gebhart/patrepeval huggingface dataset:
Enthalpy-Entropy Compensation in DNA Melting Thermodynamics (1995)

We investigate enthalpy-entropy compensation for melting of nearest-neighbor doublets in DNA. Based on data for 10 normal doublets and for doublets containing a mispaired or analog base, the correlation of delta Szero with delta Hzero follows a rectangular hyperbola. Doublet melting temperature relates linearly to delta Hzero by Tm = T(o) + delta Hzero/a, where T(o) = 273 K and a = 80 cal/mol-K. Thus Tm is proportional to delta Hzero + aTo rather than to delta Hzero alone as previously thought by assuming delta Szero to be constant. The term aTo = 21.8 kcal/mol may reflect a constant enthalpy change in solvent accompanying the DNA enthalpy change for doublet melting and is roughly equivalent to breaking four H-bonds between water molecules for each melted doublet. The solvent entropy change (aTo/Tm) declines with increasing Tm, while the DNA entropy change (delta Hzero/Tm) rises, so the combined DNA + solvent entropy change stays constant at 80 cal/K/mol of doublet. If such constancy in DNA + solvent entropy changes also holds for enzyme clefts as "solvent," then free energy differences for competing correct and incorrect base pairs in polymerase clefts may be as large as enthalpy differences and possibly sufficient to account for DNA polymerase accuracy. The hyperbolic relationship between delta Szero and delta Hzero observed in 1 M salt can be used to evaluate delta Hzero and delta Szero from Tm at lower, physiologically relevant, salt concentrations.
Simple and efficient BURS table generation (1992)

A simple and efficient algorithm for generating bottom-up rewrite system (BURS) tables is described. A small prototype implementation produces tables 10 to 30 times more quickly than the best current techniques. The algorithm does not require novel data structures or complicated algorithmic techniques. Previously published methods for the on-the-fly elimination of states are generalized and simplified to create a new method, triangle trimming , that is employed in the algorithm.
Synthesis and Biological Evaluation of 4(5)-(6-Alkylpyridin-2-yl)imidazoles as Transforming Growth Factor-β Type 1 Receptor Kinase Inhibitors (2007)

A series of 4(5)-(6-alkylpyridin-2-yl)imidazoles 13a-p, 17a, and 17b have been synthesized and evaluated for ALK5 inhibitory activity in an enzyme assay and in cell-based luciferase reporter assays. The quinoxalinyl analogue 13e inhibited ALK5 phosphorylation with an IC50 of 0.012 muM and showed more than 90% inhibition at 0.05 muM in a luciferase reporter assay using HaCaT cells transiently transfected with p3TP-luc reporter construct. The binding mode of 13e generated by flexible docking studies shows that 13e fits well into the active site cavity of ALK5 by forming several tight interactions.
Successful fertilization after superovulation and laparoscopic intrauterine insemination of the brushtail possum, Trichosurus vulpecula , and tammar wallaby, Macropus eugenii (1998)

Fertilization has been achieved in superovulated brushtail possums and tammar wallabies after laparoscopic intrauterine artificial insemination. Various superovulation protocols and insemination times were examined but a maximum of 2-5 eggs including 1-2 embryos per possum were recovered. The female possums were superovulated by treatment with 15 iu pregnant mares' serum gonadotrophin and then either GnRH (4 x 50 micrograms, at intervals of 90 min) or 4 mg LH, 3 days later. Inseminations were performed within 6 h before or 4-10 h after (pregnant mares' serum gonadotrophin-GnRH group only) the expected onset of ovulation using epididymal spermatozoa. Superovulation in wallabies was achieved by treatment with FSH (8 x 6 mg, at intervals of 12 h for 4 days) followed by 4 mg LH on day 5. Inseminations were performed 4-6 h before the expected onset of ovulation using ejaculated spermatozoa, which resulted in the recovery of 7-8 eggs including 3-4 embryos per female. All embryos recovered were from possums and wallabies examined 1-2 days after insemination and included fertilized eggs, two-cell and four-cell embryos. Motile spermatozoa were recovered from the oviducts and uteri but only immotile spermatozoa were found in the vaginal complex. Five to thirty per cent of spermatozoa recovered from the oviducts of possums examined 2-6 h after insemination had thumbtack morphology, which is thought to be correlated with capacitation. Although embryo yields per female were low, this study has established that intrauterine artificial insemination after superovulation is a feasible assisted breeding strategy for marsupials with implications for species conservation and population control.
Electron Paramagnetic Resonance Studies of Humic Acid and Related Model Compounds (1966)

