gebhart/patrepeval huggingface dataset:
Role of the epithelium in airway smooth muscle responses to relaxant agonists (1991)

We studied the role of the guinea pig tracheal epithelium in modulating tracheal smooth muscle responses to the relaxant agonists albuterol, sodium nitroprusside, and theophylline. We used an in vitro preparation that allowed separation of the fluids bathing the luminal (internal) and serosal (external) surfaces of the trachea, and bronchodilators were administered to either surface of carbachol-contracted tracheae. All three drugs produced dose-dependent relaxation. However, albuterol and nitroprusside were less potent (concentration that produced half-maximal effect increased by 100- and 32-fold, respectively) when given to the epithelial side with the epithelium intact compared with the epithelium denuded or compared with serosal administration with the epithelium intact. These differences were not observed for theophylline, where smooth muscle responses were independent of either the side of stimulation or of the presence or absence of the epithelium. Direct measurements of the diffusion of theophylline across the tracheal wall in the presence or absence of epithelium showed that after 5 h of incubation with a fixed luminal concentration of theophylline, only 1.7% had diffused across the tracheal wall with the epithelium intact. This increased to only approximately 3.3% when the epithelium was denuded. These results suggest that the epithelial is a relatively weak barrier for lipophilic agents but has a major role as a diffusion barrier to hydrophilic substances.
Development of Albumin‐binding Doxorubicin Prodrugs that are Cleaved by Prostate‐specific Antigen (2005)

Prostate-specific antigen (PSA) is a serine protease that is overexpressed in prostate carcinoma and represents a molecular target for selectively releasing an anticancer agent from a prodrug formulation. In this work, we developed albumin-binding prodrugs with the structures MT-Ser-Ser-Tyr-Tyr- Ser-Gly-DOXO, MT-Asn-Ser-Ser-Tyr-Phe-Gln-DOXO (MT = maleimidotriethyleneglycol acid; DOXO = Doxorubicin) or EMC-Arg-Arg-Ser-Ser-Tyr-Tyr-Ser-Gly-DOXO (EMC = epsilon-maleimidocaproic acid; X = amino acid). The maleimide Doxorubicin derivatives bound rapidly to the cysteine-34 position of endogenous and exogenous albumin and were efficiently cleaved by PSA at the P(1)-P'(1) scissile bond, releasing a respective Doxorubicin dipeptide (Ser-Gly-DOXO or Phe-Gln-DOXO). The derivative containing arginine residues (EMC-Arg-Arg-Ser-Ser-Tyr-Tyr-Ser-Gly-DOXO) exhibited excellent water solubility for intravenous administration. Subsequent biological evaluation was focused on a PSA-negative xenograft model (PC 3) and a PSA-positive xenograft model (CWR22) in order to assess the selectivity of our therapeutic approach. EMC-Arg-Arg-Ser-Ser-Tyr-Tyr-Ser-Gly-DOXO showed no in vivo activity in the PSA-negative PC 3 model, but good activity in the CWR22 PSA-positive model that was comparable to Doxorubicin.
Performance analysis of the covariance subtraction method for relative transfer function estimation and comparison to the covariance whitening method (2015)

Microphone array processing utilize spatial separation between the desired speaker and interference signal for speech enhancement. The transfer functions (TFs) relating the speaker component at a reference microphone with all other microphones, denoted as the relative TFs (RTFs), play an important role in beamforming design criteria such as minimum variance distortionless response (MVDR) and speech distortion weighted multichannel Wiener filter (SDW-MWF). Two common methods for estimating the RTF are surveyed here, namely, the covariance subtraction (CS) and the covariance whitening (CW) methods. We analyze the performance of the CS method theoretically and empirically validate the results of the analysis through extensive simulations. Furthermore, empirically comparing the methods performances in various scenarios evidently shows thats the CW method outperforms the CS method.
Metabolic and immunologic consequences of ABH secretor and Lewis subtype status. (2001)

