gebhart/patrepeval huggingface dataset:
Lipid-Based Delivery Systems for Improving the Bioavailability and Lymphatic Transport of a Poorly Water-Soluble LTB4 Inhibitor (1998)

Ontazolast is a potent inhibitor (IC50 = 1 nm) of calcium ionophore A23187-stimulated leukotriene B4 (LTB4) biosynthesis in human peripheral blood leukocytes. The compound is practically insoluble in water (0.14 microgram/mL) and previous studies in animals have demonstrated extensive presystemic drug clearance through hepatic first-pass metabolism. Bioavailability of a suspension formulation in rats was less than 1%, but increased to approximately 9% when administered as a 20% soybean oil-in-water emulsion. The emulsion formulation and three additional lipid-based formulations were administered by gavage to conscious, minimally restrained rats in a novel, double-cannulated model to determine the effects of formulation on systemic blood absorption and mesenteric lymph transport of ontazolast. The bioavailability of ontazolast was significantly and substantially enhanced by all of the lipid-based formulations. While these formulations also significantly increased the amount of ontazolast transported by the lymph, the total amounts transported were insufficient to account for the improvement in bioavailability, which may be due to the elimination or reduction of the barriers of poor aqueous solubility and slow dissolution to absorption of ontazolast from the gastrointestinal tract, or the effects of lipid on the gastrointestinal membrane permeability, transit time, or metabolism of ontazolast. Semisolid SEDDS formulations, composed of Peceol and Gelucire 44/14, produced bioavailability similar to the emulsion formulation. The total amount of ontazolast transported by the lymph varied directly with the amount of concurrent triglyceride transport and appeared to be favored by formulations that prolong gastric emptying time or promote rapid absorption of ontazolast from the gastrointestinal tract.
The Bacillus cereus Hbl and Nhe Tripartite Enterotoxin Components Assemble Sequentially on the Surface of Target Cells and Are Not Interchangeable (2013)

Bacillus cereus is a spore-forming, Gram-positive bacterium commonly associated with outbreaks of food poisoning. It is also known as an opportunistic pathogen causing clinical infections such as bacteremia, meningitis, pneumonia, and gas gangrene-like cutaneous infections, mostly in immunocompromised patients. B. cereus secretes a plethora of toxins of which four are associated with the symptoms of food poisoning. Two of these, the non-hemolytic enterotoxin Nhe and the hemolysin BL (Hbl) toxin, are predicted to be structurally similar and are unique in that they require the combined action of three toxin proteins to induce cell lysis. Despite their dominant role in disease, the molecular mechanism of their toxic function is still poorly understood. We report here that B. cereus strain ATCC 10876 harbors not only genes encoding Nhe, but also two copies of the hbl genes. We identified Hbl as the major secreted toxin responsible for inducing rapid cell lysis both in cultured cells and in an intraperitoneal mouse toxicity model. Antibody neutralization and deletion of Hbl-encoding genes resulted in significant reductions of cytotoxic activity. Microscopy studies with Chinese Hamster Ovary cells furthermore showed that pore formation by both Hbl and Nhe occurs through a stepwise, sequential binding of toxin components to the cell surface and to each other. This begins with binding of Hbl-B or NheC to the eukaryotic membrane, and is followed by the recruitment of Hbl-L1 or NheB, respectively, followed by the corresponding third protein. Lastly, toxin component complementation studies indicate that although Hbl and Nhe can be expressed simultaneously and are predicted to be structurally similar, they are incompatible and cannot complement each other.
Replication-defective adenovirus type 5 as an in vitro and in vivo gene transfer vector in chickens (1995)

The capacity of E1A gene-deleted and thus replication-defective adenovirus type 5 (Ad5) to transduce foreign genes in chicken embryo fibroblasts (CEF) as well as in chickens was investigated. The lacZ and luciferase genes were successfully transduced in CEF by replication-defective Ad5, demonstrating that these cells possess receptor(s) for binding and penetration of Ad5. A single intramuscular inoculation of Ad-gD, a replication-defective Ad5 harbouring the gD gene of pseudorabies virus, in adult and 1-day-old chickens led to the production of a very high titres of specific antibodies. These gD-specific antibodies persisted for at least 56 days. These results demonstrate that replication-defective Ad5, despite its mammalian origin and the deletion of the E1A gene, is a good candidate for developing non-spreading vaccines in poultry.
Courtship in Saccharomyces cerevisiae: an early cell-cell interaction during mating. (1990)