Humic acids from soils and lignites have been examined by EPR spectrometry. All samples showed a stable free organic radical content of about 1018 spins per gram. When these samples were converted to their sodium salts, a marked increase in radical content occurred. This was interpreted to indicate that a quinhydrone moiety exists in the humic acid macromolecule. Synthetic humic acid, prepared by oxidizing catechol in the presence of amino acids, also showed similar EPR spectra, as did selected quinhydrone model compounds. The radical moiety appeared to be stable to severe oxidation and hydrolytic conditions. Reduction in basic media caused an initial decrease in radical species; continued reduction generated new radical species. A proposed model for humic acid basod on a hydroxyquinone structure is proposed.
Platelet-Derived Growth Factor (PDGF)/PDGF Receptors (PDGFR) Axis as Target for Antitumor and Antiangiogenic Therapy (2010)

Angiogenesis in normal and pathological conditions is a multi-step process governed by positive and negative endogenous regulators. Many growth factors are involved in different steps of angiogenesis, like vascular endothelial growth factors (VEGF), fibroblast growth factor (FGF)-2 or platelet-derived growth factors (PDGF). From these, VEGF and FGF-2 were extensively investigated and it was shown that they significantly contribute to the induction and progression of angiogenesis. A lot of evidence has been accumulated in last 10 years that supports the contribution of PDGF/PDGFR axis in developing angiogenesis in both normal and tumoral conditions. The crucial role of PDGF-B and PDGFR-β in angiogenesis has been demonstrated by gene targeting experiments, and their expression correlates with increased vascularity and maturation of the vascular wall. PDGF and their receptors were identified in a large variety of human tumor cells. In experimental models it was shown that inhibition of PDGF reduces interstitial fluid pressure in tumors and enhances the effect of chemotherapy. PDGFR have been involved in the cardiovascular development and their loss leads to a disruption in yolk sac blood vessels development. PDGFRβ expression by pericytes is necessary for their recruitment and integration in the wall of tumor vessels. Endothelial cells of tumor-associated blood vessels can express PDGFR. Based on these data, it was suggested the potential benefit of targeting PDGFR in the treatment of solid tumors. The molecular mechanisms of PDGF/PDGFR-mediated angiogenesis are not fully understood, but it was shown that tyrosine kinase inhibitors reduce tumor growth and angiogenesis in experimental xenograft models, and recent data demonstrated their efficacy in chemoresistant tumors. The <i>in vivo</i> effects of PDGFR inhibitors are more complex, based on the cross-talk with other angiogenic factors. In this review, we summarize data regarding the mechanisms and significance of PDGF/PDGFR expression in normal conditions and tumors, focusing on this axis as a potential target for antitumor and antiangiogenic therapy.
Gene Therapy, Concepts, Current Trials and Future Directions (1993)

Since the initial human clinical trials of retroviral-mediated gene transfer in the USA in 1989, numerous additional protocols are in process or have been proposed. In the first therapeutic protocol, to treat the genetic disease ADA deficiency, encouraging signs of clinical benefit have been observed in the first two patients. Gene-marking properties are being extensively used in many protocols, particularly in the area of autologous bone marrow transplantation for various cancers. The drug delivery potential of gene therapy is initially being evaluated through delivery of various lymphokines and cytokines in cancer therapy protocols. Testing has also begun for other genetic diseases, Familial Hypercholesterolemia and Hemophilia B. Vector systems and retroviral vectors are developing rapidly, and a clinical trial using a liposome-based delivery has started. The pace of technical development and clinical application has intensified. Although significant clinical therapies are expected from these initial studies, the full potential of gene therapy for wide applications still requires innovative research programs, directed towards true in vivo vectors.
B Cell Receptor–independent Stimuli Trigger Immunoglobulin (Ig) Class Switch Recombination and Production of IgG Autoantibodies by Anergic Self-Reactive B Cells (2003)

