gebhart/patrepeval huggingface dataset:
Chronic Myelogenous Leukemia (2002)

The treatment options for chronic myelogenous leukemia (CML) continue to evolve rapidly. Imatinib mesylate (Gleevec, Glivec, formerly STI571) has continued to show remarkable clinical benefits and the updated results with this agent are reviewed. As relapses using single agent imatinib have occurred, particularly in advanced phase patients, the issue of whether combinations of other antileukemic agents with imatinib may yield improved results is addressed. In addition, data on new agents that have potential in the treatment of CML are reviewed. These agents are presented in the context of their molecular mechanism of action. The most recent data for stem cell transplantation, along with advances in nonmyeloablative transplants, are also reviewed. In Section I, Drs. Stephen O'Brien and Brian Druker update the current status of clinical trials with imatinib and review ongoing investigations into mechanisms of resistance and combinations of imatinib with other agents. They also present their views on integration of imatinib with other therapies. In Section II, Dr. Jorge Cortes describes the most recent data on novel therapies for CML, including farnesyl transferase inhibitors, arsenic trioxide, decitabine, and troxatyl, among others. These agents are discussed in the context of their molecular mechanism of action and rationale for use. In Section III, Dr. Jerald Radich updates the results of stem cell transplants for CML, including emerging data on nonmyeloablative transplants. He also presents data on using microarrays to stratify patients into molecularly defined risk groups.
Biology of breast preneoplasia (1977)

The literature dealing with mammary cancer and the presence of the identifiable preneoplastic lesions in the mammary gland of several species has been reviewed. A discrete morphologically identifiable lesion with a high malignant potential is considered preneoplastic. Lobuloalveolar lesions have been identified in the human mammary gland which fit most of the criteria for preneoplasia. The lesions, hyperplastic atypical lobules, are multicentric, have a high statistical association with breast cancer and demonstrate a morphological progression through dysplasia to frank carcinoma. Other breast lesions have a high statistical association but no morphological progression can be seen and their neoplastic potential remains unknown. The significance of these correlations is enhanced by the occurrence of homologous breast lesions in outbred and inbred animal models. Statistical correlation with breast cancer and aberrant morphology has been accepted as presumptive evidence of preneoplasia in some animals. Definitive proof of the neoplastic potential has been obtained in rodent models by transplantation of the suspected lesions and their subsequent development into cancers. Although a strong morphological and statistical analogy exists between the human and animal models, the causes and biological potential of the human lesions await experimental proof.
Evaluation of D-Dimer in the Diagnosis of Suspected Deep-Vein Thrombosis (2003)

Deep-vein thrombosis can be ruled out in a patient who is judged clinically unlikely to have deep-vein thrombosis and who has a negative D-dimer test. Ultrasound testing can be safely omitted in such patients.
Structure of the Fab Fragment of F105, a Broadly Reactive Anti-Human Immunodeficiency Virus (HIV) Antibody That Recognizes the CD4 Binding Site of HIV Type 1 gp120 (2005)

We have determined the crystal structure of the Fab fragment from F105, a broadly reactive human antibody with limited potency that recognizes the CD4 binding site of gp120. The structure reveals an extended CDR H3 loop with a phenylalanine residue at the apex and shows a striking pattern of serine and tyrosine residues. Modeling the interaction between gp120 and F105 suggests that the phenylalanine may recognize the binding pocket of gp120 used by Phe(43) of CD4 and that numerous tyrosine and serine residues form hydrogen bonds with the main chain atoms of gp120. A comparison of the F105 structure to that of immunoglobulin G1 b12, a much more potent and broadly neutralizing antibody with an overlapping epitope, suggests similarities that contribute to the broad recognition of human immunodeficiency virus by both antibodies. While the putative epitope for F105 shows significant overlap with that predicted for b12, it appears to differ from the b12 epitope in extending across the interface between the inner and outer domains of gp120. In contrast, the CDR loops of b12 appear to interact predominantly with the outer domain of gp120. The difference between the predicted epitopes for b12 and F105 suggests that the unique potency of b12 may arise from its ability to avoid the interface between the inner and outer domains of gp120.
Regioselective Synthesis of 1,3,5-Triaryl-4-alkylpyrazoles:  Novel Ligands for the Estrogen Receptor (2000)