Determining ABH secretor phenotype and/or Lewis (Le) blood group status can be useful to the metabolically-oriented clinician. For example, differences in ABH secretor status drastically alter the carbohydrates present in body fluids and secretions; this can have profound influence on microbial attachment and persistence. Lewis typing is one genetic marker which might help identify subpopulations of individuals genetically prone to insulin resistance, autoimmunity, and heart disease. Understanding the clinical significance of ABH secretor status and the Lewis blood groups can provide insight into seemingly unrelated aspects of physiology, including variations in intestinal alkaline phosphatase activity, propensities toward blood clotting, reliability of some tumor markers, the composition of breast milk, and several generalized aspects of the immune function. Since the relevance of ABH blood group antigens as tumor markers and parasitic/bacterial/viral receptors and their association with immunologically important proteins is now well established, the prime biologic role for ABH blood group antigens may well be independent and unrelated to the erythrocyte.
Gas‐Phase  CO 2 Reduction to Hydrocarbons at Metal/Solid Polymer Electrolyte Interface (1990)

La reduction electrochimique du dioxyde de carbone, en phase gazeuse, sur une electrode de platine modifiee par un polyelectrolyte solide contenant differents metaux (Ni, Ru, Rh, Pd, Ag, Re, Os, Ir, Pt, Au) qui servent de catalyseur
cGAS-mediated stabilization of IFI16 promotes innate signaling during herpes simplex virus infection (2015)

Interferon γ-inducible protein 16 (IFI16) and cGMP-AMP synthase (cGAS) have both been proposed to detect herpesviral DNA directly in herpes simplex virus (HSV)-infected cells and initiate interferon regulatory factor-3 signaling, but it has been unclear how two DNA sensors could both be required for this response. We therefore investigated their relative roles in human foreskin fibroblasts (HFFs) infected with HSV or transfected with plasmid DNA. siRNA depletion studies showed that both are required for the production of IFN in infected HFFs. We found that cGAS shows low production of cGMP-AMP in infected cells, but instead cGAS is partially nuclear in normal human fibroblasts and keratinocytes, interacts with IFI16 in fibroblasts, and promotes the stability of IFI16. IFI16 is associated with viral DNA and targets to viral genome complexes, consistent with it interacting directly with viral DNA. Our results demonstrate that IFI16 and cGAS cooperate in a novel way to sense nuclear herpesviral DNA and initiate innate signaling.
Mechanical forces regulate the interactions of fibronectin and collagen I in extracellular matrix (2015)

Despite the crucial role of extracellular matrix (ECM) in directing cell fate in healthy and diseased tissues--particularly in development, wound healing, tissue regeneration and cancer--the mechanisms that direct the assembly and regulate hierarchical architectures of ECM are poorly understood. Collagen I matrix assembly in vivo requires active fibronectin (Fn) fibrillogenesis by cells. Here we exploit Fn-FRET probes as mechanical strain sensors and demonstrate that collagen I fibres preferentially co-localize with more-relaxed Fn fibrils in the ECM of fibroblasts in cell culture. Fibre stretch-assay studies reveal that collagen I's Fn-binding domain is responsible for the mechano-regulated interaction. Furthermore, we show that Fn-collagen interactions are reciprocal: relaxed Fn fibrils act as multivalent templates for collagen assembly, but once assembled, collagen fibres shield Fn fibres from being stretched by cellular traction forces. Thus, in addition to the well-recognized, force-regulated, cell-matrix interactions, forces also tune the interactions between different structural ECM components.
Chinese herbal recipe versus diclofenac in symptomatic treatment of osteoarthritis of the knee: a randomized controlled trial [ISRCTN70292892] (2004)

DJW demonstrates clinically comparable efficacy to diclofenac after 4 weeks of treatment. However, the slow onset of action as well as approximately equal rate of adverse events to diclofenac might limit its alternative role in treatment of OA of the knee.
Tumor and liver drug uptake following hepatic artery and portal vein infusion. (1987)

Anatomic dye injection studies of the blood supply of colorectal hepatic metastases suggest that tumors are supplied predominantly by the hepatic artery. Using 13N amino acids with dynamic gamma camera imaging in patients with colorectal hepatic metastases, it has been shown that hepatic artery infusion results in a significantly greater nutrient delivery to tumor compared with portal vein infusion. However, direct measurements of drug levels in tumor following hepatic artery and portal vein infusion in humans have not previously been reported. Patients with metastatic colorectal cancer confined to the liver received fluorodeoxyuridine (FUdR) through the hepatic artery or through the portal vein. All patients had previously failed systemic chemotherapy. Five patients with hepatic artery catheters were matched (by age, serum lactic dehydrogenase levels, percent hepatic replacement, and tumor size) with five patients with portal vein catheters. At operation, 3H-FUdR (1 microCi/kg) and 99mTc-macroaggregated albumin (MAA) (6 mCi) were injected into the hepatic artery or portal vein. Liver and tumor biopsies were obtained two and five minutes later. 3H and 99mTc were measured per gram tissue by scintillation and gamma counting. The mean liver levels following hepatic artery infusion (23.9 +/- 11.4 nmol/g) and portal vein infusion (18.4 +/- 14.5 nmol/g) did not differ. However, the mean tumor FUdR level following hepatic artery infusion was 12.4 +/- 12.2 nmol/g, compared with a mean tumor FUdR level following portal vein infusion of 0.8 +/- 0.7 nmol/g (P less than .01). This low level of tumor drug uptake after portal vein infusion of FUdR predicts minimal tumor response to treatment via this route. Thus, regional chemotherapy for established colorectal hepatic metastases should be administered through the hepatic artery.
Synthetic Protein Mimics for Functional Protein Delivery (2017)