In both humans and animals, immunoglobulin (Ig)G autoantibodies are less frequent but more pathogenic than IgM autoantibodies, suggesting that controls over Ig isotype switching are required to reinforce B cell self-tolerance. We have used gene targeting to produce mice in which hen egg lysozyme (HEL)-specific B cells can switch to all Ig isotypes (SWHEL mice). When crossed with soluble HEL transgenic (Tg) mice, self-reactive SWHEL B cells became anergic. However, in contrast to anergic B cells from the original nonswitching anti-HEL x soluble HEL double Tg model, self-reactive SWHEL B cells also displayed an immature phenotype, reduced lifespan, and exclusion from the splenic follicle. These differences were not related to their ability to Ig class switch, but instead to competition with non-HEL-binding B cells generated by VH gene replacement in SWHEL mice. When activated in vitro with B cell receptor (BCR)-independent stimuli such as anti-CD40 monoclonal antibody plus interleukin 4 or lipopolysaccharide (LPS), anergic SWHEL double Tg B cells proliferated and produced IgG anti-HEL antibodies as efficiently as naive HEL-binding B cells from SWHEL Ig Tg mice. These results demonstrate that no intrinsic constraints to isotype switching exist in anergic self-reactive B cells. Instead, production of IgG autoantibodies is prevented by separate controls that reduce the likelihood of anergic B cells encountering BCR-independent stimuli. That bacteria-derived LPS could circumvent these controls may explain the well-known association between autoantibody-mediated diseases and episodes of systemic infection.
Conversion of human choriogonadotropin into a follitropin by protein engineering. (1991)

Human reproduction is dependent upon the actions of follicle-stimulating hormone (hFSH), luteinizing hormone (hLH), and chorionic gonadotropin (hCG). While the alpha subunits of these heterodimeric proteins can be interchanged without effect on receptor-binding specificity, their beta subunits differ and direct hormone binding to either LH/CG or FSH receptors. Previous studies employing chemical modifications of the hormones, monoclonal antibodies, or synthetic peptides have implicated hCG beta-subunit residues between Cys-38 and Cys-57 and corresponding regions of hLH beta and hFSH beta in receptor recognition and activation. Since the beta subunits of hCG or hLH and hFSH exhibit very little sequence similarity in this region, we postulated that these residues might contribute to hormone specificity. To test this hypothesis we constructed chimeric hCG/hFSH beta subunits, coexpressed them with the human alpha subunit, and examined their ability to interact with LH and FSH receptors and hormone-specific monoclonal antibodies. Surprisingly, substitution of hFSH beta residues 33-52 for hCG beta residues 39-58 had no effect on receptor binding or stimulation. However, substitution of hFSH beta residues 88-108 in place of the carboxyl terminus of hCG beta (residues 94-145) resulted in a hormone analog identical to hFSH in its ability to bind and stimulate FSH receptors. The altered binding specificity displayed by this analog is not attributable solely to the replacement of hCG beta residues 108-145 or substitution of residues in the "determinant loop" located between hCG beta residues 93 and 100.
A Plant-Like Kinase in Plasmodium falciparum Regulates Parasite Egress from Erythrocytes (2010)

Clinical malaria is associated with the proliferation of Plasmodium parasites in human erythrocytes. The coordinated processes of parasite egress from and invasion into erythrocytes are rapid and tightly regulated. We have found that the plant-like calcium-dependent protein kinase PfCDPK5, which is expressed in invasive merozoite forms of Plasmodium falciparum, was critical for egress. Parasites deficient in PfCDPK5 arrested as mature schizonts with intact membranes, despite normal maturation of egress proteases and invasion ligands. Merozoites physically released from stalled schizonts were capable of invading new erythrocytes, separating the pathways of egress and invasion. The arrest was downstream of cyclic guanosine monophosphate-dependent protein kinase (PfPKG) function and independent of protease processing. Thus, PfCDPK5 plays an essential role during the blood stage of malaria replication.
Alkaline Phosphatase-Positive Colony Formation Is a Sensitive, Specific, and Quantitative Indicator of Undifferentiated Human Embryonic Stem Cells (2008)

