gebhart/patrepeval huggingface dataset:
Theoretical study of interaction of winter flounder antifreeze protein with ice (2004)

Antifreeze proteins (AFPs) are synthesized by various organisms to enable their cells to survive subzero environment. These proteins bind to small ice crystals and inhibit their growth, which if left uncontrolled would be fatal to cells. The crystal structures of a number of AFPs have been determined; however, crystallographic analysis of AFP-ice complex is nearly impossible. Molecular modeling studies of AFPs' interaction with ice surface is therefore invaluable. Early models of AFP-ice interaction suggested H-bond as the primary driving force behind such interaction. Recent experimental evidence, however, suggested that hydrophobic interactions could be the main contributor to AFP-ice association. All computational studies published to date were carried out to verify the H-bond model, and no works attempting to verify the hydrophobic interaction model have been published. In this work, we Monte Carlo-minimized complexes of several AFPs with ice taking into account nonbonded interactions, H-bonds, and the hydration potential for proteins. Parameters of the hydration potential for ice were developed with the assumption that the free energy of the water-ice association should be close to zero at equilibrium melting temperature. Our calculations demonstrate that desolvation of hydrophobic groups in the AFPs upon their binding to the grooves at the ice surface is indeed the major stabilizing contributor to the free energy of AFP-ice binding. This study is consistent with available structural and mutation data on AFPs. In particular, it explains the paradoxical finding that substitution of Thr residues with Val does not affect the potency of winter flounder AFP whereas substitution with Ser abolished its antifreeze activity.
Efficacy of pharmacological treatments of neuropathic pain: an update and effect related to mechanism of drug action (1999)

Tricyclic antidepressants and carbamazepine have become the mainstay in the treatment of neuropathic pain. Within the last decade, controlled trials have shown that numerous other drugs relieve such pain. We identified all placebo-controlled trials and calculated numbers needed to treat (NNT) to obtain one patient with more than 50% pain relief in order to compare the efficacy with the current treatments, and to search for relations between mechanism of pain and drug action. In diabetic neuropathy, NNT was 1.4 in a study with optimal doses of the tricyclic antidepressant imipramine as compared to 2.4 in other studies on tricyclics. The NNT was 6.7 for selective serotonin reuptake inhibitors, 3.3 for carbamazepine, 10.0 for mexiletine, 3.7 for gabapentin, 1.9 for dextromethorphan, 3.4 for tramadol and levodopa and 5.9 for capsaicin. In postherpetic neuralgia, the NNT was 2.3 for tricyclics, 3.2 for gabapentin, 2.5 for oxycodone and 5.3 for capsaicin, whereas dextromethorphan was inactive. In peripheral nerve injury, NNT was 2.5 for tricyclics and 3.5 for capsaicin. In central pain, NNT was 2.5 for tricyclics and 3. 4 for carbamazepine, whereas selective serotonin reuptake inhibitors, mexiletine and dextromethorphan were inactive. There were no clear relations between mechanism of action of the drugs and the effect in distinct pain conditions or for single drug classes and different pain conditions. It is concluded that tricyclic antidepressants in optimal doses appear to be the most efficient treatment of neuropathic pain, but some of the other treatments may be important due to their better tolerability. Relations between drug and pain mechanisms may be elucidated by studies focusing on specific neuropathic pain phenomena such as pain paroxysms and touch-evoked pain.
An Improvement to an Algorithm for Computing Aircraft Reference Altitude (1972)

A recently developed algorithm which is being used to compute an aircraft reference altitude from air data inputs is accurate in a stationary column of air. However, pressure gradients in the atmosphere can introduce significant errors. An improvement (which corrects for pressure gradient errors) has been developed which is based on the equilibrium equation for the motion of the air mass in the presence of pressure gradients.
Systemic corticosteroid therapy---side effects and their management (1998)

