gebhart/patrepeval huggingface dataset:
Source of intrinsic innervation of canine ventricles: a functional study (1987)

Recently it has been suggested that the parasympathetic innervation of the ventricles is by way of postganglionic axones that emanate from ganglion cells in the atria, reaching the ventricles by traversing the atrioventricular (AV) groove. We designed a series of experiments to test this hypothesis. Phenol (89%) was applied to the AV groove and surrounding 5 mm of epicardium in 21 dogs on cardiopulmonary bypass. The effects of intracoronary acetylcholine (ACh; 1-5 micrograms) and intracoronary nicotine (NIC; 25-100 micrograms) on cardiac isovolumic pressures were evaluated after beta-blockade. In another series of experiments, eight dogs were exposed to phenol in the same way and allowed to recover for 7-10 days. Atrial and ventricular responses to NIC were unaffected by phenol application to the AV groove in the acute animals when compared with application of saline alone. However, in the chronic animals, pretreatment with phenol 7-10 days previously reduced the ventricular responses to NIC by 70% while leaving the atrial responses intact. These data indicate that the intrinsic cardiac nerves (ICN) of the canine ventricles consist primarily of postganglionic parasympathetic axones which arise from supraventricular ganglia and cross the AV groove.
Clinical imaging of head and neck cancer with technetium-99m-labeled monoclonal antibody E48 IgG or F(ab')2. (1994)

The present study shows that RIS with either E48 F(ab')2 or E48 IgG is as valuable as the other imaging techniques. The selective accumulation of radioactivity in tumor tissues, in combination with the known intrinsic radiosensitivity of HNSCC, justifies the development of radioimmunoconjugates for radioimmunotherapy.
Modelling and simulation in successful drug development programmes: Characterisation of exacerbation reduction with roflumilast to corroborate the importance of defining patient subsets in COPD (2011)

Background/Rationale: Roflumilast (ROF), an oral, selective PDE4 inhibitor, reduces the rate of exacerbations and improves lung function in severe COPD. During clinical development, modelling and simulation techniques were used to identify and confirm a paradigm to explore patient, disease and treatment covariates. This approach identified patient populations that will benefit most from ROF, and was used to help design confirmatory clinical trials. Methods: Data from two 1-year, randomised, double-blind, placebo-controlled, parallel-group trials [Rennard S, et al . Respir Res 2011;12(1):18] in 2686 patients were used to build exacerbation and lung function models to identify patient characteristics that significantly impacted the clinical endpoints. Results: Patients with chronic bronchitis, higher cough/sputum scores, concomitant ICS use and low predicted FEV 1 at baseline were identified as having a higher rate of exacerbations and treatment effect. Patient characteristics as defined by the models were used, in addition to a history of exacerbations, to simulate the design of two other 1-year clinical trials [Calverley PMA, et al . Lancet 2009;374:685–94], with the inclusion criteria described in the trial protocols. The models predicted that the two trials would show a 17% reduction in exacerbation rate and a 47mL gain in FEV 1 with ROF; observed results were 17% reduction and a 48mL gain. Conclusions: This modelling and simulation approach showed the importance of defining COPD subsets for drug development, and helped support phase III studies confirming exacerbation reduction with ROF.
Interaction of Escherichia coli 70with Core RNA Polymerase (1998)

The RNA polymerase of Escherichia coli is a large,multisubunit enzyme existing in two forms. The core enzyme, consisting of subunits β and β′ and an α-subunitdimer (Burgess 1969a,b), carries out processive transcription elongation followed by termination. When oneof a variety of sigma (σ) factors is added to core, theholoenzyme is formed. The σ-subunit confers promoterspecific DNA binding and transcription initiation capabilities to the enzyme (Burgess and Travers 1970; Helmann and Chamberlin 1988; Gross et al. 1992, 1996). σ70of E. coli was the first σ factor to be described and characterized (Burgess et al. 1969). Since then, numerous σfactors have been discovered throughout the eubacterialkingdom, including six alternative σ factors in E. coli.Each σ directs transcription initiation from a specific setof promoters to transcribe genes usually with relatedfunctions. This control of transcription is mediated partially through the competition of the individual σ factorsfor the core enzyme and is a major part of global generegulation in bacteria (Zhou and Gross 1992). Elucidationof the structural characteristics of the core RNA polymerase σ factor-binding interaction will be very beneficial in fully understanding this aspect of regulation...
GRIP1, a novel mouse protein that serves as a transcriptional coactivator in yeast for the hormone binding domains of steroid receptors. (1996)

