gebhart/patrepeval huggingface dataset:
Features of the adeno-associated virus origin involved in substrate recognition by the viral Rep protein (1993)

We previously demonstrated that the adeno-associated virus (AAV) Rep68 and Rep78 proteins are able to nick the AAV origin of DNA replication at the terminal resolution site (trs) in an ATP-dependent manner. Using four types of modified or mutant substrates, we now have investigated the substrate requirements of Rep68 in the trs endonuclease reaction. In the first kind of substrate, portions of the hairpinned AAV terminal repeat were deleted. Only deletions that retained virtually all of the small internal palindromes of the AAV terminal repeat were active in the endonuclease reaction. This result confirmed previous genetic and biochemical evidence that the secondary structure of the terminal repeat was an important feature for substrate recognition. In the second type of substrate, the trs was moved eight bases further away from the end of the genome. The mutant was nicked at a 50-fold-lower frequency relative to a wild-type origin, and the nick occurred at the correct trs sequence despite its new position. This finding indicated that the endonuclease reaction required a specific sequence at the trs in addition to the correct secondary structure. It also suggested that the minimum trs recognition sequence extended three bases from the cut site in the 3' direction. The third type of substrate harbored mismatched base pairs at the trs. The mismatch substrates contained a wild-type sequence on the strand normally cut but an incorrect sequence on the complementary strand. All of the mismatch mutants were capable of being nicked in the presence of ATP. However, there was substantial variation in the level of activity, suggesting that the sequence on the opposite strand may also be recognized during nicking. Analysis of the mismatch mutants also suggested that a single-stranded trs was a viable substrate for the enzyme. This interpretation was confirmed by analysis of the fourth type of substrate tested, which contained a single-stranded trs. This substrate was also cleaved efficiently by the enzyme provided that the correct strand was present in the substrate. In addition, the single-stranded substrate no longer required ATP as a cofactor for nicking. Finally, all of the substrates with mutant trss bound the Rep protein as efficiently as the wild-type did. This finding indicated that the sequence at the cut site was not involved in recognition of the terminal repeat for specific binding by the enzyme. We concluded that substrate recognition by the AAV Rep protein involves at least two and possibly as many as four features of the AAV terminal repeat.(ABSTRACT TRUNCATED AT 400 WORDS)
Conductive Inks with a “Built-In” Mechanism That Enables Sintering at Room Temperature (2011)

At present there is no metallic ink that enables formation of conductive patterns at room temperature by a single printing step. Printing conductive features by metallic nanoparticle-based inks must be followed by sintering while heating to elevated temperatures, thus preventing their utilization on most plastic substrates used in plastic electronics. In this report we present a new silver nanoparticle-based conductive ink, having a built-in sintering mechanism, which is triggered during drying of the printed pattern. The nanoparticles that are stabilized by a polymer undergo self-sintering spontaneously, due to the presence of a destabilizing agent, which comes into action only during drying of the printed pattern. The destabilizing agent, which contains Cl(-) ions, causes detachment of the anchoring groups of the stabilizer from the nanoparticles' surface and thus enables their coalescence and sintering. It was found that the new metallic ink leads to very high conductivities, by a single printing step: up to 41% of the conductivity of bulk silver was achieved, the highest reported conductivity of a printed pattern that is obtained from nanoparticles at room temperature.
Inhibition of terminal complement: a novel therapeutic approach for the treatment of systemic lupus erythematosus (2004)

The importance of the complement system in the pathophysiology of systemic lupus erythematosus (SLE) is clear although individual complement components play very different roles in the disease process. Early complement proteins are critical in the clearance of immune complexes and apoptotic bodies, and their absence predisposes individuals to SLE. Conversely, activation of terminal complement is associated with exacerbations of disease and damage to tissues and organs, particularly in lupus nephritis. Monoclonal antibodies that specifically inhibit terminal complement activation while preserving the critical functions of the early complement cascade have now been developed. These antibodies target the C5 complement protein, blocking its cleavage and the subsequent generation of potent proinflammatory molecules. Anti-C5 therapeutics have recently been investigated in an animal model of SLE and in a Phase I single dose study in humans. The results of these studies and the multiple roles of complement in SLE are discussed.
RNA-primed initiation of Moloney murine leukemia virus plus strands by reverse transcriptase in vitro (1984)