The use of proteins as biological tools and therapeutic agents is limited due to the fact that proteins do not effectively cross the plasma membrane of cells. Here, we report a novel class of protein transporter molecules based on protein transduction domain mimics (PTDMs) synthesized via ring opening metathesis polymerization (ROMP). The PTDMs reported here were specifically inspired by amphiphilic peptides known to deliver functional proteins into cells via noncovalent interactions between the peptide and the cargo. This contrasts with peptides like TAT, penetratin, and R9, which often require covalent fusion to their cargoes. Using the easily tunable synthetic ROMP platform, the importance of a longer hydrophobic segment with cationic guanidinium groups was established through the delivery of EGFP into Jurkat T cells. The most efficient of these protein transporters was used to deliver functional Cre Recombinase with ∼80% knockdown efficiency into hard to transfect human T cells. Additionally, a C-terminally deleted form of the transcription factor Runx1 (Runx1.d190) was delivered into primary murine splenocytes, producing a 2-fold increase in c-Myc mRNA production, showcasing the versatility of this platform to deliver biologically active proteins into hard to transfect cell types.
DiscoWeb: Applying Link Analysis to Web Search (1999)

How often does the search engine of your choice produce results that are less than satisfying, generating endless links to irrelevant pages even though those pages may contain the query keywords? How often are you given pages that tell you things you already know? While the search engines and related tools continue to make improvements in their information retrieval algorithms, for the most part they continue to ignore an essential part of the web – the links. We have found that link analysis can have significant contributions to web page retrieval from search engines, to web community discovery, and to the measurement of web page influence. It can help to rank results and find high-quality index/hub/link pages that contain links to the best sites on the topic of interest. Our work is based on research from IBM’s CLEVER project [7, 4, 6], Stanford’s Google [3], and the Web Archaeology research [2, 1] at Compaq’s Systems Research Center. These research teams have demonstrated some of the contributions that link analysis can make in the web. In our work, we have attempted to generalize and improve upon these approaches. Just as in citation analysis of published works, the most influential documents on the web will have many other documents recommending (pointing to) them. This idea underlies all link analysis efforts, from the straightforward technique of counting the number of incoming edges to a page, to the deeper eigenvector analysis used in our work and in those projects mentioned above. It turns out that the identification of “high-quality ” web pages reduces to a sparse eigenvalue of the adjacency matrix
Telomere-interactive agents affect proliferation rates and induce chromosomal destabilization in sea urchin embryos. (1999)

Cationic porphyrins, which interact with guanine quadruplex (G4) telomeric folds, inhibit telomerase activity in human tumor cells. In this study, we have further examined effects of porphyrins and other telomere- and telomerase-interactive agents on proliferation rates and chromosome stability in a novel in vivo model, developing sea urchin embryos. We studied two porphyrins: (i) TMPyP4, a potent telomerase inhibitor; and (ii) TMPyP2, an isomer of TMPyP4 and an inefficient telomerase inhibitor, azidothymine (AZT), the reverse transcriptase inhibitor, antisense phosphorothioate oligonucleotide to telomerase RNA (TAG6) and a control scrambled sequence (ODN). TMPyP4, AZT and TAG6 (but not TMPyP2 or ODN) decreased the rates of cell proliferation and increased the percentage of cells trapped in mitosis. Nuclear localization of TAG6, but not of ODN, was demonstrated with 5'-fluoresceinated analogs of TAG6 and ODN. Formation of elongated chromosomes incapable of separating in anaphase, induced by TMPyP4, AZT and TAG6, closely resembled phenotypes resulting from telomerase template mutation or dominant negative TRF2 allele. Our data suggest that G4-interactive agents exert their antiproliferative effects via chromosomal destabilization and warrant their further development as valuable anticancer tools.
Inter-cell interference mitigation in multi-cellular visible light communications (2016)

