gebhart/patrepeval huggingface dataset:
Synthesis of a Divalent Sialyl Lewis x O‐glycan, a Potent Inhibitor of Lymphocyte‐Endothelium Adhesion (1995)

The recognition of cell-surface L-selectin by its carbohydrate ligands causes lymphocytes to roll on capillary endothelium at sites of inflammation. As this primary contact is a prerequisite for extravasation of the leukocytes to the tissue, its inhibition by free oligosaccharides capable of competing with the natural L-selectin ligands in an attractive therapeutic possibility. The exact structures of the biological ligands of L-selectin are not yet known, but the principal carbohydrate epitopes share some structural features: they are O-glycosidically linked mucin-type oligosaccharides with N-acetyllactosamine backbone, which is 3'-sialylated or 3'-sulfated, 3-fucosylated and sometimes 6- or 6'-sulfated at the distal N-acetyllactosamine termini. Multivalency of the ligand, which is believed to enhance the binding, is achieved by a branched polylactosamine backbone or by a clustered array of O-glycans. We report here enzymic synthesis of a large oligosaccharide fulfilling several of the features characteristic to the L-selectin ligands: it is a dodecameric O-glycosidic core-2-type oligosaccharide alditol with a branched polylactosamine backbone carrying two distal alpha-2,3'-sialylated and alpha-1,3-fucosylated N-acetyl-lactosamine groups (sialyl Lewis x, sialyl Le(x)). The structure of each saccharide on the synthesis route from disaccharide Gal beta 1-3GalNAc to the dodecasaccharide alditol was established by several methods including one- and two-dimensional 1H-NMR spectroscopy. The last step of the synthesis, the alpha-1,3-fucosylation of the 6-linked arm proceeded sluggishly, and was associated with a noticeable shift in H1 resonance of the GlcNAc residue of the branch-bearing N-acetyllactosamine unit. The final synthesis product and its analogs lacking one or both of the fucose residues were tested as inhibitors of L-selectin-mediated lymphocyte-endothelium interaction in vitro in rejecting rat kidney transplant. While the non-fucosylated O-glycosidic oligosaccharide alditol did not possess any inhibitory activity, the mono-fucosylated one (i.e. monovalent sialyl Le(x)) prevented the binding significantly and the difucosylated dodecasaccharide alditol (i.e. divalent sialyl Le(x)) was a very potent inhibitor (IC50, inhibitory concentration preventing 50% of binding = 0.15 microM). Besides the multivalency, also the Gal beta 1-3GalNAc-ol sequence of the O-glycosidic core appeared to increase the affinity of the glycan to L-selectin. This was indicated by parallel inhibition experiments, where a disialylated and difucosylated branched polylactosamine decasaccharide, similar to the divalent dodecasaccharide alditol, but lacking the reduced O-glycosidic core, was a less effective inhibitor (IC50 = 0.5 microM) than the O-glycosidic dodecasaccharide alditol.
Time of day modulates low‐temperature Ca2+ signals in Arabidopsis (2006)

We tested the hypothesis that the circadian clock modulates Ca(2+)-based signalling pathways, using low-temperature (LT)-induced Ca(2+) signals. We investigated the relationship between diurnal and circadian modulation of LT-induced increases in cytosolic-free calcium ([Ca(2+)](cyt)), and regulation of [Ca(2+)](cyt)-dependent outputs of the LT-signalling network (RD29A transcript abundance and stomatal closure). We measured [Ca(2+)](cyt) non-invasively using aequorin, and targeted aequorin to the guard cell using a guard cell-specific GAL4-green fluorescent protein enhancer trap line. LT caused transient increases in whole plant and guard cell [Ca(2+)](cyt). In guard cells, the LT-induced [Ca(2+)](cyt) elevation preceded stomatal closure. In whole plants, the magnitude of LT-induced [Ca(2+)](cyt) transients, measured from the entire plant or specifically the guard cell, varied with the time of day: LT-induced [Ca(2+)](cyt) transients were significantly higher during the mid-photoperiod than at the beginning or end. Diurnal variation in LT-induced guard cell [Ca(2+)](cyt) increases was not correlated to diurnal variation in LT-induced stomatal closure. There was circadian modulation of LT-induced whole plant [Ca(2+)](cyt) increases, which were correlated to the circadian pattern of RD29A induction. In order to understand the significance of LT-induced [Ca(2+)](cyt) increases, we used a computer simulation to demonstrate that, in guard cells, LT-induced [Ca(2+)](cyt) increases measured from a population of cells are likely to represent the summation of cold-induced single-cell [Ca(2+)](cyt) oscillations.
A discriminative learning framework with pairwise constraints for video object classification (2006)

