were not affected by initial ATRA concentration but were affected by the type of oil, where oleic acid showed the highest release rate of ATRA from lipid emulsions.
Disentangling Genetic Variation for Resistance and Tolerance to Infectious Diseases in Animals (2007)

Hosts can in principle employ two different strategies to defend themselves against parasites: resistance and tolerance. Animals typically exhibit considerable genetic variation for resistance (the ability to limit parasite burden). However, little is known about whether animals can evolve tolerance (the ability to limit the damage caused by a given parasite burden). Using rodent malaria in laboratory mice as a model system and the statistical framework developed by plant-pathogen biologists, we demonstrated genetic variation for tolerance, as measured by the extent to which anemia and weight loss increased with increasing parasite burden. Moreover, resistance and tolerance were negatively genetically correlated. These results mean that animals, like plants, can evolve two conceptually different types of defense, a finding that has important implications for the understanding of the epidemiology and evolution of infectious diseases.
Using Crowdsourcing to Investigate Perception of Narrative Similarity (2014)

For many applications measuring the similarity between documents is essential. However, little is known about how users perceive similarity between documents. This paper presents the first large-scale empirical study that investigates perception of narrative similarity using crowdsourcing. As a dataset we use a large collection of Dutch folk narratives. We study the perception of narrative similarity by both experts and non-experts by analyzing their similarity ratings and motivations for these ratings. While experts focus mostly on the plot, characters and themes of narratives, non-experts also pay attention to dimensions such as genre and style. Our results show that a more nuanced view is needed of narrative similarity than captured by story types, a concept used by scholars to group similar folk narratives. We also evaluate to what extent unsupervised and supervised models correspond with how humans perceive narrative similarity.
A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data (2013)

Source code and executables are available from github.com/brendanofallon/SNPSVM/
Effect of ribose on thallium-201 myocardial redistribution. (1988)

Myocardial 201Tl redistribution after transient ischemia may be too slow to allow identification of a reversible myocardial defect within the routine 201Tl imaging period. To determine whether 201Tl redistribution could be affected by a metabolic intervention, intravenous ribose was administered postischemia. Seventeen domestic swine were subjected to a 10-min ischemic period followed by either a 30-min i.v. ribose (n = 8) or saline (n = 9) infusion. Thallium-201 was injected during ischemia and myocardial 201Tl activity was continuously monitored in ischemic and nonischemic regions with miniature CdTe radiation detection probes. Coronary flow in the ischemic region was reduced to 25% of that in the nonischemic regions in both saline and ribose groups. The 201Tl time-activity curves demonstrated a significant enhancement of % 201Tl redistribution in the ribose-treated animals at the end of ribose infusion: Ribose (48 +/- 11%), Saline (20 +/- 4%), p less than 0.05. Alteration of 201Tl kinetics by ribose may permit earlier recognition of 201Tl myocardial redistribution after transient ischemia.
Image‐directed, tissue‐preserving focal therapy of prostate cancer: a feasibility study of a novel deformable magnetic resonance‐ultrasound ( <scp>MR‐US</scp> ) registration system (2013)

Non-rigid MR-US registration is feasible, efficient and can locate lesions on US. The process has potential for improved accuracy of focal treatments, and improved diagnostic sampling strategies for prostate cancer. Further work on whether deformable MR-US registration impacts on efficacy is required.
Handbook for Matrix Computations (1988)

1. A Subset of Fortran 77. Basics, Logical Operations, Loops, Arrays, Subprograms, Input/Output, Complex Arithmetic, Programming Tips, Fortran 77 Built-in Functions 2. The BLAS. Bookkeeping Operations, Vector Operations, Norm Computations, Givens Rotations, Double Precision and Complex Versions 3.LINPACK. Triangular Systems, General Systems, Symmetric Systems, Banded Systems, The QR Factorization, The Singular Value Decomposition, Double Precision and Complex Versions 4. MATLAB. Basics, Loops and Conditionals, Built-in Functions, Working with Submatrices, Functions, Factorizations, Miscellaneous.
Polar coding for secure transmission and key agreement (2010)

Wyner's work on wiretap channels and the recent works on information theoretic security are based on random codes. Achieving information theoretical security with practical coding schemes is of definite interest. In this note, the attempt is to overcome this elusive task by employing the polar coding technique of Arikan. It is shown that polar codes achieve nontrivial perfect secrecy rates for binary-input degraded wiretap channels while enjoying their low encoding-decoding complexity. In the special case of symmetric main and eavesdropper channels, this coding technique achieves the secrecy capacity. Next, fading erasure wiretap channels are considered and a secret key agreement scheme is proposed, which requires only the statistical knowledge of the eavesdropper channel state information (CSI). The enabling factor is the creation of advantage over Eve, by blindly using the proposed scheme over each fading block, which is then exploited with privacy amplification techniques to generate secret keys.
Major Response to Imatinib Mesylate in <i>KIT</i>-Mutated Melanoma (2008)

two primary malignancies that originated outside of the CNS. In addition, this is the first reported case of a synchronous malignant melanoma and a small-cell lung cancer metastasizing to the same anatomic location. This case illustrates the necessity of proper pathologic evaluation in a brain lesion assumed to be a metastasis. In this case, had the patient's performance status improved after her motor vehicle accident, she would have been offered systemic chemotherapy for her extensive-stage smallcell lung cancer, which can markedly improve survival, even in advanced disease. If this brain lesion had proven to be solely melanoma, it is unlikely that any systemic treatment would have been offered.
Double lateral shearing interferometer for the quantitative measurement of tear film topography (2005)

A lateral shearing interferometer designed and built for the study of the precorneal tear film topography dynamics and its effect on visual performance is presented. Simple data processing algorithms are discussed and tested on data illustrating different tear topography features: postblink tear undulation, tear breakup, eyelid-produced bumps and ridges, bubbles, and rough precontact lens tear surfaces.
Joint source-channel decoding using the residual redundancy in compressed images (2002)

A joint source-channel decoding approach is described, which utilizes the residual redundancy in the bit stream of a source-coded image by employing a modified APRI-SOVA (a priori soft-output Viterbi algorithm) at the channel decoder. The source coders used are the nonadaptive discrete cosine transform coding and subband coding with Lloyd-Max (1960) quantization. The log-likelihood ratio describing the a priori information is linearized. The reliability of the current bit is computed as a proper linear combination of the soft values characterizing statistical dependency of the zero-th order (probability of 1s or 0s) and the first order (bit correlation among neighboring samples). Substantial subjective and objective performance gains can be obtained by using this method. It is demonstrated that especially in a noisy environment, it may be better to keep the residual redundancy in the data and use it at the receiver side in order to achieve a more reliable decoding, rather than to further remove it by using a variable length coding. The trade-off between the allocation of bits for source and channel coding is also addressed.