Inter-cell interference hinders multi-cellular optical wireless communication to support various applications. We proposed and experimentally demonstrated a multicarrier-based cell partitioning scheme, combined with frequency reuse, which could be effective in optical communications although it is inefficient in RF wireless communications. For multicarrier-based cell partitioning, Orthogonal frequency division multiplexing-based multiple access (OFDMA) was employed to accommodate multi-cellular optical wireless communications without a large guard band between adjacent cells and without additional RF components. Moreover, we employed filter bank-based multicarrier (FBMC) to mitigate inter-cell interference generated in OFDMA-based cell partitioning due to asynchronous signals originated from RF path difference. By using FBMC-based cell partitioning, inter-cell interference could be effectively mitigated as well as capacity and spectral efficiency were improved about 1.5 times compared to those of OFDMA. Because no cyclic prefix (CP) is required in FBMC, the improvement factor could be increased if there is a large RF path difference between lighting cells. Moreover, it could be a stronger solution when many neighboring cells exist causing large interference. The proposed multicarrier-based cell partitioning combined with FBMC will effectively support visible light communication (VLC)-based localization-based services (LBS) and indoor positioning system by transparently providing trilateration-based positioning method.
Imidazo[1,2-a]-s-triazine nucleosides. Synthesis and antiviral activity of the N-bridgehead guanine, guanosine, and guanosine monophosphate analogs of imidazo[1,2-a]-s-triazine (1978)

The first chemical synthesis of 2-aminoimidazo[1,2-a]-s-triazin-4-one (8), the corresponding nucleoside and nucleotide, and certain related derivatives of a new class of purine analogues containing a bridgehead nitrogen atom is described. Condensation of 2-amino-4-chloro-6-hydroxy-s-triazine (2) with aminoacetaldehyde dimethyl acetal followed by the ring annulation gave the guanine analogue 8. A similar ring annulation of 4-(2,2-dimethoxyethylamino)-s-triazine-2,6-dione (5) gave imidazo[1,2-a]-s-triazine-4,6-dione (9). Direct glycosylation of the trimethylsilyl derivative of 8 with 1-O-acetyl-2,3,5-tri-O-benzoyl-beta-D-ribofuranose in the presence of stannic chloride, followed by debenzoylation, gave the guanosine analogue 2-amino-8-(beta-D-ribofuranosyl)imidazo[1,2-a]-s-triazin-4-one (12b), which on deamination gave the xanthosine analogue 13. Phosphorylation of 12b gave 2-amino-8-(beta-D-ribofuranosyl)imidazo[1,2-a]-s-triazin-4-one 5'-monophosphate (II). The anomeric configuration has been determined unequivocally by using NMR of the 2',3'-O-isopropylidene derivate 10 and the site of ribosylation has been established by using 13C NMR spectroscopy. These compounds were tested against type 1 herpes, type 13 rhino, and type 3 parainfluenza viruses in tissue culture. Moderate rhinovirus activity was observed for several compounds at nontoxic dosage levels.
Epidermal Growth Factor Receptor Inhibitors in the Treatment of Non–Small-Cell Lung Cancer (2005)

Remarkable developments in the systemic treatment of advanced non-small-cell lung cancer have taken place in the past few years. Targeted therapies have been largely employed in patients with far advanced disease, and some of them have demonstrated consistent activity in this setting. Epidermal growth factor receptor (EGFR) inhibitors cause dramatic response in approximately 10% of white patients who had received prior chemotherapy. Responses are higher in Asians. These findings are at least partly caused by the substantially higher incidence of EGFR mutations in Asians compared with whites. Studies of EGFR inhibitors in combination chemotherapy in front-line therapy of advanced non-small-cell lung cancer have, however, failed to improve survival, and better understanding of interactions between chemotherapeutic agents and EGFR inhibitors will be essential in the development of more effective strategies.
Electron spectroscopy and atomic force microscopy studies of DNA adsorption on mica. (1994)