The anti-inflammatory effects of corticosteroids cannot be separated from their metabolic effects as all cells use the same glucocorticoid receptor; therefore when corticosteroids are prescribed measures should be taken to minimise their side effects. Clearly, the chance of significant side effects increases with the dose and duration of treatment and so the minimum dose necessary to control the disease should be given. Before embarking on a long term course of corticosteroids the factors summarised in Table 1 should be considered. A full discussion with the patient is necessary in order to explain the benefits and risks of corticosteroid treatment. A patient information leaflet is now provided by the manufacturers of all systemic corticosteroid preparations. As emphasised by the recent publication by the Committee on the Safety of Medicines, advice to patients is the key to the safe use of long term systemic corticosteroids and it recommends discussing the following points with the patient: not to stop taking corticosteroids suddenly to see a doctor if they become unwell of the increased susceptibility to infections, especially chickenpox of the serious side effects that may occur to read and keep the patient information leaflet to always carry the steroid treatment card and to show it to any health professional involved in their treatment. In addition the following suggestions may help to minimise some side effects: a single morning dose early dietary modification--low calorie, low sodium, and high potassium awareness of possible errors of judgment on high doses. Once started on corticosteroids the patient should be regularly reviewed to assess the response to the treatment with adjustments to keep the dose at a minimum.
Preparation of Trojan Horse Liposomes (THLs) for Gene Transfer across the Blood-Brain Barrier (2010)

Nonviral plasmid DNA is delivered to the brain via a transvascular route across the blood-brain barrier (BBB) following intravenous administration of DNA encapsulated within Trojan horse liposomes (THLs), also called PEGylated immunoliposomes (PILs). The liposome surface is covered with several thousand strands of polymer (e.g., polyethylene glycol [PEG]), and the tips of 1%-2% of the polymer strands are conjugated with a targeting monoclonal antibody that acts as a molecular Trojan horse (MTH). The MTH binds to a receptor (e.g., for transferrin or insulin) on the BBB and brain cell membrane, triggering receptor-mediated transcytosis of the THL across the BBB in vivo, and receptor-mediated endocytosis into brain cells beyond the BBB. The persistence of transgene expression in the brain is inversely related to the rate of degradation of the episomal plasmid DNA. THL technology enables an exogenous gene to be widely expressed in the majority of cells in adult brain (or other organs) within 1 d of a single intravenous administration. Applications of the THLs include tissue-specific gene expression with tissue-specific promoters, complete normalization of striatal tyrosine hydroxylase in experimental Parkinson's disease following intravenous tyrosine hydroxylase gene therapy, a 100% increase in survival time of mice with brain tumors following weekly intravenous antisense gene therapy using THLs, and a 90% increase in survival time with weekly intravenous RNA interference (RNAi) gene therapy in mice with intracranial brain tumors. This protocol describes the preparation of THLs for use in gene transfer in vitro or in vivo.
Methanococcus jannaschii Flap Endonuclease: Expression, Purification, and Substrate Requirements (1998)

The flap endonuclease (FEN) of the hyperthermophilic archaeon Methanococcus jannaschii was expressed in Escherichia coli and purified to homogeneity. FEN retained activity after preincubation at 95 degrees C+ for 15 min. A pseudo-Y-shaped substrate was formed by hybridization of two partially complementary oligonucleotides. FEN cleaved the strand with the free 5' end adjacent to the single-strand-duplex junction. Deletion of the free 3' end prevented cleavage. Hybridization of a complementary oligonucleotide to the free 3' end moved the cleavage site by 1 to 2 nucleotides. Hybridization of excess complementary oligonucleotide to the free 5' end failed to block cleavage, although this substrate was refractory to cleavage by the 5'-3' exonuclease activity of Taq DNA polymerase. For verification, the free 5' end was replaced by an internally labeled hairpin structure. This structure was a substrate for FEN but became a substrate for Taq DNA polymerase only after exonucleolytic cleavage had destabilized the hairpin. A circular duplex substrate with a 5' single-stranded branch was formed by primer extension of a partially complementary oligonucleotide on virion phiX174. This denaturation-resistant substrate was used to examine the effects of temperature and solution properties, such as pH, salt, and divalent ion concentration on the turnover number of the enzyme.
Isolation and characterization of the human gene for ADP-ribosylation factor 3, a 20-kDa guanine nucleotide-binding protein activator of cholera toxin. (1991)