A 190-base-pair DNA-RNA hybrid containing the Moloney murine leukemia virus origin of plus-strand DNA synthesis was constructed and used as a source of template-primer for the reverse transcriptase in vitro. Synthesis was shown to initiate precisely at the known plus-strand origin. The observation that some of the origin fragments retained ribonucleotide residues on their 5' ends suggests that the primer for chain initiation is an RNA molecule left behind by RNase H during the degradation of the RNA moiety of the DNA-RNA hybrid. If the RNase H is responsible for creating the correct primer terminus, then it must possess a specific endonucleolytic activity capable of recognizing the sequence in the RNA where plus strands are initiated. The 16-base RNase A-resistant fragment which spans the plus-strand origin can also serve as a source of the specific plus-strand primer RNA. Evidence is presented that some of the plus-strand origin fragments synthesized in the endogenous reaction contain 5' ribonucleotides, suggesting that specific RNA primers for plus-strand initiation may be generated during reverse transcription in vivo as well.
Plasma membrane localization and function of the estrogen receptor α variant (ER46) in human endothelial cells (2003)

Estrogen receptor (ER) alpha variants have been identified in an array of nonendothelial cells. We previously demonstrated that estrogen rapidly induces nitric oxide release via a phosphatidylinositol 3-kinase/Akt/endothelial nitric-oxide synthase (eNOS) pathway in EA.hy926 cells (immortalized human endothelial cells), which express a 46-kDa ER. We now confirm that, due to alternative splicing, the 46-kDa endothelial cell protein (ER46) is an amino-terminal truncated product of full-length ER alpha (ER66). ER46 is expressed in the plasma membrane, cytosol, and nucleus of resting, estrogen-deprived cells. Flow cytometric and immunofluorescence microscopic analyses demonstrated that the ER46 C but not N terminus is Ab-accessible in the plasma membrane. Inhibition of palmitoylation with tunicamycin and [(3)H]palmitic acid labeling demonstrated an estrogen-induced, palmitoylation-dependent plasma membrane ER46 recruitment, with reorganization into caveolae. In reconstituted, estrogen-stimulated COS-7 (ER-null) cells, membrane ER46 more efficiently triggered membrane eNOS phosphorylation than ER66. Conversely, ER66 more efficiently mediated estrogen response element reporter-gene transactivation than ER46. These results demonstrate that ER46 is localized and further dynamically targeted to the plasma membrane in a palmitoylation-dependent manner. ER46 more efficiently modulates membrane-initiated estrogen actions, including eNOS activation, than full-length ER66. These findings may have important implications in vascular-specific targeting of estrogen receptor agonists.
Therapeutic Potential of Hericium erinaceus for Depressive Disorder (2019)

Depression is a common and severe neuropsychiatric disorder that is one of the leading causes of global disease burden. Although various anti-depressants are currently available, their efficacies are barely adequate and many have side effects. <i>Hericium erinaceus,</i> also known as Lion's mane mushroom, has been shown to have various health benefits, including antioxidative, antidiabetic, anticancer, anti-inflammatory, antimicrobial, antihyperglycemic, and hypolipidemic effects. It has been used to treat cognitive impairment, Parkinson's disease, and Alzheimer's disease. Bioactive compounds extracted from the mycelia and fruiting bodies of <i>H. erinaceus</i> have been found to promote the expression of neurotrophic factors that are associated with cell proliferation such as nerve growth factors. Although antidepressant effects of <i>H. erinaceus</i> have not been validated and compared to the conventional antidepressants, based on the neurotrophic and neurogenic pathophysiology of depression, <i>H. erinaceus</i> may be a potential alternative medicine for the treatment of depression. This article critically reviews the current literature on the potential benefits of <i>H. erinaceus</i> as a treatment for depressive disorder as well as its mechanisms underlying the antidepressant-like activities.
Oncogenic Alterations in Papillary Thyroid Cancers of Young Patients (2011)

PTCs in young patients display a low prevalence of the already identified oncogenic alterations. The increasing prevalence with age is mainly due to V600E BRAF mutation. There is no relation between tumor aggressiveness and BRAF mutation. There is a relation between the presence of RET/PTC (1 and 3) and the histological and clinical short-term aggressiveness of PTC in the population of young adults. Such a relation is not found in children and adolescents.
Multiple Primary Cancers (2017)