Various methods for the deposition of deoxyribonucleic acid (DNA) molecules on mica are investigated to determine their reproducibility, and to quantify their ability to bind DNA. The use of these deposition methods for sample preparation for biological scanning tunneling microscopy (STM) and atomic force microscopy (AFM) studies is discussed. Auger electron spectroscopy (AES) and electron spectroscopy for chemical analysis (ESCA) were used to investigate the quantity of DNA adsorbed. AFM images of DNA deposited using the methods investigated are presented. The combination of AFM results with AES and ESCA results provides a basic understanding of the deposition techniques studied and illustrates that electron spectroscopy can be a useful addition to studies of this nature.
Synthesis and Diagnostic Electrochemistry of Nanocrystalline Li[sub 1+x]Mn[sub 2−x]O[sub 4] Powders of Controlled Li Content (2000)

Fine powders of cathode materials were synthesized by a nitrate route based on the Lux‐Flood principle. The method involves the reaction of with an excess of nitrate from a nitrate bath. The reaction consists of three steps, dehydration, oxidation, and lithiation. Cathode powders with a grain size of ∼100 nm were made and tested in rechargeable lithium batteries for their capacity retention and high discharge current behavior. Despite the small diffusion path offered by these nanosized grains during lithium insertion, the electrochemical performance of the cathode was not improved. The observed discharge profiles are interpreted in terms of current density—dependent mixed insertion into tetrahedral and octahedral sites. A quantitative analysis of the capacity retention data for Li‐substituted and stoichiometric cathodes suggests that is immune to dissolution in the electrolyte. These results are interpreted as establishing that the dissolution of the cathode and the structural fatigue induced by the Jahn‐Teller distortion are correlated through the formation of at the grain surface. © 2000 The Electrochemical Society. All rights reserved.
Advanced buffer materials for indoor air CO<sub>2</sub>control in commercial buildings (2017)

In this study, we evaluated solid sorbents for their ability to passively control indoor CO<sub>2</sub> concentration in buildings or rooms with cyclic occupancy (eg, offices, bedrooms). Silica supported amines were identified as suitable candidates and systematically evaluated in the removal of CO<sub>2</sub> from indoor air by equilibrium and dynamic techniques. In particular, sorbents with various amine loadings were synthesized using tetraethylenepentamine (TEPA), poly(ethyleneimine) (PEI) and a silane coupling agent 3-aminopropyltriethoxysilane (APS). TGA analysis indicates that TEPA impregnated silica not only displays a relatively high adsorption capacity when exposed to ppm level CO<sub>2</sub> concentrations, but also is capable of desorbing the majority of CO<sub>2</sub> by air flow (eg, by concentration gradient). In 10 L flow-through chamber experiments, TEPA-based sorbents reduced outlet CO<sub>2</sub> by up to 5% at 50% RH and up to 93% of CO<sub>2</sub> adsorbed over 8 hours was desorbed within 16 hours. In 8 m<sup>3</sup> flow-through chamber experiments, 18 g of the sorbent powder spread over a 2 m<sup>2</sup> area removed approximately 8% of CO<sub>2</sub> injected. By extrapolating these results to real buildings, we estimate that meaningful reductions in the CO<sub>2</sub> can be achieved, which may help reduce energy requirements for ventilation and/or improve air quality.
Noninvasive Quantification of Coronary Blood Flow Reserve in Humans Using Myocardial Contrast Echocardiography (2001)

CBF reserve can be measured in humans using MCE. This method may allow the noninvasive assessment of coronary stenosis severity and the detection of microvascular dysfunction.
dna2vec: Consistent vector representations of variable-length k-mers (2017)

One of the ubiquitous representation of long DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding of k-mer as a one-hot vector is vulnerable to the curse of dimensionality. Worse yet, the distance between any pair of one-hot vectors is equidistant. This is particularly problematic when applying the latest machine learning algorithms to solve problems in biological sequence analysis. In this paper, we propose a novel method to train distributed representations of variable-length k-mers. Our method is based on the popular word embedding model word2vec, which is trained on a shallow two-layer neural network. Our experiments provide evidence that the summing of dna2vec vectors is akin to nucleotides concatenation. We also demonstrate that there is correlation between Needleman-Wunsch similarity score and cosine similarity of dna2vec vectors.
LOCALLY RECURRENT PROSTATE TUMORS FOLLOWING EITHER RADIATION THERAPY OR RADICAL PROSTATECTOMY HAVE CHANGES IN KI-67 LABELING INDEX, P53 AND BCL-2 IMMUNOREACTIVITY (1998)

Recurrent tumors following either radiation or surgery differ significantly from the corresponding pretreatment tumors with respect to cellular proliferation and p53 nuclear reactivity.