gebhart/patrepeval huggingface dataset:
Miscibility of Rigid-Rod and Random-Coil Macromolecules through Acid−Base Interactions (1999)

Acid−base interactions can be used to overcome the free energy barrier to the mixing of rods and coils, originating primarily from the reduced entropy of the coil conformation in the presence of rods. A study of rigid-rod polydiacetylene, carrying pyridine side groups, and sulfonated polystyrene blends, in conjunction with a modified Flory theory, shows a rich variety of observed and expected phase behavior.
HALOGENATION OF AROMATIC METHYL KETONES USING OXONE® AND SODIUM HALIDE (2001)

Aromatic methyl ketones undergo α-halogenation on treatment with sodium halide in the presence of oxone® in aqueous methanol. However, electron-rich hetero aromatic methyl ketones afford ring bromination products preferentially.
Simple Method for Quantitative Analysis of N-Linked Glycoproteins in Hepatocellular Carcinoma Specimens (2009)

Changes in N-linked glycan structures are related to the initiation and progression of hepatocellular carcinoma (HCC), one of the most common fatal cancers worldwide. In this study, we describe a simple and an efficient strategy for the selective identification and quantitation of N-linked glycoproteins that does not require extensive enrichment steps prior to MS/MS analysis. With this approach, N-linked glycoprotein differences between the plasma of healthy and HCC patients were selectively quantified after iTRAQ labeling. We identified a total of 14 N-linked glycopeptides with higher expression in HCC patient plasma than in healthy controls (>or=1.5 fold). Additionally, we characterized alterations in the glycan structures of vitronectin (Asn-169, 242) and antithrombin III (Asn-225) that were identified in HCC patient plasma. The intact glycopeptides with native glycan structures were also elevated in HCC tumor tissue. Taken together, these data support the utility of our approach for high throughput global profiling and quantification of the N-linked glycopeptides to identify disease biomarkers.
Trends in Pharmaceutical Taste Masking Technologies: A Patent Review (2009)

According to the year 2003 survey of pediatricians by the American Association of Pediatrics, unpleasant taste was the biggest barrier for completing treatment in pediatrics. The field of taste masking of active pharmaceutical ingredients (API) has been continuously evolving with varied technologies and new excipients. The article reviews the trends in taste masking technologies by studying the current state of the art patent database for the span of year 1997 to 2007. The worldwide database of European patent office (http://ep.espacenet.com) was employed to collect the patents and patent applications. It also discusses the possible reasons for the change of preferences in the taste masking technologies with time. The prime factors critical to the selection of an optimal taste masking technique such as the extent of drug bitterness, solubility, particle characteristics, dosage form and dose are briefly discussed.
122. The interaction of o-chloromethylphenacyl chloride and primary amines: a novel formation of the isoindoline system (1959)

I. G. Hinton, F. G. Mann and A. Vanterpool, J. Chem. Soc., 1959, 610 DOI: 10.1039/JR9590000610
Cellular Anti-Melanogenic Effects of a Euryale ferox Seed Extract Ethyl Acetate Fraction via the Lysosomal Degradation Machinery (2015)

The aim of this study was to investigate the effect of ethyl acetate fraction of Euryale ferox seed extracts (Efse-EA) on melanogenesis in immortalized mouse melanocyte cell line, melan-a. Efse-EA showed strong dose-dependent mushroom tyrosinase inhibitory activity. Treatment of melan-a cells with 30 μg/mL Efse-EA produced strong inhibition of cellular tyrosinase and melanin synthesis. Efse-EA significantly reduced the levels of melanogenesis-related proteins, such as tyrosinase, tyrosinase-related proteins 1 and 2, and microphthalmia-associated transcription factor. Because Efse-EA treatment reduced tyrosinase protein levels without changing its mRNA expression, we investigated whether this decrease was related to proteasomal or lysosomal degradation of tyrosinase. We found that chloroquine, a lysosomal proteolysis inhibitor, almost completely abolished both the down-regulation of tyrosinase and the inhibition of melanin synthesis induced by Efse-EA. These results suggested that Efse-EA may contribute to the inhibition of melanogenesis by altering lysosomal degradation of tyrosinase, and that this extract may provide a new cosmetic skin-whitening agent.
Motion compensated frame interpolation based on H.264 decoder (2007)