To deal with the problem of insufficient labeled data in video object classification, one solution is to utilize additional pairwise constraints that indicate the relationship between two examples, i.e., whether these examples belong to the same class or not. In this paper, we propose a discriminative learning approach which can incorporate pairwise constraints into a conventional margin-based learning framework. Different from previous work that usually attempts to learn better distance metrics or estimate the underlying data distribution, the proposed approach can directly model the decision boundary and, thus, require fewer model assumptions. Moreover, the proposed approach can handle both labeled data and pairwise constraints in a unified framework. In this work, we investigate two families of pairwise loss functions, namely, convex and nonconvex pairwise loss functions, and then derive three pairwise learning algorithms by plugging in the hinge loss and the logistic loss functions. The proposed learning algorithms were evaluated using a people identification task on two surveillance video data sets. The experiments demonstrated that the proposed pairwise learning algorithms considerably outperform the baseline classifiers using only labeled data and two other pairwise learning algorithms with the same amount of pairwise constraints.
MSNovo:  A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007)

Tandem mass spectrometry (MS/MS) has become the experimental method of choice for high-throughput proteomics-based biological discovery. The two primary ways of analyzing MS/MS data are database search and de novo sequencing. In this paper, we present a new approach to peptide de novo sequencing, called MSNovo, which has the following advanced features. (1) It works on data generated from both LCQ and LTQ mass spectrometers and interprets singly, doubly, and triply charged ions. (2) It integrates a new probabilistic scoring function with a mass array-based dynamic programming algorithm. The simplicity of the scoring function, with only 6-10 parameters to be trained, avoids the problem of overfitting and allows MSNovo to be adopted for other machines and data sets easily. The mass array data structure explicitly encodes all possible peptides and allows the dynamic programming algorithm to find the best peptide. (3) Compared to existing programs, MSNovo predicts peptides as well as sequence tags with a higher accuracy, which is important for those applications that search protein databases using the de novo sequencing results. More specifically, we show that MSNovo outperforms other programs on various ESI ion trap data. We also show that for high-resolution data the performance of MSNovo improves significantly. Supporting Information, executable files and data sets can be found at http://msms.usc.edu/supplementary/msnovo.
The relationship between the down-regulation of DNA-PKcs or Ku70 and the chemosensitization in human cervical carcinoma cell line HeLa (2007)

The aim of this study was to clarify the function of non-homologous end-joining (NHEJ) in tumorigenesis and chemoresistance, and to explore the potential of DNA-PK as a target of reversal of chemoresistance and enhancing the sensitivity of cells to chemotherapeutic agents. Plasmid vectors pSIREN-Ku70shRNA and pSIREN-DNA-PKcssh-RNA, which coded small interfering RNA of Ku70 and DNA-PKcs, were constructed and transfected into human cervical cancer cell line HeLa. The relationship between the down-regulation of Ku70 or DNA-PKcs and tumor cell proliferation and the sensitivity of cells to chemotherapeutic agents were analyzed. Down-regulation of Ku70 and DNA-PKcs expression inhibited cell proliferation, and increased cell apoptosis in DDP-treated HeLa cells. DNA-PK might play an important role in drug resistance, and inhibition of the DNA-PK expression suppressed the growth of tumor cells and enhanced the sensitivity of cells to chemotherapeutic agents.
A Novel Peptide-Based Encoding System for “One-Bead One-Compound” Peptidomimetic and Small Molecule Combinatorial Libraries (2002)