Human embryonic stem cells (hESCs) can be maintained in vitro as immortal pluripotent cells but remain responsive to many differentiation-inducing signals. Investigation of the initial critical events involved in differentiation induction would be greatly facilitated if a specific, robust, and quantitative assay for pluripotent hESCs with self-renewal potential were available. Here we describe the results of a series of experiments to determine whether the formation of adherent alkaline phosphatase-positive (AP(+)) colonies under conditions optimized for propagating undifferentiated hESCs would meet this need. The findings can be summarized as follows. (a) Most colonies obtained under these conditions consist of >or=30 AP(+) cells that coexpress OCT4, NANOG, SSEA3, SSEA4, TRA-1-60, and TRA-1-81. (b) Most such colonies are derived from SSEA3(+) cells. (c) Primary colonies contain cells that produce secondary colonies of the same composition, including cells that initiate multilineage differentiation in embryoid bodies (EBs). (d) Colony formation is independent of plating density or the colony-forming cell (CFC) content of the test population over a wide range of cell concentrations. (e) CFC frequencies decrease when differentiation is induced by exposure either to retinoic acid or to conditions that stimulate EB formation. Interestingly, this loss of AP(+) clonogenic potential also occurs more rapidly than the loss of SSEA3 or OCT4 expression. The CFC assay thus provides a simple, reliable, broadly applicable, and highly specific functional assay for quantifying undifferentiated hESCs with self-renewal potential. Its use under standardized assay conditions should enhance future elucidation of the mechanisms that regulate hESC propagation and their early differentiation.
Cloning of a Gene Cluster Encoding Enzymes Responsible for the Mevalonate Pathway from a Terpenoid-antibiotic-producing Streptomyces Strain (2001)

A gene cluster encoding enzymes responsible for the mevalonate pathway was isolated from Streptomyces griseolosporeus strain MF730-N6, a terpenoid-antibiotic terpentecin producer, by searching a flanking region of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase gene, which had been previously isolated by complementation. By DNA sequencing of an 8.9-kb BamHI fragment, 7 genes encoding geranylgeranyl diphosphate synthase (GGDPS), mevalonate kinase (MK), mevalonate diphosphate decarboxylase (MDPD), phosphomevalonate kinase (PMK), isopentenyl diphosphate (IPP) isomerase, HMG-CoA reductase, and HMG-CoA synthase were suggested to exist in that order. Heterologous expression of these genes in E. coli and Streptomyces lividans, both of which have only the nonmevalonate pathways, suggested that the genes for the mevalonate pathway were included in the cloned DNA fragment. The GGDPS, MK, MDPD, PMK, IPP isomerase, and HMG-CoA synthase were expressed in E. coli. Among them, the recombinant GGDPS, MK, and IPP isomerase were confirmed to have the expected activities. This is the first report, to the best of our knowledge, about eubacterial MK with direct evidence.
Protein thermostability above 100°C: A key role for ionic interactions (1998)

The discovery of hyperthermophilic microorganisms and the analysis of hyperthermostable enzymes has established the fact that multisubunit enzymes can survive for prolonged periods at temperatures above 100 degreesC. We have carried out homology-based modeling and direct structure comparison on the hexameric glutamate dehydrogenases from the hyperthermophiles Pyrococcus furiosus and Thermococcus litoralis whose optimal growth temperatures are 100 degreesC and 88 degreesC, respectively, to determine key stabilizing features. These enzymes, which are 87% homologous, differ 16-fold in thermal stability at 104 degreesC. We observed that an intersubunit ion-pair network was substantially reduced in the less stable enzyme from T. litoralis, and two residues were then altered to restore these interactions. The single mutations both had adverse effects on the thermostability of the protein. However, with both mutations in place, we observed a fourfold improvement of stability at 104 degreesC over the wild-type enzyme. The catalytic properties of the enzymes were unaffected by the mutations. These results suggest that extensive ion-pair networks may provide a general strategy for manipulating enzyme thermostability of multisubunit enzymes. However, this study emphasizes the importance of the exact local environment of a residue in determining its effects on stability.
Atom Transfer Radical Polymerization and the Synthesis of Polymeric Materials (1998)

The development of new controlled radical polymerization methods has progressed rapidly over the last five years. One of the most useful of these methods, atom transfer radical polymerization (ATRP), a powerful technique for the design and synthesis of new polymeric materials with novel structures, is reviewed. The Figure represents a hyperbranched polymer resulting from ATRP of p-chloromethylstyrene.
EFFECT OF REDUCING SPERM NUMBERS PER INSEMINATION DOSE ON FERTILITY OF CRYOPRESERVED BUFFALO BULL SEMEN (2006)