The yeast two-hybrid system was used to isolate a clone from a 17-day-old mouse embryo cDNA library that codes for a novel 812-aa long protein fragment, glucocorticoid receptor-interacting protein 1 (GRIP1), that can interact with the hormone binding domain (HBD) of the glucocorticoid receptor. In the yeast two-hybrid system and in vitro, GRIP1 interacted with the HBDs of the glucocorticoid, estrogen, and androgen receptors in a hormone-regulated manner. When fused to the DNA binding domain of a heterologous protein, the GRIP1 fragment activated a reporter gene containing a suitable enhancer site in yeast cells and in mammalian cells, indicating that GRIP1 contains a transcriptional activation domain. Overexpression of the GRIP1 fragment in mammalian cells interfered with hormone-regulated expression of mouse mammary tumor virus-chloramphenicol acetyltransferase gene and constitutive expression of cytomegalovirus-beta-galactosidase reporter gene, but not constitutive expression from a tRNA gene promoter. This selective squelching activity suggests that GRIM can interact with an essential component of the RNA polymerase II transcription machinery. Finally, while a steroid receptor HBD fused with a GAL4 DNA binding domain did not, by itself, activate transcription of a reporter gene in yeast, coexpression of this fusion protein with GRIP1 strongly activated the reporter gene. Thus, in yeast, GRIP1 can serve as a coactivator, potentiating the transactivation functions in steroid receptor HBDs, possibly by acting as a bridge between HBDs of the receptors and the basal transcription machinery.
Design, power, and interpretation of studies in the standard murine model of ALS (2008)

Identification of SOD1 as the mutated protein in a significant subset of familial amyotrophic lateral sclerosis (FALS) cases has led to the generation of transgenic rodent models of autosomal dominant SOD1 FALS. Mice carrying 23 copies of the human SOD1(G93A) transgene are considered the standard model for FALS and ALS therapeutic studies. To date, there have been at least 50 publications describing therapeutic agents that extend the lifespan of this mouse. However, no therapeutic agent besides riluzole has shown corresponding clinical efficacy. We used computer modeling and statistical analysis of 5429 SOD1(G93A) mice from our efficacy studies to quantify the impact of several critical confounding biological variables that must be appreciated and should be controlled for when designing and interpreting efficacy studies. Having identified the most critical of these biological variables, we subsequently instituted parameters for optimal study design in the SOD1(G93A) mouse model. We retested several compounds reported in major animal studies (minocycline, creatine, celecoxib, sodium phenylbutyrate, ceftriaxone, WHI-P131, thalidomide, and riluzole) using this optimal study design and found no survival benefit in the SOD1(G93A) mouse for any compounds (including riluzole) administered by their previously reported routes and doses. The presence of these uncontrolled confounding variables in the screening system, and the failure of these several drugs to demonstrate efficacy in adequately designed and powered repeat studies, leads us to conclude that the majority of published effects are most likely measurements of noise in the distribution of survival means as opposed to actual drug effect. We recommend a minimum study design for this mouse model to best address and manage this inherent noise and to facilitate more significant and reproducible results among all laboratories employing the SOD1(G93A) mouse.
Deinococcus cellulosilyticus sp. nov., isolated from air (2007)

A pink-coloured bacterial strain, 5516J-15(T), was isolated from an air sample from Jeju Island, Republic of Korea. The organism was found to have resistance to UV radiation typical of members of the genus Deinococcus, and it was placed within the radiation of the Deinococcus on a phylogenetic tree based on 16S rRNA gene sequences. Strain 5516J-15(T) shared low 16S rRNA gene sequence similarity (84.5-87.8 %) with Deinococcus species, showing highest sequence similarity to Deinococcus deserti VCD115(T) (87.8 %) and Deinococcus indicus Wt/1a(T) (87.8 %). Strain 5516J-15(T) had type A3 beta peptidoglycan with l-ornithine, menaquinone 8 (MK-8) as the major quinone and iso-C(12 : 0), anteiso-C(13 : 0), iso-C(16 : 0) and C(16 : 0) as the major fatty acids. Its polar lipid profile contained three unknown aminophospholipids, two unknown polar lipids, one unknown phospholipid and one unknown glycolipid. The DNA G+C content of strain 5516J-15(T) was 61.3 mol%. Based on the phylogenetic and phenotypic data presented, it is proposed that the unknown strain should be classified within a novel species in the genus Deinococcus with the name Deinococcus cellulosilyticus sp. nov. The type strain is 5516J-15(T) (=KACC 11606(T) =DSM 18568(T)).
[Expression of human VEGF165 gene in rat bone marrow stromal cells in vitro]. (2005)