[reaction: see structure] A regioselective synthesis of 4-alkyl-1,3,5-triarylpyrazoles has been developed for the preparation of unsymmetrically substituted systems of interest as ligands for the estrogen receptor.
Synthesis, Structure−Activity Relationships, and Pharmacological Profile of 9-Amino-4-oxo-1-phenyl-3,4,6,7-tetrahydro[1,4]diazepino[6,7,1-hi]indoles:  Discovery of Potent, Selective Phosphodiesterase Type 4 Inhibitors (2000)

The synthesis, structure-activity relationships, and biological properties of a novel series of potent and selective phosphodiesterase type 4 (PDE4) inhibitors are described. These new aminodiazepinoindoles displayed in vitro PDE4 activity with submicromolar IC(50) values and PDE4 selectivity vs PDE1, -3, and -5. Specifically, one compound (CI-1044, 10e) provided efficient in vitro inhibition of TNFalpha release from hPBMC and hWB with IC(50) values of 0.34 and 0.84 microM, respectively. This compound was found to exhibit potent in vivo activity in antigen-induced eosinophil recruitment in Brown-Norway rats (ED(50) = 3.2 mg/kg po) and in production of TNFalpha in Wistar rats (ED(50) = 2.8 mg/kg po). No emetic side effects at therapeutic doses were observed in ferrets.
Achievements and Limitations of Complement Inhibition by Eculizumab in Paroxysmal Nocturnal Hemoglobinuria: The Role of Complement Component 3 (2011)

Paroxysmal nocturnal hemoglobinuria (PNH) is a hematological disorder characterized by complementmediated hemolytic anemia, thrombophilia and bone marrow failure. The clinical hallmark of PNH is evident chronic hemolysis due to the absence of the complement regulators CD55 and CD59 on PNH erythrocytes. Intravascular hemolysis drives the major clinical features of PNH, including anemia, hemoglobinuria, fatigue and other hemolysisrelated disabling symptoms, such as painful abdominal crises, dysphagia and erectile dysfunction. A peculiar thromboembolic risk has been associated with the hemolysis in PNH, but its pathophysiologic cause remains unclear. The treatment of PNH has remained supportive until a few years ago, when the first complement inhibitor, designated eculizumab, became available. Chronic treatment with eculizumab results in sustained control of intravascular hemolysis, leading to hemoglobin stabilization and transfusion independence in half of the patients. However, residual anemia may persist in a substantial fraction of patients. Recent observations by different groups, including our own, have demonstrated that residual hemolysis may be due to persistent activation of the early phases of the complement cascade, leading to progressive C3-deposition on PNH erythrocytes and possible subsequent extravascular hemolysis through the reticuloendothelial system. Here we critically review the available clinical results of eculizumab treatment for PNH patients, pointing out the recent insights into the pathophysiology of the disease. We discuss the role of the different components of the complement cascade leading to hemolysis, in both the absence and presence of the terminal effector pathway inhibition by eculizumab. Finally, we provide a theoretical rationale for the development of novel strategies of complement inhibition which could in the future further improve on the already substantial efficacy of eculizumab.
Identification of a subgroup of tardive dyskinesia patients by pharmacologic probes (1980)

Some patients with tardive dyskinesia fit the cholinergic-dopaminergic imbalance theory, but some do not. In an attempt to study his heterogeneity further, the authors measured the responses of 10 patients with tardive dyskinesia to intravenous challenge doses of drugs that facilitate or inhibit acetylcholine transmission (physostigmine or benztropine, respectively). They then measured the response of these patients to an open outpatient deanol trial. They found that the responses of half of the patients followed the classic theory, 2 responded paradoxically, and 3 responsed inconsistently. They suggest that there is a subgroup of tardive dyskinesia patients who fit the theory but that more research is needed to identify the subgroups who do not.
Band Gap Control in Conjugated Oligomers via Lewis Acids (2009)