A low complexity motion compensated frame interpolation method using compressed-domain information based on an H.264 decoder is presented. In the proposed method, the motion vectors are estimated using the constant acceleration motion model, and the interpolation algorithm is applied based on the macroblock coded types. Results show that the proposed method provides high quality interpolation frames.
The Effects of Pathogens on the Immune System: Viral Hepatitis (2005)

This chapter contains sections titled: Introduction The Viruses and the Disease Genomic Organization Prevalence Hepatic Disease and Chronicity After Infection Importance of CD4 and CD8 T Cells in HBV and HCV Control Limitations of Existing Data Low Frequency of HBV- and HCV-specific T Cells Pre-selection of Epitopes Stage of Infection Variations in Viral Inoculum Hierarchy of T-cell Responses During HBV Infection: Helper CD4 T-cell Response Hierarchy of T-cell Responses During HBV Infection: Cytotoxic T-cell Response Hierarchy of HCV Proteins Hierarchy of HCV Epitopes Immunodominance and Liver Pathology Concluding Remarks
Magnetic imaging system in smartphones based on built-in magnetometer (2017)

Summary form only given. Magnetometers have recently become a built-in feature in most tablets and smartphones around the globe. The sensor is usually based on GMR/AMR (Giant/ Anisotropic Magneto Resistance) materials, which are produced as magnetometer integrated circuits that cost less than USD 1. Although they are not as sensitive as the magnetometers used in the geomagnetic survey, their omnipresence and low price tag, as well as the readily available computing power of tablets/smartphones, drive our interest to develop a subsurface imaging system based on built-in magnetometers.
Topology discovery in heterogeneous IP networks (2002)

Knowledge of the up-to-date physical topology of an IP network is crucial to a number of critical network management tasks, including reactive and proactive resource management, event correlation, and root-cause analysis. Given the dynamic nature of today's IP networks, keeping track of topology information manually is a daunting (if not impossible) task. Thus, effective algorithms for automatically discovering physical network topology are necessary. Earlier work has typically concentrated on either: (a) discovering logical (i.e., layer-3) topology, which implies that the connectivity of all layer-2 elements (e.g., switches and bridges) is ignored; or (b) proprietary solutions targeting specific product families. In this paper, we present novel algorithms for discovering physical topology in heterogeneous (i.e., multi-vendor) IP networks. Our algorithms rely on standard SNMP MIB information that is widely supported by modern IP network elements and require no modifications to the operating system software running on elements or hosts. We have implemented the algorithms presented in this paper in the context of a topology discovery tool that has been tested on Lucent's own research network. The experimental results clearly validate our approach, demonstrating that our tool can consistently discover the accurate physical network topology in time that is roughly quadratic in the number of network elements.
Design of biologically active peptides with non-peptidic structural elements. Biological and physical properties of a synthetic analogue of beta-endorphin with unnatural amino acids in the region 6-12. (1986)

Modelling studies with beta-endorphin have clearly demonstrated that an amphiphilic secondary structural segment is a salient feature of the biologically active conformation of this 31-residue opioid peptide hormone. Here, we have initiated the synthesis of peptide models using unnatural building blocks by designing a beta-endorphin analogue (peptide 6) in which the hydrophilic linker region between the NH2-terminal enkephalin (residues 1-5) and the COOH-terminal helix (residues 10-28, sequence identical to that of peptide 3 in region 13-31, Fig. 1) consists of four units of gamma-amino-gamma-hydroxymethylbutyric acid connected by isopeptidic linkages. Peptide 6 has physical properties similar to that of peptide 3, as shown by surface monolayer and circular dichroism studies. The binding affinities of the two peptides to delta- and mu-receptors are also similar. In rat vas deferens assays, the present model is equipotent to peptide 3. The most striking result of all is the potent analgesic activity displayed by peptide 6 when injected intracerebroventricularly into mice. The potencies of peptides 6 and 3 are comparable in these assays. These studies clearly illustrate that one can use unusual building blocks to construct structural regions of synthetic analogues and still preserve the biological activity of peptide hormones.
COMPARATIVE MICROSTRUCTURE OF RED MEAT, POULTRY AND FISH MUSCLE (1990)

ABSTRACT Since muscle food researchers tend to focus on disciplines such as red meats, poultry or fish; there is little shared information across commodity lines. Comparisons among these three groups of muscle foods are discussed.
Cyclin A-CDK Phosphorylation Regulates MDM2 Protein Interactions (2001)