The objective of this study was to evaluate the effect of reducing sperm numbers per insemination dose on fertility of cryopreserved buffalo bull semen. For this purpose, semen was collected at weekly intervals from a Nili-Ravi buffalo bull (Bubalus bubalis) using an artificial vagina in two batches. The ejaculates were split-sampled and diluted at 37°C with tris-citric acid extender having 15x10 6 or 30x10 6 motile spermatozoa/0.5 ml. After dilution, the semen was cooled to 4°C, equilibrated for 4 hours, packaged in 0.5 ml straws and frozen in programmable cell freezer. Fertility test based on 75-days first service pregnancy rate was determined under field conditions. A total of 500 buffaloes were inseminated with frozen semen and out of these 431 could be followed, 209 for semen straws packaged with 15x10 6 spermatozoa/straw and 222 for doses filled with 30x10 6 spermatozoa/straw. The inseminations were performed in two batches and each batch was spread over a period of three months. The fertility rate for sperm concentration of 15x10 6 spermatozoa/0.5 ml vs. 30x10 6 spermatozoa/0.5 ml (49.28 vs. 56.75%) was similar (P>0.05). The fertility rates were also similar (P>0.05) in the first and second batch of inseminations performed with 15x10 6 or 30x10 6 spermatozoa/0.5 ml straw of cryopreserved semen. In conclusion, reduction of sperm number from 30x10 6 to 15x10 6 spermatozoa/0.5 ml dose of insemination did not affect fertility of cryopreserved buffalo bull semen.
Five new TTF1/NKX2.1 mutations in brain-lung-thyroid syndrome: rescue by PAX8 synergism in one case (2009)

Thyroid transcription factor 1 (NKX2-1/TITF1) mutations cause brain-lung-thyroid syndrome, characterized by congenital hypothyroidism (CH), infant respiratory distress syndrome (IRDS) and benign hereditary chorea (BHC). The objectives of the present study were (i) detection of NKX2-1 mutations in patients with CH associated with pneumopathy and/or BHC, (ii) functional analysis of new mutations in vitro and (iii) description of the phenotypic spectrum of brain-lung-thyroid syndrome. We identified three new heterozygous missense mutations (L176V, P202L, Q210P), a splice site mutation (376-2A-->G), and one deletion of NKX2-1 at 14q13. Functional analysis of the three missense mutations revealed loss of transactivation capacity on the human thyroglobulin enhancer/promoter. Interestingly, we showed that deficient transcriptional activity of NKX2-1-P202L was completely rescued by cotransfected PAX8-WT, whereas the synergistic effect was abolished by L176V and Q210P. The clinical spectrum of 6 own and 40 published patients with NKX2-1 mutations ranged from the complete triad of brain-lung-thyroid syndrome (50%), brain and thyroid disease (30%), to isolated BHC (13%). Thyroid morphology was normal (55%) and compensated hypothyroidism occurred in 61%. Lung disease occurred in 54% of patients (IRDS at term 76%; recurrent pulmonary infections 24%). On follow-up, 20% developed severe chronic interstitial lung disease, and 16% died. In conclusion, we describe five new NKX2.1 mutations with, for the first time, complete rescue by PAX8 of the deficient transactivating capacity in one case. Additionally, our review shows that the majority of affected patients display neurological and/or thyroidal problems and that, although less frequent, lung disease is responsible for a considerable mortality.
Recombinant human J-chain: Fix the protein aggregations and yield maximize (2006)

Polymeric immunoglobulin (dimeric IgA and pentameric IgM) molecules can assembly by using the immunoglobulin J (joining) chain and across the epithelial cell layers. Based on its amino acid and gene sequences data, disulfide bond (2 bonds) assignment secondary structure predictions, and chemical properties, a model for J-chain folding has been proposed. However, the crystal structure of the J-chain protein is still far from obtained, because the J-chain expression and its protein downstream has a permanent aggregation problems, due to its two free thiol groups. Our work focused on the chemical blocking of free cysteines-SH or to mutate these cysteines into serine residues. The chemical blocking yielded partially soluble proteins with new structures (carboxyamidomethyl cysteine and carboxyamidomethyl methionine) at cysteine and methionine residues. While mutate the cysteines into serine has been yielded a complete soluble (11.5 mg/l) J-chain protein which migrate (SDS-PAGE) at 27 KDa. We were used pET22b expression vector and E. coli BL21 (DE3) to produce the J-chain protein. For maximization the production yield of j-chain foreign protein, the batch culture was developed. We described the scaling-up production in term of kinetic behavior to the recombinant E.coli and optimization of cultivation parameters in 3-L bench-top bioreactor. The process was automated through a computer aided data bioprocessing system AFS-BioCommand multi-process management program to regulate the cell growth rate, temperature, pH and agitation speed based on dissolved oxygen. The results showed an obvious increasing in biomass by 5.98 g/L after about 27 h [corrected]