A simple and effective strategy for optical band gap control is demonstrated through the use of a novel small acceptor/donor/acceptor molecule, 1, and group-13 Lewis acids. Chromophore 1 contains a dithienolesilole donor unit end-capped with benzo-2,1,3-thiadiazole (BT) acceptor units. Addition to 1 of stoichiometeric quantities of Lewis acids of varying strength resulted in the formation of Lewis adducts with progressively red-shifted primary charge-transfer absorption bands. These complexes have absorption spectra that approach those of known conjugated copolymers containing related units. NMR spectroscopy and X-ray diffraction studies revealed that 1 binds 2 equiv of Lewis acid via the nitrogen at the 3-position of BT.
Production of Polyketides by Saccharomyces cerevisiae (2007)

Polyketides are a group of natural products that have gained much interest due to their use as antibiotics, cholesterol lowering agents, immunosuppressors and as other drugs. Many organisms that naturally produce polyketides are difficult to cultivate and only produce these metabolites in small amounts. It is therefore of general interest to transfer polyketide synthase (PKS) genes from their natural sources into heterologous hosts that can overproduce the corresponding polyketides. In this study we demonstrate the heterologous expression of 6-methylsalicylic acid synthase (6-MSAS), naturally produced by Penicillium patulum, in the yeast Saccharomyces cerevisiae. In order to activate the PKS a 4 -phosphopantetheinyl transferase (PPTase) is required. We therefore co-expressed PPTases encoded by either sfp from Bacillus subtilis or by npgA from Aspergillus nidulans. The different strains were grown in batch cultures. Growth and product concentration were measured and kinetic parameters were calculated. It was shown that both PPTases could be efficiently used for activation of PKSs in yeast as good yields of 6MSA were obtained with both enzymes. * Corresponding auther: ael@biocentrum.dtu.dk 1 Center for Microbial Biotechnology, BioCentrum-DTU, Denmark 2 Department of Biology, University of Iceland, Iceland
Mutational analysis of Wnt signaling molecules in ameloblastoma with aberrant nuclear expression of β‐catenin (2008)

Mutations in CTNNB1, APC, AXIN1, and AXIN2 are not implicated in nuclear accumulation of beta-catenin, and that the expression of cyclin D1 is accelerated independently of beta-catenin in ameloblastomas. Other Wnt signaling members or alternative pathways involved in the degradation of beta-catenin should be subject of further investigation.
Functional Expression of the High Affinity Receptor for IgE (FcɛRI) in Human Platelets and Its’ Intracellular Expression in Human Megakaryocytes (1999)

Abstract The high affinity IgE receptor (FcɛRI) expressed on the cell surface of mast cells and basophils is the key molecule in triggering the IgE-mediated allergic reaction. Recently, it was elucidated that the FcɛRI is expressed on a variety of other cells like Langerhans cells, monocytes, and eosinophils, and the functional importance of the FcɛRI expression in Langerhans cells was also shown. Some studies suggest that human platelets may play important roles in allergic inflammation through the cell-surface expression of the FcɛRII and FcγRII. Here, we report that human platelets and megakaryocytes constitutively express the messenger RNA and protein for the FcɛRI. Although the FcɛRI is expressed on the cell surface of human platelets, it is only detected in the cytoplasm of human megakaryocytes. We also confirmed that human platelets express the genes for the , β, and γ chains of the FcɛRI without any defined mutations. Furthermore, stimulation of human platelets via the FcɛRI induced the release of serotonin and RANTES (Regulated on Activation, Normal T Expressed, and presumably Secreted). Taken together, these results suggest a novel and important role for human platelets in perpetuating allergic inflammation through the expression of and activation via the FcɛRI.
Identification and in vitro expression of mutations causing dihydropteridine reductase deficiency (1993)