The experiment demonstrated that rhVEGF165 was successfully expressed in BMSC. This result could serve as a basis for the next step of revascularization of bone tissue engineering.
Abstract B41: The angiotensin receptor blocker telmisartan inhibits the growth of pancreatic ductal adenocarcinoma and improves survival (2016)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal forms of cancer with a 5-year survival rate of less than 5%. PDAC is highly resistant to chemotherapy, which impels search for novel approaches for treatment. Our group has previously shown in PDAC models that the angiotensin II type 1 receptor (AT1R) blocker losartan decreases desmoplasia and solid stress, which enhances blood flow, and improves the delivery and effectiveness of cytotoxic agents (Chauhan et al, Nature Comm 2013). In contrast to losartan, which had no effects on the growth of primary PDAC, we recently found that the AT1R blocker telmisartan significantly reduces the growth of PDAC. In addition to inhibiting AT1R activity telmisartan is also a partial agonist of Peroxisome Proliferator Activated Receptor γ (PPARγ). We determined in a panel of PDAC cell lines the effects of telmisartan on cellular viability. Our findings suggest that the sensitivity to telmisartan treatment correlates with low steady-state expression of PPARγ and a mesenchymal morphology. Furthermore, telmisartan induced a transcriptional profile distinct from the response to the direct PPARγ agonist pioglitazone. In support of our correlative results, the genetic knockdown of PPARγ increased the sensitivity to telmisartan and stimulated epithelial to mesenchymal transition (e.g. decreased expression of E-cadherin, increased expression of the mesenchymal markers Snail and N-cadherin). We also tested the effects of telmisartan in orthotopically implanted and genetically engineered mouse models of PDAC. Telmisartan inhibited the growth of primary tumors, decreased the incidence of metastasis and improved mice survival. In summary, our findings show that telmisartan reduces the viability of PDAC cells with a mesenchymal morphology and low expression of PPARγ, inhibits PDAC growth and improves the survival of mice. Citation Format: Jelena Grahovac, Shiwei Han, Hao Liu, Rakesh Jain, Yves Boucher.{Authors}. The angiotensin receptor blocker telmisartan inhibits the growth of pancreatic ductal adenocarcinoma and improves survival. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B41.
From Lundberg to SIM-ICP: Computational Physiology and Modeling Intracranial Pressure (2012)

A simplified dynamic model generates patient-specific estimates of intracranial pressure and suggests a path forward for bringing simulated (SIM) physiologic models to the patient's bedside.
Structural Basis of a Potent Peptide Inhibitor Designed for Kv1.3 Channel, a Therapeutic Target of Autoimmune Disease (2008)

The potassium channel Kv1.3 is an attractive pharmacological target for immunomodulation of T cell-mediated autoimmune diseases. Potent and selective blockers of Kv1.3 are potential therapeutics for treating these diseases. Here we describe the design of a new peptide inhibitor that is potent and selective for Kv1.3. Three residues (Gly(11), Ile(28), and Asp(33)) of a scorpion toxin BmKTX were substituted by Arg(11), Thr(28), and His(33), resulting in a new peptide, named ADWX-1. The ADWX-1 peptide blocked Kv1.3 with picomolar affinity (IC(50), 1.89 pM), showing a 100-fold increase in activity compared with the native BmKTX toxin. The ADWX-1 also displayed good selectivity on Kv1.3 over related Kv1.1 and Kv1.2 channels. Furthermore, alanine-scanning mutagenesis was carried out to map the functional residues of ADWX-1 in blocking Kv1.3. Moreover, computational simulation was used to build a structural model of the ADWX-1-Kv1.3 complex. This model suggests that all mutated residues are favorable for both the high potency and selectivity of ADWX-1 toward Kv1.3. While Arg(11) of ADWX-1 interacts with Asp(386) in Kv1.3, Thr(28) and His(33) of ADWX-1 locate right above the selectivity filter-S6 linker of Kv1.3. Together, our data indicate that the specific ADWX-1 peptide would be a viable lead in the therapy of T cell-mediated autoimmune diseases, and the successful design of ADWX-1 suggests that rational design based on the structural model of the peptide-channel complex should accelerate the development of diagnostic and therapeutic agents for human channelopathies.
Radiolabeled alpha(v)beta3 integrin antagonists: a new class of tracers for tumor targeting. (1999)