As prognosis following a cancer diagnosis has improved and survival has increased, so has the occurrence of multiple primary cancers diagnosed in the same individual. In the United States, one in five cancer diagnoses involves an individual with a previous history of cancer. These new primary cancer diagnoses, or “subsequent neoplasms” (SN), are a substantial cause of morbidity and mortality in cancer survivors. The risk of developing SN varies substantially depending on age, the type of initial primary cancer, chemotherapy, radiotherapy, genetic susceptibility, and exposure to other cancer risk factors. Childhood cancer survivors have particularly elevated SN risks associated with radiotherapy and, to a lesser extent, systemic therapy. Genetic susceptibility to cancer is also thought to play an important role in SN development after childhood cancer. Survivors of many adulthood cancers also have elevated SN risks, likely with a multifactorial etiology.
Stretchable Supercapacitors Based on Buckled Single‐Walled Carbon‐Nanotube Macrofilms (2009)

A reversibly stretchable supercapacitor using buckled single-walled carbon-nanotube (SWNT) macrofilms as the electrodes is demonstrated. A controllable wavy geometry and an extremely high stretchability (up to 30%) is achieved utilizing poly(dimethylsiloxane) (PDMS) as an elastomeric substrate (see image). The stretchable supercapacitors exhibit very stable capacitance under cyclic stretching and releasing, with capacitance values comparable to that of a supercapacitor assembled with pristine SWNT films.
Generation of Intramolecular and Intermolecular Sulfenamides, Sulfinamides, and Sulfonamides by Hypochlorous Acid:  A Potential Pathway for Oxidative Cross-Linking of Low-Density Lipoprotein by Myeloperoxidase (2001)

Oxidized low-density lipoprotein (LDL) is implicated in atherogenesis, and human atherosclerotic lesions contain LDL oxidized by myeloperoxidase, a heme protein secreted by activated phagocytes. Using hydrogen peroxide (H(2)O(2)), myeloperoxidase generates hypochlorous acid (HOCl), a powerful oxidant. We now demonstrate that HOCl produces sulfenamides, sulfinamides, and sulfonamides in model peptides, which suggests a potential mechanism for LDL oxidation and cross-linking. When we exposed the synthetic peptide PFKCG to HOCl, the peptide's thiol residue reacted rapidly, generating a near-quantitative yield of products. Tandem mass spectrometric analysis identified the products as the sulfenamide, sulfinamide, and sulfonamide, all formed by intramolecular cross-linking of the peptide's thiol and lysine residues. An intramolecular sulfinamide was also observed after the peptide PFRCG was exposed to HOCl, indicating that the guanidine group of arginine can also form a sulfur-nitrogen cross-link. The synthetic peptide PFVCG, which contains a free thiol residue but lacks nucleophilic amino acid side chains, formed an intermolecular sulfonamide when exposed to HOCl. Tandem mass spectrometric analysis of the dimer revealed that the free N-terminal amino group of one PFVCG molecule cross-linked with the thiol residue of another. This peptide also formed intermolecular sulfonamide cross-links with N(alpha)-acetyllysine after exposure to HOCl, demonstrating that the epsilon-amino group of a lysine residue can undergo a similar reaction. Moreover, human neutrophils used the myeloperoxidase-H(2)O(2) system to generate sulfinamides in model peptides containing lysine or arginine residues. Collectively, our observations raise the possibility that HOCl generated by myeloperoxidase contributes to intramolecular and intermolecular protein cross-linking in the artery wall. Myeloperoxidase might also use this mechanism to form sulfur-nitrogen cross-links in other inflammatory conditions.
A new murine monoclonal antibody reports an activation-dependent change in the conformation and/or microenvironment of the platelet glycoprotein IIb/IIIa complex. (1985)