During conjugation in Saccharomyces cerevisiae, two cells of opposite mating type (MATa and MAT alpha) fuse to form a diploid zygote. Conjugation requires that each cell locate an appropriate mating partner. To investigate how yeast cells select a mating partner, we developed a competition mating assay in which wild-type MAT alpha cells have a choice of two MATa cell mating partners. We first demonstrated that sterile MAT alpha 1 cells (expressing no a- or alpha-specific gene products) do not compete with fertile MATa cells in the assay; hence, wild-type MATa and MAT alpha cells can efficiently locate an appropriate mating partner. Second, we showed that a MATa strain need not be fertile to compete with a fertile MATa strain in the assay. This result defines an early step in conjugation, which we term courtship. We showed that the ability to agglutinate is not necessary in MATa cells for courtship but that production of a-pheromone and response to alpha-pheromone are necessary. Thus, MATa cells must not only transmit but must also receive and then respond to information for effective courtship; hence, there is a "conversation" between the courting cells. We showed that the only alpha-pheromone-induced response necessary in MATa cells for courtship is production of a-pheromone. In all cases tested, a strain producing a higher level of a-pheromone was more proficient in courtship than one producing a lower level. We propose that during courtship, a MAT alpha cell selects the adjacent MATa cell producing the highest level of a-pheromone.
Development of a tethered epicardial crawler for minimally invasive cardiac therapies (2004)

This paper describes the development of a robotic surgical device to facilitate minimally invasive, beating-heart cardiac therapies that can be performed within the pericardium. The concept we propose is that the device be equipped with the ability to adhere to the surface of the epicardium and locomote to any position and orientation under the direct control of a physician. As compared to current minimally invasive cardiac robotics, our approach obviates cardiac stabilization, lung deflation, differential lung ventilation, and reinsertion of laparoscopic tools. These advantages will result in greater efficiency and reduced trauma for the administration of intrapericardial therapies. This paper describes the current design of the robotic device and presents preliminary results.
Transcriptional regulation via cysteine thiol modification: A novel molecular strategy for chemoprevention and cytoprotection (2006)

Chemoprevention refers to the use of defined nontoxic chemical regimens to inhibit, reverse, or retard the process of multistage carcinogenesis that involves multiple signal transduction events. Identification of signaling molecules associated with carcinogenesis as prime targets of chemopreventive agents has become an area of great interest. Recent studies have implicated cysteine thiols present in various transcription factors, such as NF-kappaB, AP-1, and p53 as redox sensors in transcriptional regulation of many genes essential for maintaining cellular homeostasis. Some chemopreventive and cytoprotective agents have been found to target cysteine thiols present in key transcription factors or their regulators, thereby suppressing aberrant over-activation of carcinogenic signal transduction or restoring/normalizing or even potentiating cellular defense signaling. The focus of this review is the oxidation or covalent modification of thiol groups present in key representative redox-sensitive transcription factors and their regulating molecules as a unique strategy for molecular target-based chemoprevention and cytoprotection.
Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire (2019)

The αβ T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3β, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires.
Genome‐wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice (2008)

Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation.
HYCRON, an Allylic Anchor for High-Efficiency Solid Phase Synthesis of Protected Peptides and Glycopeptides (1997)

The recently developed allylic HYCRON anchor1 exhibits excellent properties for the solid phase synthesis of protected peptides and glycopeptides. Model reactions with analogous low molecular weight compounds assessed the acid- and base-stability of the polar and flexible HYCRON linkage. The new anchor is available in a two-step synthesis and allows the use of both the Boc- and the Fmoc-strategy, which can even be combined within one synthesis. Protected glycopeptides are released under almost neutral conditions, taking advantage of the Pd(0)-catalyzed allyl transfer to a weakly basic nucleophile such as N-methylaniline. The highly efficient synthesis of O-αGalNAc(TN)-peptides of the MUC-1 repeating unit is described. Acid- and base-stability of the allyl ester linkage enabled the synthesis of an O-glucosylated peptide by first removing a threonine tert-butyl group on the solid phase and subsequently glycosylating the liberated resin-bound hydroxyl component.
JNK inhibition reduces apoptosis and neovascularization in a murine model of age-related macular degeneration (2013)