[125I]P2 exhibits high affinity and selectivity for the alpha(v)beta3 integrin in vitro and in vivo and, thus, represents the first radiolabeled alpha(v)beta3 antagonist for the investigation of angiogenesis and metastasis in vivo.
Characterization and distribution of prolactin releasing peptide (PrRP) binding sites in the rat – evidence for a novel binding site subtype in cardiac and skeletal muscle (2000)

Prolactin releasing peptide (PrRP) was recently purified from bovine hypothalamus and binds to the orphan receptor, UHR-1. We examined the distribution and kinetics of (125)I-PrRP binding in rat tissues together with molecular characterization by chemical cross-linking and Northern blotting. In this study (125)I-PrRP binding showed specificity and rapid association and dissociation. Specific binding was found in membranes from rat tissues including brain (hypothalamus, medulla oblongata and cerebellum), pituitary, heart, soleus muscle, adipose tissue, kidney, adrenal gland, testis and small intestine. In hypothalamus, pituitary, heart and soleus competition analysis indicated only one class of binding site in each tissue. Binding affinity for PrRP (IC(50)) and binding site density (B(max)) respectively were 5.2+/-0.9 nM and 674+/-97 fmol mg protein(-1) in hypothalamus (n = 5), 1.4+/-0.6 nM and 541+/-126 fmol mg protein(-1) in pituitary (n = 3), 6.6+/-0.7 nM and 628+/-74 fmol mg protein(-1) in heart (n = 4) and 9.8+/-0.9 nM and 677+/-121 fmol mg protein(-1) in soleus muscle (n = 4). Analysis of (125)I-PrRP-binding site complexes by chemical cross-linking showed a binding site M(r) of 69,000 in hypothalamus and 41,000 in heart and soleus. Northern analysis of polyA(+) RNA from hypothalamus showed a 4.2 kb band as expected for UHR-1, but heart and soleus showed a 4.8 kb band. Taken together these results indicate that there may be different subtypes of PrRP binding sites in rat tissues which may differ from UHR-1.
A protective epitope of Moraxella catarrhalis is encoded by two different genes (1997)

The high-molecular-weight UspA protein of Moraxella catarrhalis has been described as being both present on the surface of all M. catarrhalis disease isolates examined to date and a target for a monoclonal antibody (MAb 17C7) which enhanced pulmonary clearance of this organism in a mouse model system (M. E. Helminen et al., J. Infect. Dis. 170:867-872, 1994). A recombinant bacteriophage that formed plaques which bound MAb 17C7 was shown to contain a M. catarrhalis gene, designated uspA1, that encoded a protein with a calculated molecular weight of 88,271. Characterization of an isogenic uspA1 mutant revealed that elimination of expression of UspA1 did not eliminate the reactivity of M. catarrhalis with MAb 17C7. In addition, N-terminal amino acid analysis of internal peptides derived from native UspA protein and Southern blot analysis of M. catarrhalis chromosomal DNA suggested the existence of a second UspA-like protein. A combination of epitope mapping and ligation-based PCR methods identified a second M. catarrhalis gene, designated uspA2, which also encoded the MAb 17C7-reactive epitope. The UspA2 protein had a calculated molecular weight of 62,483. Both the isogenic uspA1 mutant and an isogenic uspA2 mutant possessed the ability to express a very-high-molecular-weight antigen that bound MAb 17C7. Southern blot analysis indicated that disease isolates of M. catarrhalis likely possess both uspA1 and uspA2 genes. Both UspA1 and UspA2 most closely resembled adhesins produced by other bacterial pathogens.
Meganucleases and DNA Double-Strand Break-Induced Recombination: Perspectives for Gene Therapy (2007)