Considerable evidence indicates that the glycoprotein (GP) IIb/IIIa complex on human platelets functions as a receptor for fibrinogen, but little is known about the mechanism of receptor "exposure." To investigate this mechanism, our previously described murine monoclonal antibody (10E5) and a new monoclonal antibody (7E3), both of which block the binding of fibrinogen to platelets and bind to GPIIb and/or GPIIIa, were radiolabeled and their rates of binding to native and ADP-activated platelets were studied. At low concentrations, 125I-10E5 bound nearly equally rapidly to both native and activated platelets, whereas 125I-7E3 bound slowly to native platelets and much more rapidly to activated platelets. This increased rate of 7E3 binding is unlikely to be due to an increase in the number of GPIIb/IIIa sites on the surface of activated platelets because: (a) the rate of 10E5 binding was unchanged; (b) the total number of surface GPIIb/IIIa sites increased by only 2-10% with activation as judged by equilibrium binding of near-saturating concentrations of 10E5 and 7E3, and (c) there was less than 1% release of platelet factor 4 with activation, indicating minimal fusion of alpha-granule membranes (a potential source of GPIIb/IIIa) with the plasma membrane. Other activators (epinephrine, thrombin, and ionophore A 23187) also increased the rate of 7E3 binding, as did digestion of platelets with chymotrypsin. Aspirin did not affect the rate of binding of 7E3, whereas apyrase, prostaglandin E1, and dibucaine all inhibited the enhancement of the 7E3-binding rate produced by ADP. These data provide evidence for an activation-dependent change in the conformation and/or microenvironment of the GPIIb/IIIa complex, and offer a method of studying the receptor exposure mechanism that does not rely on the binding of fibrinogen itself.
Adjustable Locks and Flexible Keys: Plasticity of Epitope–Paratope Interactions in Germline Antibodies (2014)

Ag recognition by independent primary Abs against a small flexible Ag with overlapping epitopes was analyzed to address the determinants of Ag specificity during the initial encounter. Crystal structures of two distinct dodecapeptide Ags, GDPRPSYISHLL and PPYPAWHAPGNI, in complex with the germline mAb 36-65 were determined and compared with the structures of the same Ags bound to another independent germline mAb, BBE6.12H3. For each peptide Ag, the two germline mAbs recognized overlapping epitopes, but in different topologies. The peptide structures differed, and the two paratopes attained discrete conformations, leading to different surface topologies, in a mode that can be described as adjustable locks and flexible keys. This is in contrast to mature mAbs, in which conformational convergence of different paratopes while binding to a common epitope in a similar conformation has been reported. These results suggest that the primary immune receptor repertoire is highly versatile as compared with its mature counterpart. Germline and mature mAbs adopt distinct mechanisms for recognizing a flexible epitope. Whereas conservation of conformational repertoire is a key characteristic of mature mAbs achieved through affinity maturation, the germline mAbs, at the initial stages of Ag encounter, maintain substantial plasticity, accommodating a broad specificity repertoire.
Review and Reflection on the Translation History of Traditional Chinese Medicine (2006)

The brief translation history of traditional Chinese medicine(TCM),as well as the achievements,is reviewed in the paper in four different stages: the beginning,the early time,the difficult developing time,and the gradual mature time.The paper mainly focuses on the achievements in dictionaries,collected books,textbooks,and the formation of translation theory in the translation field of TCM in the latest 30 years since China's open-door policy.
[Asymmetric somatic hybridization between mixed wheat and Psathyrostachys juncea]. (2004)

Psathyrostachys juncea is a potential source of useful genes, such as the barley yellow dwarf virus resistance, salt tolerance and drought tolerance, for wheat improvement. Conventional sexual hybridization between wheat and Psathyrostachys juncea is very difficult to occur as the two are sexual incompatible. Somatic hybridization is a promising technique for creating hybrids across the sexual border. Here we report a fusion system for somatic hybridization of wheat using PEG method. Mixed protoplasts of two wheat (Triticum aestivum L. cv. Jinan 177) culture cells (cha9 and 176) were used as the recipients to fuse with the donors, the protoplasts of Psathyrostachys juncea (Fisch.) Nevski irradiated with ultraviolet light (UV) at an intensity of 380 microW/cm2 for 1 min or 2 min. Sixteen clones were generated in the combination I, (wheat 176 + wheat cha9 + P. juncea 1 min UV treatment) and five of the hybrid clones could differentiate to green plants. All the regenerated clones were confirmed as somatic hybrids by cytological, isozyme, chromosome and random amplified polymorphic DNA (RAPD) analysis. Chloroplast genome of the hybrids was analyzed using 7 pairs of wheat-specific chloroplast microsatellite (SSR) primers. Three clones were obtained from the combination II (wheat 176 + wheat cha9 + P. juncea 2 min UV treatment), and all browned slowly and died in 3 months. This result indicated that the mixed wheat cells was helpful to the formation and regeneration of hybrid callus and the dosage of the UV had significant effect on the development of the fusion products.
Possible modes of action of nimesulide in controlling neutrophilic inflammation. (1995)