Age-related macular degeneration (AMD) is the leading cause of registered blindness among the elderly and affects over 30 million people worldwide. It is well established that oxidative stress, inflammation, and apoptosis play critical roles in pathogenesis of AMD. In advanced wet AMD, although, most of the severe vision loss is due to bleeding and exudation of choroidal neovascularization (CNV), and it is well known that vascular endothelial growth factor (VEGF) plays a pivotal role in the growth of the abnormal blood vessels. VEGF suppression therapy improves visual acuity in AMD patients. However, there are unresolved issues, including safety and cost. Here we show that mice lacking c-Jun N-terminal kinase 1 (JNK1) exhibit decreased inflammation, reduced CNV, lower levels of choroidal VEGF, and impaired choroidal macrophage recruitment in a murine model of wet AMD (laser-induced CNV). Interestingly, we also detected a substantial reduction in choroidal apoptosis of JNK1-deficient mice. Intravitreal injection of a pan-caspase inhibitor reduced neovascularization in the laser-induced CNV model, suggesting that apoptosis plays a role in laser-induced pathological angiogenesis. Intravitreal injection of a specific JNK inhibitor decreased choroidal VEGF expression and reduced pathological CNV. These results suggest that JNK1 plays a key role in linking oxidative stress, inflammation, macrophage recruitment apoptosis, and VEGF production in wet AMD and pharmacological JNK inhibition offers a unique and alternative avenue for prevention and treatment of AMD.
Rheumatoid factors, B cells and immunoglobulin genes (1995)

The paradigm of self, non-self discrimination in the immune system is under review as autoreactive B or T cells are increasingly delineated within normal individuals. The products of autoreactive B cells are, mostly, polyspecific IgM antibodies of low affinity. These 'natural' antibodies include rheumatoid factors (RF) encoded by unmutated germline immunoglobulin genes. In rheumatoid arthritis (RA) the RF may be of the IgM, IgG or IgA isotype, show evidence of somatic mutation and have increased affinity; consistent with maturation of an antigen driven immune response. This response could be initiated or driven by an auto-immunogenic form of IgG or an exogenous cross-reactive antigen. Changes in galactosylation of IgG have been reported to be a valuable diagnostic and prognostic indicator in RA. Speculation that these changes may precipitate some of the disease processes is critically reviewed.
Photoperiod and Temperature Responses in Early‐Maturing, Near‐Isogenic Soybean Lines (2001)

While photoperiod responses have been studied in soybean [ Glycine max (L.) Merr.] isolines, identification of temperature and photo–thermal responses are lacking in early‐maturing soybean. This study was conducted to quantify photoperiod and temperature responses of early‐maturing soybean. Six ‘Harosoy’ isolines with different combinations of alleles at the E1 , E3 , E4 , and E7 loci were grown in growth cabinets with 10‐, 12‐, 14‐, 16‐, and 20‐h photoperiods and with either 18 or 28°C constant temperature. Under the most inductive conditions (10 and 12 h, 28°C), all isolines flowered in about 26 d. Under the least inductive conditions (20 h, 28°C), there was a 50 d difference in flowering time between the early‐ and late‐flowering isolines. Interestingly, the late‐flowering isolines flowered earlier under cool than under warm temperatures. A mathematical model was developed to quantify the effects of temperature and photoperiod on days to first flower. This model related the rate of phenological development from planting to flowering to temperature, photoperiod and the interaction between temperature and photoperiod. The equation was integrated analytically, resulting in an inverse time (1/time) equation, or numerically resulting in the development of a Growing Photothermal Day (G PTD ) similar to a heat unit. The model had a base temperature (5.8°C) below which the rate of phenological development was zero, a critical or base photoperiod (13.5 h) below which photoperiod had no effect, and two genetic coefficients, one of which varied with isoline. The isoline photoperiod sensitivity coefficient was linearly related to the number of dominant (late flowering, photoperiod sensitive) alleles. The model fit the observed data well ( R 2 = 0.96).
Music and Vibroacoustic Stimulation in People with Rett Syndrome: A Neurophysiological Study (2011)

VII ACKNOWLEDGEMENTS IX TABLE OF CONTENTS XI LIST OF TABLES XVI LIST OF FIGURES XVIII LIST OF APPENDICES XX LIST OF ABBREVIATIONS XXI CHAPTER ONE 1
Experimental evaluation of impact ionization in dilute nitride GaInNAs diodes (2013)

The anomalous behavior of impact ionization in dilute-nitride GaInNAs photodiodes with a range of nitrogen content below 4% is investigated. The ratio of hole- and electron-initiated ionization coefficients, k = β/α, is enhanced by a factor up to ∼4 with increasing nitrogen content. The absolute ionization coefficients are suppressed by up to two orders of magnitude at low electric fields in samples with 3% N. The narrow band gap, suppressed impact ionization, and increased breakdown voltage characteristics of GaInNAs make it a suitable material for use as part of a composite collector in GaAs-based heterojunction bipolar transistors.
Peptidomics approach to elucidate the proteolytic regulation of bioactive peptides (2012)