The "one-bead one-compound" (OBOC) combinatorial library method is highly efficient, especially when used with well-established on-bead binding or functional assays. Literally, millions of compounds can be screened concurrently within 1 to 2 days. However, structure determination of peptidomimetic and small molecule compounds on one single bead is not trivial. A novel, highly efficient, and robust peptide-based encoding system has been developed for OBOC peptidomimetic and small molecule combinatorial libraries. In this system, topologically segregated bifunctional beads, which are made by a simple biphasic solvent strategy, are employed for the preparation and screening of an OBOC combinatorial peptidomimetic and small molecule libraries. Testing molecules are on the outer layer, and the coding tags in the interior of the bead do not interfere with screening. The coding tag is a peptide containing a large number of unnatural alpha-amino acids derived from different building blocks used for generating the peptidomimetic or small molecule. By coupling common building blocks simultaneously to the scaffold of the testing compound and to the side chains of the alpha-amino acids on the coding peptide, extra synthetic steps are eliminated and the amount of undesirable side products is minimized. Positive bead decoding is easy and straightforward as there is no need for cleavage and retrieval of the coding tag, and positive beads can be sequenced directly with Edman degradation. To demonstrate the efficiency and simplicity of our encoding system, an encoded 158 400-member model peptidomimetic library has been generated and screened for ligands that bind to streptavidin. Potent and novel ligands with clear motifs have been identified.
The incorporation of marinen-3 PUFA into platelets and adipose tissue in pre- and postmenopausal women: a randomised, double-blind, placebo-controlled trial (2010)

The primary aim of the trial was to investigate the influence of menopause on the incorporation of marine n-3 PUFA into platelets and adipose tissue. A secondary aim was to evaluate whether marine n-3 PUFA may change levels of circulating oestrogens in women. Ninety-two pre- and postmenopausal women were randomly assigned to consume 2.2 g of marine n-3 PUFA or control oil daily for 12 weeks. Adipose tissue biopsies and blood samples were collected at baseline and after intervention. Eighty-nine women completed the study. Baseline contents of total marine n-3 PUFA and each of the major long-chained n-3 PUFA, EPA, docosapentaenoic acid and DHA were all significantly lower (P < 0.05) in the premenopausal group both in platelets and adipose tissue, except for EPA in platelets (P = 0.05). After supplementation with fish oil, the content of all marine n-3 PUFA increased significantly in platelets and adipose tissue in both pre- and postmenopausal women. The increase in platelets and adipose tissue was, however, the same in both groups. There was no effect of fish oil on oestrogen levels in postmenopausal women. We found a significant difference in premenopausal women, in whom oestradiol (P < 0.04) and oestrone (P < 0.02) serum concentrations increased after the fish oil supplement. This trial did not reveal any difference in the ability of pre- and postmenopausal women to incorporate marine n-3 PUFA into platelets or adipose tissue. However, supplementation with fish oil increased oestrogen levels in premenopausal women.
Recombinant human factor IX: replacement therapy, prophylaxis, and pharmacokinetics in canine hemophilia B (1996)