ADP-ribosylation factors (ARFs) are approximately 20-kDa guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin in vitro. Five different human ARFs have been identified by cDNA cloning. Northern analysis using ARF 3-specific oligonucleotides identified two mRNAs of 3.7 and 1.2 kilobases (kb). We report here the complete nucleotide sequence of the 3.7-kb ARF 3 mRNA derived from three overlapping cDNAs isolated from human hippocampus and fetal brain cDNA libraries, as well as the structure of human ARF 3 gene. Sequences of two overlapping genomic clones indicated that the ARF 3 gene spans approximately 18.3 kb and contains five exons and four introns. The conserved amino acid sequences involved in guanine nucleotide binding by ARF 3 are distributed among separate exons, as found in other GTP-binding protein genes. Translation initiates in exon 2 which includes the sequence GXXXXGK that probably participates in phosphate binding and GTP hydrolysis. The sequence DVGG in exon 3 coordinates binding of Mg2+ and the beta-phosphate of GDP. In the ARF 3 gene in contrast to those of other GTP-binding proteins, the sequence NKXD (which is thought to contribute to the specificity of interaction with the guanine ring) is divided between exons 4 and 5. The latter encodes the COOH-terminal 53 amino acids of ARF 3 and contains greater than 2500 base pairs of untranslated DNA. The sequence AATTAA is 19 bases 5' to the polyadenylation addition site of the 3.7-kb mRNA. Multiple transcription start sites were identified by primer extension and S1 and mung bean nuclease analyses. The 5'-flanking region of exon 1 contains neither a TATA nor a CAAT box, but is high in GC content (greater than 70%) and includes three potential Sp1-binding sites (GC box), consistent with the promoters described for several housekeeping genes. The 1.2-kb ARF 3 mRNA is shown to arise by use of an alternative polyadenylation signal (AACAAA) at nucleotide 1091 within the ARF 3 cDNA.
High Efficiency Gene Transfer to Human Hematopoietic SCID-Repopulating Cells Under Serum-Free Conditions (1998)

Stable gene transfer to human pluripotent hematopoietic stem cells (PHSCs) is an attractive strategy for the curative treatment of many genetic hematologic disorders. In clinical trials, the levels of gene transfer to this cell population have generally been low, reflecting deficiencies in both the vector systems and transduction conditions. In this study, we have used a pseudotyped murine retroviral vector to transduce human CD34+ cells purified from bone marrow (BM) and umbilical cord blood (CB) under optimized conditions. After transduction, 71% to 97% of the hematopoietic cells were found to express a low-affinity nerve growth factor receptor (LNGFR) marker gene. Six weeks after transplantation into immunodeficient NOD/LtSz-scid/scid (NOD/SCID) mice, LNGFR expression was detected in 6% to 57% of CD45+ cells in eight of nine engrafted animals. Moreover, proviral DNA was detected in 8.3% to 45% of secondary colonies derived from BM cells of engrafted NOD/SCID mice. Our data show consistent transduction of SCID-repopulating cells (SRCs) and suggest that the efficiency of gene transfer to human hematopoietic repopulating cells can be improved using existing retroviral vector systems and carefully optimized transduction conditions. © 1998 by The American Society of Hematology.
Synthesis and Pharmacological Characterization of All Sixteen Stereoisomers of 2-(2‘-Carboxy-3‘-phenylcyclopropyl)glycine. Focus on (2S,1‘S,2‘S,3‘R)-2-(2‘-Carboxy-3‘-phenylcyclopropyl)glycine, a Novel and Selective Group II Metabotropic Glutamate Receptors Antagonist (1996)

All 16 2-(2‘-carboxy-3‘-phenylcyclopropyl)glycine (PCCGs) stereoisomers 32−47 have been prepared from the corresponding racemic aldehydes 12−15 following an enantiodivergent synthetic protocol. Compounds 32−47 were evaluated by a number of binding and functional experiments as potential ligands for several classes of excitatory amino acid receptors, including metabotropic glutamate receptors (mGluR1a, mGluR2, mGluR4) and ionotropic glutamate receptors (NMDA, KA, AMPA) as well as sodium-dependent and calcium/chloride-dependent glutamate transport systems. The stereolibrary of compounds 32−47 appears to be endowed with a peculiar pharmacological profile. PCCG-2 (33) and PCCG-3 (34) displaced labeled kainate at low micromolar concentration; PCCG-9 (40) and PCCG-11 (42) weakly interacted with the NMDA site; PCCG-5 (36), PCCG-10 (41), and PCCG-12 (43) showed to be potent inhibitors of Ca2+/Cl--dependent glutamate transport system. Most interestingly, PCCG-4 (35) has been shown to be able to antagonize (IC50 = 8 μM) the effects of glutamate on forskolin-stimulated cAMP formation in BHK cells expressing mGluR2. Uneffective at mGluR1, 35 is a weak mGluR4 agonist (EC50 = 156 μM) and has no effect on either ionotropic receptors or glutamate transport systems, thus demonstrating to be a novel selective mGluR2 antagonist with a 6-fold increase in potency over previously reported antagonists.
Inhibition of Influenza Virus Infection in Human Airway Cell Cultures by an Antisense Peptide-Conjugated Morpholino Oligomer Targeting the Hemagglutinin-Activating Protease TMPRSS2 (2010)