Peptide hormones and neuropeptides have important roles in physiology and therefore the regulation of these bioactive peptides is of great interest. In some cases proteolysis controls the concentrations and signaling of bioactive peptides, and the peptidases that mediate this biochemistry have proven to be extremely successful drug targets. Due to the lack of any general method to identify these peptidases, however, the role of proteolysis in the regulation of most neuropeptides and peptide hormones is unknown. This limitation prompted us to develop an advanced peptidomics-based strategy to identify the peptidases responsible for the proteolysis of significant bioactive peptides. The application of this approach to calcitonin gene-related peptide (CGRP), a neuropeptide associated with blood pressure and migraine, revealed the endogenous CGRP cleavage sites. This information was then used to biochemically purify the peptidase capable of proteolysis of CGRP at those cleavage sites, which led to the identification of insulin-degrading enzyme (IDE) as a candidate CGRP-degrading enzyme. CGRP had not been identified as an IDE substrate before and we tested the physiological relevance of this interaction by quantitative measurements of CGRP using IDE null (IDE(-/-)) mice. In the absence of IDE, full-length CGRP levels are elevated in vivo, confirming IDE as an endogenous CGRP-degrading enzyme. By linking CGRP and IDE, this strategy uncovers a previously unknown pathway for CGRP regulation and characterizes an additional role for IDE. More generally, this work suggests that this may be an effective general strategy for characterizing these pathways and peptidases moving forward.
An Antigenic Analysis of the Adenovirus Type 2 Fibre Polypeptide (1988)

Twenty-seven monoclonal antisera were generated against the SDS-denatured fibre of adenovirus type 2. The antisera were characterized using radioimmune assay, fluorescent antibody tests, immune precipitation, Western blotting, haemagglutination and neutralization, and formed six groups as follows: A, type-specific neutralizing antisera which exhibited haemagglutination inhibition (Hi+); B, type-specific non-neutralizing antisera which did not exhibit haemagglutination inhibition (Hi-); C, subgroup-specific neutralizing antisera Hi+; D, a subgroup-specific neutralizing antiserum Hi-; E, subgroup-specific non-neutralizing antisera Hi-; F, a subgroup-specific neutralizing antiserum Hi- which did not react in Western blotting tests. The C-terminal 201 amino acids of the fibre were expressed in Escherichia coli and a total of six antisera from groups A, B and C recognized five epitopes carried on this region which in several models is thought to form the knob of the fibre. At least eight epitopes were expressed by the entire native fibre. The five epitopes of the C-terminal end of the fibre formed three antigenic sites. Two sites each consisted of a neutralizing type-specific and a neutralizing group-specific epitope which overlapped in position. The remaining site consisted of a type-specific, non-neutralizing epitope.
Interaction between fibronectin and purified staphylococcal clumping factor (1987)

Clumping of Staphylococcal aureus was observed in the presence of fibrinogen as well as fibronectin. In order to elucidate the mechanism of this clumping, binding of radiolabelled fibrinogen and fibronectin to S. aureus cultures was studied. Cultures of S. aureus reacted with 125I-labelled fibrinogen as well as fibronectin. The binding of labelled fibrinogen to S. aureus could be completely inhibited by unlabelled fibronectin, whereas the binding of labelled fibronectin was only partially inhibited by unlabelled fibrinogen. This suggested an interaction of fibronectin with clumping factor which is the binding protein for fibrinogen in staphylococci. The clumping factor was purified from S. aureus strain K 807 by affinity chromatography on fibrinogen-Sepharose followed by HPLC. The purified clumping factor inhibited the binding of fibrinogen and fibronectin to staphylococci. In western blots the purified clumping factor reacted with fibrinogen as well as fibronectin. Thus, the direct interaction of clumping factor with fibronectin might be responsible for the clumping of staphylococci in fibrinogen depleted plasma or serum.
Discovery of a Potent Small Molecule IL-2 Inhibitor through Fragment Assembly (2003)

Using a site-directed fragment discovery method called tethering, we have identified a 60 nM small molecule antagonist of a cytokine/receptor interaction (IL-2/IL2Ralpha) with cell-based activity. Starting with a low micromolar hit, we employed a combination of tethering, structural biology, and computational analysis to design a focused set of 20 compounds. Eight of these compounds were at least 5-fold more active than the original hit. One of these compounds showed a 50-fold enhancement and represents the highest affinity inhibitor reported against this protein-protein target class. This method of coupling selected fragments with a low micromolar hit shows great potential for generating high-affinity lead compounds.