Recombinant human factor IX (rFIX) has been expressed in transduced cultured cell systems since 1985. Because there has been limited in vivo testing of rFIX in hemophilia B subjects, this study was undertaken using the severe hemophilia B canines of the Chapel Hill strain. Three groups of hemophilic dogs received either 50, 100, or 200 IU/kg of rFIX. As a control, a fourth group of hemophilic dogs received 50 IU/kg of a high purity, plasma-derived human FIX (pdFIX). The coagulant and hemostatic effects of rFIX and pdFIX were similar with all comparative dosing regimens. Based on activity data, the elimination half-life of rFIX was 18.9 +/- 2.3 hours and pdFIX was 17.9 +/- 2.1 hours. A prophylactic regimen administering rFIX daily resulted in a continuous therapeutic level of plasma FIX and was accompanied by a two-fold increase in recovery levels by day 5, compared to that observed with administration of a single bolus. The mechanisms of the high to complete recovery of FIX with the prophylactic regimen could depend not only on the degree of saturation of the vascular endothelial binding sites but also on the altered dynamics of the balance of FIX distribution between the intravascular and extravascular compartments. The pharmacokinetic (PK) parameters for rFIX and pdFIX were similar. However, the relative PK values for V1 and V5s of both products on day 5 differed greatly from day 1 and may reflect the changing equilibrium of FIX between compartments with elevated levels of plasma FIX. Neutralizing antihuman FIX antibodies resulting from human FIX antigen being administered to FIX deficient dogs were observed beginning at 14 days. The antigenicity of rFIX and pdFIX appeared to be comparable. Despite the very different procedures used for production of rFIX and pdFIX products, in vivo testing in hemophilia B dogs showed the functional behavior of these products is similar; they are highly effective for replacement therapy and for prophylaxis.
Synthesis and cleavage of core‐labile poly(alkyl methacrylate) star polymers (2003)

Abstract Core‐cleavable star polymers were synthesized by the coupling of living anionic poly(alkyl methacrylate) arms with either dicumyl alcohol dimethacrylate (DCDMA) or 2,5‐dimethyl‐2,5‐hexanediol dimethacrylate (DHDMA). This synthetic methodology led to the formation of star polymers that exhibited high molecular weights and relatively narrow molecular weight distributions. The labile tertiary alkyl esters in the DCDMA and DHDMA star polymer cores were readily hydrolyzed under acidic conditions. High‐molecular‐weight star polymer cleavage led to well‐defined arm polymers with lower molecular weights. Hydrolysis was confirmed via 1 H NMR spectroscopy and gel permeation chromatography. Thermogravimetric analysis (TGA) of the star polymers demonstrated that the DCDMA and DHDMA star polymer cores also thermally degraded in the absence of acid catalysts at 185 and 220 °C, respectively, and the core‐cleavage temperatures were independent of the arm polymer composition. The difference in the core‐degradation temperatures was attributed to the increased reactivity of the DCDMA‐derived cores. TGA/mass spectrometry detected the evolution of the diene byproduct of the core degradation and confirmed the proposed degradation mechanism. The DCDMA monomer exhibited a higher degradation rate than DHDMA under identical reaction conditions because of the additional resonance stabilization of the liberated byproduct, which made it a more responsive cleavable coupling monomer than DHDMA. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3083–3093, 2003
Role of the Carboxy Terminus of Herpes Simplex Virus Type 1 DNA Polymerase in its Interaction With UL42 (1994)

Several recent reports implicate sequences at or near the C terminus of the catalytic subunit (POL) of herpes simplex virus type 1 (HSV-1) DNA polymerase in its interaction with the accessory protein UL42. We have investigated further the involvement of this region by three different approaches: anti-idiotype antibodies, a competition ELISA and inhibition of the interaction by peptides. Antibodies raised in rabbits to peptides corresponding to regions of POL all reacted in Western blots with POL. Surprisingly, the sera raised against C-terminal peptides (amino acids 1221 to 1235 and 1224 to 1235) also reacted with UL42. The UL42 reactivity was shown to be due to the presence of anti-idiotype antibodies, providing direct evidence for complementarity of the structure of the extreme C terminus of POL to a region of UL42. To measure the contribution of the C terminus of POL to UL42 binding we developed a competition ELISA using POL, a truncated polymerase lacking the carboxyl-terminal 27 amino acids (POLd1) and UL42. UL42 binding to immobilized POL was inhibited approximately four times more effectively by competition, in solution, with POL than with POLd1, indicating that the C-terminal 27 amino acids of POL are responsible for at least 75% of the binding energy. A peptide corresponding to these 27 amino acids (residues 1209 to 1235) inhibited both the POL-UL42 interaction and the stimulation of POL by UL42 and did so more effectively than peptides corresponding to amino acids just away from the C terminus (residues 1195 to 1223 and 1177 to 1195).
Prodrugs of Anthracyclines in Cancer Chemotherapy (2006)