Even in recent years the development of new non-steroidal anti-inflammatory drugs (NSAIDs) appears to be essentially driven by the archaic idea to protect humans from pain and other symptoms of inflammation. Very few attempts have been made to understand if any of these drugs can limit the tissue injury during one or several forms of inflammatory reaction. In studying the events underlying the development of the tissue injury during neutrophilic inflammation, it was found that at least a NSAID, i.e. nimesulide (CAS 51803-78-2), has high potential to interfere efficiently with the major pathway responsible for neutrophil-dependent histotoxicity. Other chemically related drugs, not classified as NSAIDs but used in disease conditions characterized by neutrophilic inflammation, i.e. dapsone and sulfapyridine, have similar activities. Therefore, it is suggested that derivates from sulfanilamide (nimesulide, dapsone and sulfapyridine) are the major candidates for developing rational therapeutic anti-inflammatory strategies for controlling the development of tissue injury during neutrophilic inflammation. Also, these molecules might serve to drive the synthesis of new histoprotective antiinflammatory drugs.
Monoaminergic anorectic agents (2001)

Catecholamine, dopamine, serotonine (5HT) and neuronal histamine are anorectic monoamines and act as anorectic neurotransmitters. The anorectic agents as modulators of these monoamines inhibit appetite by activating release together with suppressing reuptake of those monoamines. The anorectic agents were classified in clinical use into either alpha 1, beta-adrenergic receptor agonists or 5HT-receptor agonist. Dexfenfluramine, a 5HT-receptor agonist, was inhibited in clinical use because of its cardiac complications including pulmonary hypertension and valvelar disease. Mazindol is an adrenergic agonist and the solitary anti-obesity drug used clinically in Japan. Sibutramine shows the effects of both beta-adrenergic and serotonergic receptor agonists. Sibutramine induces not only appetite suppression but also acceleration of peripheral energy expenditure. No histaminergic anorectics have been employed in the clinical situation to date. L-Histizine, precursor amino acid of endogenous neuronal histamine, is useful for suppression of food intake, lipolytic acceleration of peripheral adipose tissues and enhanced energy expenditure in both animals and humans. L-Histizine thus inspires development of more effective and safer anorectics that can be used without suffering from the rebound phenomenon of body weight.
Conserved Sequences in a Tissue-Specific Regulatory Region of the pdx-1 Gene Mediate Transcription in Pancreatic β Cells: Role for Hepatocyte Nuclear Factor 3β and Pax6 (2002)

Pancreas duodenum homeobox 1 (PDX-1) is absolutely required for pancreas development and the maintenance of islet beta-cell function. Temporal and cell-type-specific transcription of the pdx-1 gene is controlled by factors acting upon sequences found within its 5'-flanking region. Critical cis-acting transcriptional control elements are located within a nuclease hypersensitive site that contains three conserved subdomains, termed areas I, II, and III. We show that area II acts as a tissue-specific regulatory region of the pdx-1 gene, directing transgene expression to a subpopulation of islet cells. Mutation of the area II hepatocyte nuclear factor 3 (HNF3) binding element in the larger area I- and area II- containing PstBst fragment also decreases PB(hsplacZ) transgene penetrance. These two results indicate possible ontogenetic and/or functional heterogeneity of the beta-cell population. Several other potential positive- and negative-acting control elements were identified in area II after mutation of the highly conserved sequence blocks within this subdomain. Pax6, a factor essential for islet alpha-cell development and islet hormone gene expression, was shown to bind in area II in vitro. Pax6 and HNF3 beta were also found to bind to this region in vivo by using the chromatin immunoprecipitation assay. Collectively, these data suggest an important role for both HNF3 beta and Pax6 in regulating pdx-1 expression in beta cells.