The product of the MDM2 gene interacts with and regulates a number of proteins, in particular the tumor suppressor p53. The MDM2 protein is likely to be extensively modified in vivo, and such modification may regulate its functions in cells. We identified a potential cyclin-dependent kinase (CDK) site in murine MDM2, and found the protein to be efficiently phosphorylated in vitro by cyclin A-containing complexes (cyclin A-CDK2 and cyclin A-CDK1), but MDM2 was either weakly or not phosphorylated by other cyclin-containing complexes. Moreover, a peptide containing a putative MDM2 cyclin recognition motif specifically inhibited phosphorylation by cyclin A-CDK2. The site of cyclin A-CDK2 phosphorylation was identified as Thr-216 by two-dimensional phosphopeptide mapping and mutational analysis. Phosphorylation of MDM2 at Thr-216 both weakens its interaction with p53 and modestly augments its binding to p19(ARF). Interestingly, an MDM2-specific monoclonal antibody, SMP14, cannot recognize MDM2 phosphorylated at Thr-216. Changes in SMP14 reactivity of MDM2 in staged cell extracts indicate that phosphorylation of MDM2 at Thr-216 in vivo is most prevalent at the onset of S phase when cyclin A first becomes detectable.
Density functional theory studies of the adsorption of ethylene and oxygen on Pt(111) and Pt3Sn(111) (2001)

Density functional theory, employing periodic slab calculations, was used to investigate the interactions of ethylene and oxygen with Pt(111) and Pt3Sn(111). The predicted energetics and structures of adsorbed species on Pt(111) are in good agreement with experimental data. The binding energies of π-bonded ethylene, di-σ-bonded ethylene, and ethylidyne species are weaker on Pt3Sn(111) than on Pt(111) by 21, 31, and 50 kJ/mol, respectively. Hence, the electronic effect of Sn on the adsorption of ethylene depends on the type of adsorption site, with adsorption on three-fold site weakened more than adsorption on two-fold and one-fold sites. Oxygen atoms bond as strongly on Pt3Sn(111) as on Pt(111), and these atoms prefer to adsorb near Sn atoms on the surface. The addition of Sn to Pt(111) leads to a surface heterogeneity, wherein ethylidyne species prefer to adsorb away from Sn atoms and oxygen atoms prefer to adsorb near Sn atoms. Implications of this surface heterogeneity on hydrocarbon reaction selectivity on Pt-based catalysts are discussed.
Posttraumatic Epilepsy: A Major Problem in Desperate Need of Major Advances (2006)

This brief review is meant to provide an update on the data from clinical and laboratory studies that have provided insight into the mechanisms underlying the development of epilepsy following traumatic brain injury (TBI). The link between severe brain trauma and epilepsy in humans is well recognized. However, we have yet to identify an effective intervention to prevent the development of epilepsy in patients who are at risk after TBI. Laboratory studies, which have relied primarily on the fluid-percussion model, have documented long-term hyperexcitability associated with TBI, and recent studies are shedding light on the structural and electrophysiological abnormalities that may underlie epileptogenesis in this setting. Nonetheless, given the extent of the clinical problem and our current state of knowledge, this area of epilepsy research deserves far more attention.
Synthesis of 1-Acyl-1,2-dihydro-1-benzazocine Derivatives (1981)

Substituted 1 , 2 , 3 , 4 -t e t r a h y d r o q u m l i n -3 -o n e ( 1 1 was synthesized Erom nitrobenzene derivatives (A1 in several steps.The compound (Za) was converted the pyrrolidine enamine, and then treated with dimethyl acetylenedicarbonylat-e (DMADl to give a ring expanded heterocyclx product ; dimethyl l-acetyl-
Performance Characteristics of the Fluorescence Optrode Cure Sensor (1988)

The autoclave curing of carbon-epoxy laminates is the most critical and costly stage in the fabrication of composites. A reliable, low-cost cure sensor suitable for use in manufacturing is needed to implement realtime control of the process. A second-generation FOCS which measures fluorescence intensity and wavelength with a fiber-optic spectrofluorometer and a tool-mounted optrode were used to monitor the curing of Hercules 3501-6 laminates. Changes of fluorescence intensity during cure follow changes in resin viscosity up to the gel-point, after which it increases in proportion to the degree of cure (DOC). The fluorescence wavelength as a function of cure-time produces a highly characteristic signal profile which is reproducible and independent of fluctuations in fluorescence intensity. Both FOCS signals detect changes in DOC during late stages of cure. Factors affecting the performance of the second-generation FOCS are discussed.
Synthesis and Biological Activity of the Mono- and Diamino Analogues of 2′-Deoxyadenosine, Cordycepin, 9-(3-Deoxy-α-D-Threo-Pentofuranosyl)-Adenine (A Structural Component of Agrocin 84) and 9-(2-Deoxy-α-D-Threo-Pentofuranosyl)Adenine (1989)