Influenza A viruses constitute a major and ongoing global public health concern. Current antiviral strategies target viral gene products; however, the emergence of drug-resistant viruses highlights the need for novel antiviral approaches. Cleavage of the influenza virus hemagglutinin (HA) by host cell proteases is crucial for viral infectivity and therefore presents a potential drug target. Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMO) are single-stranded-DNA-like antisense agents that readily enter cells and can act as antisense agents by sterically blocking cRNA. Here, we evaluated the effect of PPMO targeted to regions of the pre-mRNA or mRNA of the HA-cleaving protease TMPRSS2 on proteolytic activation and spread of influenza viruses in human Calu-3 airway epithelial cells. We found that treatment of cells with a PPMO (T-ex5) designed to interfere with TMPRSS2 pre-mRNA splicing resulted in TMPRSS2 mRNA lacking exon 5 and consequently the expression of a truncated and enzymatically inactive form of TMPRSS2. Altered splicing of TMPRSS2 mRNA by the T-ex5 PPMO prevented HA cleavage in different human seasonal and pandemic influenza A viruses and suppressed viral titers by 2 to 3 log(10) units, strongly suggesting that TMPRSS2 is responsible for HA cleavage in Calu-3 airway cells. The data indicate that PPMO provide a useful reagent for investigating HA-activating proteases and may represent a promising strategy for the development of novel therapeutics to address influenza infections.
Maltose-Binding Protein as a Solubility Enhancer (2003)

A major impediment to the production of recombinant proteins in Escherichia coli is their tendency to accumulate in the form of insoluble and biologically inactive aggregates known as inclusion bodies. Although it is sometimes possible to convert aggregated material into native, biologically-active protein, this is a time consuming, labor-intensive, costly, and uncertain undertaking (1). Consequently, many tricks have been employed in an effort to circumvent the formation of inclusion bodies (2). One approach that shows considerable promise is to exploit the innate ability of certain proteins to enhance the solubility of their fusion partners. Although it was originally thought that virtually any highly soluble protein could function as a general solubilizing agent, this has not turned out to be the case. In a direct comparison with glutathione S-transferase (GST) and thioredoxin, maltose-binding protein (MBP) was decidedly superior at solubilizing a diverse collection of aggregation-prone passenger proteins (3). Moreover, some of these proteins were able to fold into their biologically active conformations when fused to MBP. It is not entirely clear why MBP is such a spectacular solubilizing agent, but there is some evidence to suggest that it may be able to function as a general molecular chaperone in the context of a fusion protein by temporarily sequestering aggregation-prone folding intermediates of its fusion partners and preventing their self association (3–6).
Human lupus autoantibody–DNA complexes activate DCs through cooperation of CD32 and TLR9 (2005)

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by pathogenic autoantibodies against nucleoproteins and DNA. Here we show that DNA-containing immune complexes (ICs) within lupus serum (SLE-ICs), but not protein-containing ICs from other autoimmune rheumatic diseases, stimulates plasmacytoid DCs (PDCs) to produce cytokines and chemokines via a cooperative interaction between Toll-like receptor 9 (TLR9) and FcgammaRIIa (CD32). SLE-ICs transiently colocalized to a subcellular compartment containing CD32 and TLR9, and CD32+, but not CD32-, PDCs internalized and responded to SLE-ICs. Our findings demonstrate a novel functional interaction between Fc receptors and TLRs, defining a pathway in which CD32 delivers SLE-ICs to intracellular lysosomes containing TLR9, inducing a signaling cascade leading to PDC activation. These data demonstrate that endogenous DNA-containing autoantibody complexes found in the serum of patients with SLE activate the innate immune system and suggest a novel mechanism whereby these ICs contribute to the pathogenesis of this autoimmune disease.
Synthesis of Annelated Azaheterocycles Containing a 5‐Carbamoylpyrazin‐3‐one Fragment by a Modification of the Four‐Component Ugi Reaction (2005)

Abstract A convenient synthesis of novel imidazole‐ and pyrrole‐fused 1‐oxo‐1,2,3,4‐tetrahydropyrazine heterocyclic structures by a novel modification of the four‐component Ugi condensation is described. The usefulness and versatility of the developed approach for the synthesis of variously substituted compounds is demonstrated and the scope and limitations of the chemistry involved are discussed. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Two-neutron capture reactions and therprocess (2006)