Six mutations resulting in the recessive inherited disorder dihydropteridine reductase deficiency are reported, five of which are previously unknown. Two are nonsense mutations, resulting in premature termination of the protein, with the remaining four being missense mutations. The mutations found lie in the middle to 3' end of the dihydropteridine reductase reading frame, with the exception of one mutation which lies at codon 23, which is the only mutation found in more than one patient. The mutation pattern can be described as heterogeneous. The wild type and several of the mutant DHPR cDNA's were expressed in E. coli and the proteins purified and examined by a variety of techniques, including calculation of kinetic constants. One mutation (Gly23-->Asp) results in completely inactive protein, while a second (Trp108-->Gly) has substantial activity but does not completely dimerize. Both this mutant and a third, His158-->Tyr, are extremely susceptible to in vitro protease digestion, indicating that their three-dimensional structure has been altered. The protein studies underline the heterogeneous nature of DHPR mutations, in that the effects of different amino acid substitutions on the DHPR enzyme are varied.
Crystal Structure and Mutational Analysis of Heparan Sulfate 3-O-Sulfotransferase Isoform 1 (2004)

Heparan sulfate interacts with antithrombin, a protease inhibitor, to regulate blood coagulation. Heparan sulfate 3-O-sulfotransferase isoform 1 performs the crucial last step modification in the biosynthesis of anticoagulant heparan sulfate. This enzyme transfers the sulfuryl group (SO(3)) from 3'-phosphoadenosine 5'-phosphosulfate to the 3-OH position of a glucosamine residue to form the 3-O-sulfo glucosamine, a structural motif critical for binding of heparan sulfate to antithrombin. In this study, we report the crystal structure of 3-O-sulfotransferase isoform 1 at 2.5-A resolution in a binary complex with 3'-phosphoadenosine 5'-phosphate. This structure reveals residues critical for 3'-phosphoadenosine 5'-phosphosulfate binding and suggests residues required for the binding of heparan sulfate. In addition, site-directed mutagenesis analyses suggest that residues Arg-67, Lys-68, Arg-72, Glu-90, His-92, Asp-95, Lys-123, and Arg-276 are essential for enzymatic activity. Among these essential amino acid residues, we find that residues Arg-67, Arg-72, His-92, and Asp-95 are conserved in heparan sulfate 3-O-sulfotransferases but not in heparan N-deacetylase/N-sulfotransferase, suggesting a role for these residues in conferring substrate specificity. Results from this study provide information essential for understanding the biosynthesis of anticoagulant heparan sulfate and the general mechanism of action of heparan sulfate sulfotransferases.
The HER2 Receptor in Breast Cancer: Pathophysiology, Clinical Use, and New Advances in Therapy (2012)

Human epidermal growth factor receptor 2 (HER2) is overexpressed in around 20-30% of breast cancer tumors. It is associated with a more aggressive disease, higher recurrence rate, and increased mortality. Trastuzumab is a HER2 receptor blocker that has become the standard of care for the treatment of HER2 positive breast cancer. The effectiveness of Trastuzumab has been well validated in research as well as in clinical practice. The addition of Trastuzumab to standard of care chemotherapy in clinical trials has been shown to improve outcomes for early stage as well as metastatic HER2 positive breast cancer. The most clinically significant side effect of Trastuzumab is the risk of cardiac myocyte injury, leading to the development of congestive heart failure. The emergence of patterns of resistance to Trastuzumab has led to the discovery of new monoclonal antibodies and other targeted agents aimed at overcoming Trastuzumab resistance and improving survival in patients diagnosed with HER2 positive breast cancers.
Pneumococcal Virulence Factors: Structure and Function (2001)