Meganucleases are sequence-specific endonucleases recognizing large (>12 bp) sequence sites and several laboratories have used these proteins to induce highly efficient gene targeting in mammalian cells. The recent development of artificial endonucleases with tailored specificities has opened the door for a wide range of new applications, including therapeutic ones: redesigned endonucleases cleaving chosen sequences could be used to in gene therapy to correct mutated genes or introduce transgenes in chosen loci. Such "targeted" approaches markedly differ from current gene therapy strategies based on the random insertion of a complementing virus-borne transgene. As a consequence, they should bypass the odds of random insertion. Artificial fusion proteins including Zinc-Finger binding domains have provided important proofs of concept, however the toxicity of these proteins is still an issue. Today custom-designed homing endonucleases, the natural meganucleases, could represent an efficient alternative. After a brief description of the origin of the technology, current systems based on redesigned endonucleases will be presented, with a special emphasis on the recent advances in homing endonuclease engineering. Finally, we will discuss the main issues that will need to be addressed in order to bring this promising technology to the patient.
Interferon-τ Modulates Phorbol Ester-Induced Production of Prostaglandin and Expression of Cyclooxygenase-2 and Phospholipase-A2 from Bovine Endometrial Cells1 (2000)

Antiluteolytic actions of bovine interferon-tau (bIFN-tau) require suppression of prostaglandin F(2 alpha) (PGF(2 alpha)) production. Our objective was to test whether bIFN-tau could block PGF(2 alpha) production and synthesis of phospholipase A(2) (PLA(2)) and cyclooxygenase-2 (COX-2) enzymes induced by a protein kinase C (PKC) stimulator (phorbol 12,13 dibutyrate; PDBu). Bovine endometrial epithelial (BEND) cells were treated with PDBu in the presence or absence of bIFN-tau. Medium samples were analyzed for concentrations of PGF(2 alpha), whole-cell extracts were analyzed for abundance of PLA(2) and COX-2 by immunoblotting, and RNA extracts were examined for steady-state levels of COX-2 mRNA by Northern blotting. The PDBu stimulated production of PGF(2 alpha) between 3 and 12 h, levels of COX-2 mRNA by 3 h and protein expression of COX-2 and PLA(2) by 6 and 12 h, respectively. Added concomitantly with PDBu, bIFN-tau suppressed PGF(2 alpha) production, steady-state levels of COX-2 mRNA, and expression of COX-2 and PLA(2) proteins. Added after a 3-h stimulation with PDBu alone, bIFN-tau suppressed PGF(2 alpha) production after 1 h. Bovine IFN-tau inhibited intracellular mechanisms responsible for PGF(2 alpha) production in BEND cells, and this could be through both cytosolic and nuclear actions.
The other pigment cell: specification and development of the pigmented epithelium of the vertebrate eye (2006)

Vertebrate retinal pigment epithelium (RPE) cells are derived from the multipotent optic neuroepithelium, develop in close proximity to the retina, and are indispensible for eye organogenesis and vision. Recent advances in our understanding of RPE development provide evidence for how critical signaling factors operating in dorso-ventral and distal-proximal gradients interact with key transcription factors to specify three distinct domains in the budding optic neuroepithelium: the distal future retina, the proximal future optic stalk/optic nerve, and the dorsal future RPE. Concomitantly with domain specification, the eye primordium progresses from a vesicle to a cup, RPE pigmentation extends towards the ventral side, and the future ciliary body and iris form from the margin zone between RPE and retina. While much has been learned about the molecular networks controlling RPE cell specification, key questions concerning the cell proliferative parameters in RPE and the subsequent morphogenetic events still need to be addressed in greater detail.
Design and Synthesis of Tesirine, a Clinical Antibody–Drug Conjugate Pyrrolobenzodiazepine Dimer Payload (2016)

Pyrrolobenzodiazepine dimers are an emerging class of warhead in the field of antibody-drug conjugates (ADCs). Tesirine (SG3249) was designed to combine potent antitumor activity with desirable physicochemical properties such as favorable hydrophobicity and improved conjugation characteristics. One of the reactive imines was capped with a cathepsin B-cleavable valine-alanine linker. A robust synthetic route was developed to allow the production of tesirine on clinical scale, employing a flexible, convergent strategy. Tesirine was evaluated <i>in vitro</i> both in stochastic and engineered ADC constructs and was confirmed as a potent and versatile payload. The conjugation of tesirine to anti-DLL3 rovalpituzumab has resulted in rovalpituzumab-tesirine (Rova-T), currently under evaluation for the treatment of small cell lung cancer.