The mono- and diamino analogues of 9-(2-deoxy-0-D-erythro-pen-tofuranosyl)adenine J_a, 9-(2-deoxy-8-D-threo-pentofuranosyl)adenine 4a, 9-(3-deoxy-B-D-erythro-pentofuranosyl)adenine 2a and 9-(3-deoxy-0-D-threo-pentofuranosyl)adenine 3a were synthesized by triphenylphosphine reduction of the corresponding azido compounds. The azido group was introduced by a substitution reaction with lithium azide on mesylates or, more directly, by reaction with lithium azide, triphenylphosphine and carbon tetrabromide. Of the newly synthesized compounds, only 3*-amino-21,3'-dideoxyadenosine proved, albeit slightly, inhibitory to murine leukemia L1210 and mammary carcinoma FM3A, and human B-lymphoblast Raji, T-lymphoblast Molt/4F and T-Iymphocyte MT-4 cell proliferation in vitro (50 % inhibitory dose : 43.1-323 pM). None of the compounds inhibited human immunodeficiency virus-induced cytopathogenicity in MT-4 cells. © 1989, Taylor & Francis Group, LLC. All rights reserved.
{BLAS-on-flash}: An Efficient Alternative for Large Scale {ML} Training and Inference? (2019)

Many large scale machine learning training and inference tasks are memory-bound rather than compute-bound. That is, on large data sets, the working set of these algorithms does not fit in memory for jobs that could run overnight on a few multi-core processors. This often forces an expensive redesign of the algorithm for distributed platforms such as parameter servers and Spark. We propose an inexpensive and efficient alternative based on the observation that many ML tasks admit algorithms that can be programmed with linear algebra subroutines. A library that supports BLAS and sparseBLAS interface on large SSD-resident matrices can enable multi-threaded code to scale to industrial scale datasets on a single workstation. We demonstrate that not only can such a library provide near in-memory performance for BLAS, but can also be used to write implementations of complex algorithms such as eigensolvers that outperform in-memory (ARPACK) and distributed (Spark) counterparts. Existing multi-threaded in-memory code can link to our library with minor changes and scale to hundreds of gigabytes of training or inference data at near in-memory processing speeds. We demonstrate this with two industrial scale use cases arising in ranking and relevance pipelines: training large scale topic models and inference for extreme multi-label learning. This suggests that our approach could be an efficient alternative to expensive distributed big-data systems for scaling up structurally complex machine learning tasks. © 2019 by The USENIX Association. All Rights Reserved.
International Society of Geriatric Oncology Consensus on Geriatric Assessment in Older Patients With Cancer (2014)

There is mounting data regarding the utility of GA in oncology practice; however, additional research is needed to continue to strengthen the evidence base.
Methionine 500, the site of covalent attachment of an active site-directed reagent of beta-galactosidase (1978)

The site of attachment to beta-galactosidase of the active site-directed inhibitor, beta-D-galactopyranosylmethyl p-nitrophenyl triazene, was determined. When the enzyme is completely inactivated, 1 mol of the galactopyranosylmethyl group is bound per mol of monomer with retention of the tetrameric structure. After reaction with the [14C]methyl reagent, labeled peptides were isolated and analyzed. The radioactive label was found to be covalently bound to methionine residue 500.
γ‐Subunit of mouse retinal cyclic‐GMP phosphodiesterase: cDNA and corresponding amino acid sequence (1988)

The cDNA nucleotide and corresponding amino acid sequences of the gamma-subunit of cyclic-GMP phosphodiesterase (cGMP-PDE gamma) from mouse retina have been determined. The cDNA translated region was found to be 91.5% homologous to the cDNA coding region for the enzyme from bovine retina [(1986) FEBS Lett. 204, 288-292]. On Northern blots of normal mouse retinal RNAs this cDNA hybridized the cGMP-PDE gamma mRNA which is 900 bp long. The mouse gamma-subunit contains 87 amino acid residues which share 97.7% homology with the bovine polypeptide [(1986) FEBS Lett. 204, 288-292]. Only two amino acids have been changed, Ala 8 to Gly and Met 17 to Ile.
[Anti-osteopenic effect of taurine: possible involvement of activated MEK-ERK-Cbfa1 signaling]. (2002)