The overall goal for this review is to summarize the current body of knowledge about the structure and function of major known antigens of Streptococcus pneumoniae, a major gram-positive bacterial pathogen of humans. This information is then related to the role of these proteins in pneumococcal pathogenesis and in the development of new vaccines and/or other antimicrobial agents. S. pneumoniae is the most common cause of fatal community-acquired pneumonia in the elderly and is also one of the most common causes of middle ear infections and meningitis in children. The present vaccine for the pneumococcus consists of a mixture of 23 different capsular polysaccharides. While this vaccine is very effective in young adults, who are normally at low risk of serious disease, it is only about 60% effective in the elderly. In children younger than 2 years the vaccine is ineffective and is not recommended due to the inability of this age group to mount an antibody response to the pneumococcal polysaccharides. Antimicrobial drugs such as penicillin have diminished the risk from pneumococcal disease. Several pneumococcal proteins including pneumococcal surface proteins A and C, hyaluronate lyase, pneumolysin, autolysin, pneumococcal surface antigen A, choline binding protein A, and two neuraminidase enzymes are being investigated as potential vaccine or drug targets. Essentially all of these antigens have been or are being investigated on a structural level in addition to being characterized biochemically. Recently, three-dimensional structures for hyaluronate lyase and pneumococcal surface antigen A became available from X-ray crystallography determinations. Also, modeling studies based on biophysical measurements provided more information about the structures of pneumolysin and pneumococcal surface protein A. Structural and biochemical studies of these pneumococcal virulence factors have facilitated the development of novel antibiotics or protein antigen-based vaccines as an alternative to polysaccharide-based vaccines for the treatment of pneumococcal disease.
Declining Age of Onset of Type 2 Diabetes Mellitus in the North-West (2011)

Context: Diabetes mellitus, an inherited metabolic disorder which is associated with devastating complications, is one of the biggest burdens on the society, in terms of the expenditure of money on health care and wastage of the prime years of life. The increasing prevalence of diabetes mellitus is attributed to adverse lifestyles like obesity and physical inactivity and this is prevalent even among school going children, thus making them vulnerable to the disease at an earlier age. Aim: The present study was designed to decipher the prevalence of type 2 diabetes mellitus in various age groups of the north west Punjabi population. Settings and design: The subjects were selected by conducting a door to door survey of a few villages of the border belt of Amritsar and the Tarn Taran district. One patient of diabetes mellitus was considered as one family unit and the offsprings of these diabetic patients, who were siblings amongst themselves, were recruited for the study. Material and Method: All the selected families were required to fill up a consent form by the head of the family. Fasting samples of the participating families were collected and analyzed for fasting plasma glucose, glycated haemoglobin, complete lipid profile, serum insulin and C-peptide. Statistical analysis was done by using the Student’s t test. Results and conclusions The prevalence of diabetes mellitus in the north-west Punjabi population was found to be 25%. IFG was more prevalent in females as compared to the males and the age of onset of diabetes mellitus was observed to decline both in males and females, as was evident from its occurrence in the age group of 19-24 years. .
Comparison of the efficacy of mechanistically different antioxidants in the rat hemorrhagic shock model. (1991)

Four pharmacological mechanisms for antagonizing free radical generation or reactions were compared in terms of their efficacy in attenuating hemorrhagic shock in rats. These included opposing superoxide generation by xanthine oxidase (e.g., oxypurinol), inhibiting arachidonic acid oxidation by cyclooxygenase (e.g., ibuprofen), chelating iron (e.g., desferal), and inhibiting lipid peroxidation (e.g., tirilazad mesylate [U-74006F] and U-78517G). Animals were hemorrhaged to a mean arterial pressure (MAP) of 43-45 mmHg where they were held for 2 hr. Five minutes prior to the end of the hemorrhage period, either vehicle, U-74006F (10 mg/kg), U-78517G (10 mg/kg), oxypurinol (10 or 25 mg/kg), desferal (10 or 25 mg/kg), or ibuprofen (10 mg/kg) was administered i.v., followed by the reinfusion of shed blood. In vehicle-treated animals, MAP declined progressively over the 2 hr post-reinfusion. Ibuprofen, desferal, and oxypurinol treatments each failed to attenuate this decline. In contrast, both U-74006F and U-78517G resulted in a significantly improved maintenance of MAP. Evidence of shock-induced lipid peroxidation was observed in terms of a 73.8% depletion in liver vitamin E content at 2 hr post-reinfusion in vehicle-treated rats. This decrease was prevented by both U-74006F and U-78517G. Inhibition of free radical-induced lipid peroxidation appears more effective for attenuating free radical pathophysiology in hemorrhagic shock that attempting to inhibit specific pathways of oxygen radical generation.