Rates for the $^{4}\mathrm{He}$$(2n,\ensuremath{\gamma})$$^{6}\mathrm{He}$ and $^{6}\mathrm{He}$$(\ensuremath{\alpha},n)$$^{9}\mathrm{Be}$ reactions have been calculated, including both resonant and nonresonant contributions. The sequential two-neutron capture process on $^{4}\mathrm{He}$ has also been reevaluated on the basis of new experimental results. It is shown that a one-step dineutron capture reaction may enhance the sequential two-neutron reaction rate by several orders of magnitude. This opens the possibility that reaction flow through $^{4}\mathrm{He}$$({}^{2}n,\ensuremath{\gamma})$$^{6}\mathrm{He}$$(\ensuremath{\alpha},n)$$^{9}\mathrm{Be}$ may occur in competition with the bottle-neck three-body reactions $^{4}\mathrm{He}$(2$\ensuremath{\alpha},\ensuremath{\gamma})$$^{12}\mathrm{C}$ and the $^{4}\mathrm{He}$$(\ensuremath{\alpha}n,\ensuremath{\gamma})$$^{9}\mathrm{Be}$ that initiate the \ensuremath{\alpha} process and provide seed nuclei for the $r$ process. Here we explore the effect of such dineutron capture on $r$-process nucleosynthesis. We show that such reactions have little effect on the final abundance and would change only $r$-process abundances in an extremely neutron-rich low-temperature $r$ process.
Carotid Atherosclerosis and Risk of Subsequent Coronary Event in Outpatients With Atherothrombosis (2013)

Carotid atherosclerosis was an independent predictor of coronary events across all types of symptomatic vascular disease and had an incremental effect on risk regardless of risk factors or location of vessel disease.
Long- and short-term effects of biological hydrogels on capsule microvascular density around implants in rats (2001)

Fibrous capsule formation around implants can inhibit solute exchange between implantable devices and the circulation. Parylene-n coated polycarbonate disks surrounded with growth factor reduced Matrigel (MG) or several gelatin-based matrices were implanted intramuscularly into rats for 21 or 50 days. MG supplemented with vascular endothelial growth factor (VEGF) or basic fibroblast growth factor (bFGF) increased capsule microvascular density at 21 days (p < 0.05) when compared to bare parylene-coated polycarbonate disks (control). The increased microvascular density around VEGF- and bFGF-treated implants regressed by 50 days and was no longer significantly different from controls. The microvascular density induced by the gelatin-based matrices was not significantly different from controls at 21 days, but was increased at 50 days (p < 0.05), suggesting a slower, long-term effect. Disks treated with MG and gelatin-based matrices had thinner capsules at 21 days (p < 0.05). By 50 days, the capsule thicknesses around these implants were no longer statistically thinner than controls. The capsule thickness around implants treated with VEGF, bFGF, and essential gelatin-based matrix was thinner than controls at 50 days (p < 0.05). These results indicate that it is possible to increase functional microvascular density within fibrous capsules using angiogenic growth factors and gelatin-based matrices. However, this effect may be short-lived, requiring chronic administration of growth factors.
Two-pronged Binding with Bromodomain-containing Protein 4 Liberates Positive Transcription Elongation Factor b from Inactive Ribonucleoprotein Complexes (2011)

The positive transcription elongation factor b (P-TEFb) exists in two forms in cells as follows: an inactive form where the core components cyclin T1 and CDK9 are incorporated in the 7SK small nuclear ribonucleoprotein complex containing the inhibitory molecule HEXIM1, and an active form, part of which associates with the bromodomain-containing protein BRD4. Here, we define a novel interaction between P-TEFb and BRD4 involving tri-acetylated cyclin T1 (acK380, acK386, and acK309) and the second bromodomain in BRD4. This interaction is observed with the short splice variant of BRD4 (amino acids 1-722) lacking a previously defined C-terminal P-TEFb-interacting domain (PID). Notably, P-TEFb complexes associated with short BRD4 contain HEXIM1 and 7SK snRNA, implicating the PID in the liberation of P-TEFb from the 7SK small nuclear ribonucleoprotein complex (7SK snPNP). Overexpression of the PID alone in cells dissociates HEXIM1 and 7SK snRNA from P-TEFb, but it is not sufficient to activate P-TEFb-dependent transcription of the HIV LTR. Our data support a model where two BRD4 domains, the second bromodomain and the PID, bind P-TEFb and are required for full transcriptional activation of P-TEFb response genes.