Previously we first noted that taurine (TR) has anti-osteopenic effect on low Ca diet-induced osteopenia in rats (1). Employing osteoblastic MC3T3-E1 cells, the mechanism of the anti-osteopenic effect was explored in vitro. TR (1 mM) was found to promote mineralization of extracellular matrices, without affecting alkaline phosphataase activity. Gel shift assay using 32P-labeled OSE2 (osteoblast-specific cis-element 2: the consensus sequence for Cbfa1, refer to 2) indicated that TR (1 mM) increased the nuclear localization of Cbfa1, just as TPH (1-34) (3,4) and bisphosphonates did (5). In addition, TR was found to stimulate ERK phosphorylation. PD98059, a MEK inhibitor, suppressed effects of TR on both Cbfa1 transactivation and ERK activation. The results strongly suggest that TR first activates intracellular MEK-ERK-Cbfa1 signaling system thereby promoting mineralization and finally leading to its bone anabolic action.
The use of finite fields to compute convolutions (1975)

A transform is defined in the Galois field of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q^2</tex> elements <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GF(q^2)</tex> , a finite field analogous to the field of complex numbers, when <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</tex> is a prime such that (--1) is not a quadratic residue. It is shown that the action of this transform over <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GF(q^2)</tex> is equivalent to the discrete Fourier transform of a sequence of complex integers of finite dynamic range. If <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</tex> is a Mersenne prime, one can utilize the fast Fourier transform (FFT) algorithm to yield a fast convolution without the usual roundoff problem of complex numbers.
Effective electron mobility in Si inversion layers in metal–oxide–semiconductor systems with a high-κ insulator: The role of remote phonon scattering (2001)

The high dielectric constant of insulators currently investigated as alternatives to SiO2 in metal–oxide–semiconductor structures is due to their large ionic polarizability. This is usually accompanied by the presence of soft optical phonons. We show that the long-range dipole field associated with the interface excitations resulting from these modes and from their coupling with surface plasmons, while small in the case of SiO2, for most high-κ materials causes a reduction of the effective electron mobility in the inversion layer of the Si substrate. We study the dispersion of the interfacial coupled phonon-plasmon modes, their electron-scattering strength, and their effect on the electron mobility for Si-gate structures employing films of SiO2, Al2O3, AlN, ZrO2, HfO2, and ZrSiO4 for “SiO2-equivalent” thicknesses ranging from 5 to 0.5 nm.
Developmental Assembly of Transduction Apparatus in Chick Basilar Papilla (2003)

Hair cells, the sensory receptors of auditory and vestibular systems, use a transducer apparatus that renders them remarkably sensitive to mechanical displacement as minute as 1 nm. To study the embryonic development of the transducer apparatus in hair cells of the chick auditory papilla, we examined hair cells that have been labeled with N-(3-triethylammoniumpropyl)-4-(4-(dibutylamino)styryl) pyridiniumdibromide, which has been shown to permeate the transducer channels. In addition, mechanotransduction currents were recorded directly using whole-cell patch-clamp techniques. The structure of the hair bundle was examined using scanning electron microscopy, and immunofluorescence labeling for myosin 1c, myosin 7a, and plasma membrane Ca2+ ATPase 2 was studied to determine the developmental expression of these proteins in embryonic chick papillas. We demonstrate that the transducer apparatus is assembled jointly at embryonic day 11 (E11) of the developing chick basilar papilla. The resting open probability of the transducer channels was high at E12 (approximately 0.5) and remained substantially elevated at E14-16; it then declined to the mature value of approximately 0.15 at E21. The displacement sensitivity of the transduction apparatus, the gating force, increased from E12 to E21. Although the expression of different components of the transducer apparatus and the transduction current peaked at approximately E14-16, marked refinement occurred beyond E16. For example, myosin 1c appeared diffusely localized in hair bundles from E12 to E16, but subsequently consolidated into punctate pattern. The fine temporal and precise spatial assembly of the transducer apparatus likely contributes toward the exquisite sensitivity of the transduction ensemble.