Designing and developing truly tumor-specific prodrugs remains a challenge in the field of cancer chemotherapy. Active targeting strategies, on the one hand, aim at exploiting membrane-associated receptors or antigens for drug delivery; on the other hand, the enhanced vascular permeability and retention of macromolecules in tumor tissue substantiates the concept of passive targeting. Consequently, research efforts have concentrated on conjugating anticancer agents with a wide spectrum of carriers including antibodies, peptides, serum proteins, and synthetic polymers. Conversely, low-molecular weight prodrugs of anticancer agents have been developed that do not bear an active or passive targeting moiety, but are activated by tumor-associated enzymes at the tumor site. Anthracyclines probably represent the class of anticancer agents that has been most widely used for the development of prodrugs. This overview gives an update of the various low- and high-molecular weight prodrugs of anthracyclines, e.g. with antibodies, peptides, carbohydrates, serum proteins or synthetic polymers, that have been developed over the past 20 years and that exemplify the salient features of a respective drug delivery system. A detailed description will be dedicated to anthracycline prodrugs that have reached an advanced stage of preclinical testing or that have entered clinical trials.
Online Adaptive Estimation of Sparse Signals: Where RLS Meets the $\ell_1$-Norm (2010)

Using the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ℓ</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -norm to regularize the least-squares criterion, the batch least-absolute shrinkage and selection operator (Lasso) has well-documented merits for estimating sparse signals of interest emerging in various applications where observations adhere to parsimonious linear regression models. To cope with high complexity, increasing memory requirements, and lack of tracking capability that batch Lasso estimators face when processing observations sequentially, the present paper develops a novel time-weighted Lasso (TWL) approach. Performance analysis reveals that TWL cannot estimate consistently the desired signal support without compromising rate of convergence. This motivates the development of a time- and norm-weighted Lasso (TNWL) scheme with <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ℓ</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -norm weights obtained from the recursive least-squares (RLS) algorithm. The resultant algorithm consistently estimates the support of sparse signals without reducing the convergence rate. To cope with sparsity-aware recursive real-time processing, novel adaptive algorithms are also developed to enable online coordinate descent solvers of TWL and TNWL that provably converge to the true sparse signal in the time-invariant case. Simulated tests compare competing alternatives and corroborate the performance of the novel algorithms in estimating time-invariant signals, and tracking time-varying signals under sparsity constraints.
Clostridium spores for tumor-specific drug delivery (2002)

Insufficient blood supply of rapidly growing tumors leads to the presence of hypoxia, a well-known feature in solid tumors. Hypoxia is known to decrease the efficiency of currently used anti-cancer modalities like surgery, chemotherapy and radiotherapy. Therefore, hypoxia seems to be a major limitation in current anti-cancer therapy. The use of non-pathogenic clostridia to deliver toxic agents to the tumor cells takes advantage of this unique physiology. These strictly anaerobic, Gram-positive, spore-forming bacteria give, after systemic administration, a selective colonization of hypoxic/necrotic areas within the tumor. Moreover, they can be genetically modified to secrete therapeutic proteins like cytosine deaminase or tumor necrosis factor-alpha. The specificity of this protein delivery system can be further increased when expression is controlled by the use of a radio-inducible promoter, leading to increased spatial and temporal regulation of protein expression. This approach of bacterial vector systems to target protein expression to the tumor can be considered very safe since bacteria can be eliminated at any moment by the addition of proper antibiotics. The Clostridium-based delivery system thus presents an alternative therapeutic modality to deliver anti-tumor agents specifically to the tumor site. This high selectivity offers a major advantage in comparison with the classical gene therapy systems.
Visualization and quantitative analysis of leukocyte dynamics in retinal microcirculation of rats. (1996)

This study demonstrates that microcirculatory dynamics of leukocytes can be visualized and analyzed quantitatively in rats in vivo with acridine orange fluorography. This method may be a promising tool to reveal how leukocytes contribute to retinal flow disturbances under various pathologic conditions.