gebhart/patrepeval huggingface dataset:
Red Fluorescent Protein (DsRed) as a Reporter in Saccharomyces cerevisiae (2001)

We describe the utilization of a red fluorescent protein (DsRed) as an in vivo marker for Saccharomyces cerevisiae. Clones expressing red and/or green fluorescent proteins with both cytoplasmic and nuclear localization were obtained. A series of vectors are now available which can be used to create amino-terminal (N-terminal) and carboxyl-terminal (C-terminal) fusions with the DsRed protein.
In vivo genome editing of the albumin locus as a platform for protein replacement therapy (2015)

Site-specific genome editing provides a promising approach for achieving long-term, stable therapeutic gene expression. Genome editing has been successfully applied in a variety of preclinical models, generally focused on targeting the diseased locus itself; however, limited targeting efficiency or insufficient expression from the endogenous promoter may impede the translation of these approaches, particularly if the desired editing event does not confer a selective growth advantage. Here we report a general strategy for liver-directed protein replacement therapies that addresses these issues: zinc finger nuclease (ZFN) -mediated site-specific integration of therapeutic transgenes within the albumin gene. By using adeno-associated viral (AAV) vector delivery in vivo, we achieved long-term expression of human factors VIII and IX (hFVIII and hFIX) in mouse models of hemophilia A and B at therapeutic levels. By using the same targeting reagents in wild-type mice, lysosomal enzymes were expressed that are deficient in Fabry and Gaucher diseases and in Hurler and Hunter syndromes. The establishment of a universal nuclease-based platform for secreted protein production would represent a critical advance in the development of safe, permanent, and functional cures for diverse genetic and nongenetic diseases.
Soluble V Domain of Nectin-1/HveC Enables Entry of Herpes Simplex Virus Type 1 (HSV-1) into HSV-Resistant Cells by Binding to Viral Glycoprotein D (2005)

Interaction of herpes simplex virus (HSV) glycoprotein D (gD) with specific cellular receptors is essential for HSV infection of susceptible cells. Virus mutants that lack gD can bind to the cell surface (attachment) but do not enter, implying that interaction of gD with its receptor(s) initiates the postattachment (entry) phase of HSV infection. In this report, we have studied HSV entry in the presence of the gD-binding variable (V) domain of the common gD receptor nectin-1/HveC to determine whether cell association of the gD receptor is required for HSV infection. In the presence of increasing amounts of the soluble nectin-1 V domain (sNec1(123)), increasing viral entry into HSV-resistant CHO-K1 cells was observed. At a multiplicity of 3 in the presence of optimal amounts of sNec1(123), approximately 90% of the cells were infected. The soluble V domain of nectin-2, a strain-specific HSV entry receptor, promoted entry of the HSV type 1 (HSV-1) Rid-1 mutant strain, but not of wild-type HSV-1. Preincubation and immunofluorescence studies indicated that free or gD-bound sNec1(123) did not associate with the cell surface. sNec1(123)-mediated entry was highly impaired by interference with the cell-binding activities of viral glycoproteins B and C. While gD has at least two functions, virus attachment to the cell and initiation of the virus entry process, our results demonstrate that the attachment function of gD is dispensable for entry provided that other means of attachment are available, such as gB and gC binding to cell surface glycosaminoglycans.
Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections (2008)

Acute HIV infection is characterized by massive loss of CD4 T cells from the gastrointestinal (GI) tract. Th17 cells are critical in the defense against microbes, particularly at mucosal surfaces. Here we analyzed Th17 cells in the blood, GI tract, and broncheoalveolar lavage of HIV-infected and uninfected humans, and SIV-infected and uninfected sooty mangabeys. We found that (1) human Th17 cells are specific for extracellular bacterial and fungal antigens, but not common viral antigens; (2) Th17 cells are infected by HIV in vivo, but not preferentially so; (3) CD4 T cells in blood of HIV-infected patients are skewed away from a Th17 phenotype toward a Th1 phenotype with cellular maturation; (4) there is significant loss of Th17 cells in the GI tract of HIV-infected patients; (5) Th17 cells are not preferentially lost from the broncheoalveolar lavage of HIV-infected patients; and (6) SIV-infected sooty mangabeys maintain healthy frequencies of Th17 cells in the blood and GI tract. These observations further elucidate the immunodeficiency of HIV disease and may provide a mechanistic basis for the mucosal barrier breakdown that characterizes HIV infection. Finally, these data may help account for the nonprogressive nature of nonpathogenic SIV infection in sooty mangabeys.
Enhancement of immune response to naked DNA vaccine by immunization with transfected dendritic cells (1997)

Immunization with plasmid DNA encoding various proteins promises to be a valuable vaccine approach especially if its immunogenicity could be optimized. In this study we show that the intramuscular delivery in dendritic cells (DC) of naked plasmid DNA encoding two proteins of herpes simplex virus (HSV) leads to the induction of significantly enhanced levels of resistance to viral challenge. Whereas DC transfected in vitro with DNA induced enhanced immunity, similarly transfected macrophage (M phi) populations lacked immunogenicity even though plasmid expression occurred in vitro. The enhanced immunity induced by DC-delivered DNA appeared to be associated mainly with an increased Th1 CD4+ T cell response. Our results add evidence that DC are the essential antigen-presenting cell types involved in immune responses to intramuscularly administered DNA vaccines.
T‐Fix anchor sutures for arthroscopic meniscal repair (1997)

The results of arthroscopically repaired meniscal tears with the T-Fix system in a short-term follow-up of 6 months was assessed in a non-comparative, prospective study. The T-Fix device consists of a short, rigid Delrin T attached to a braided, non-absorbable, polyester suture which is preloaded inside and deployed through a delivery (spinal) needle. The T grabs inside the tissue and provides an anchor for the suture. Twenty menisci in 20 patients (mean age 29 years) were repaired. Sports-related injuries were documented in 18 patients. In 15 patients, meniscus tears were repaired 6 months or more after injury. Half of the patients had isolated meniscus injuries. Associated injuries included anterior cruciate ligament (ACL), medial or lateral collateral ligament ruptures. These were not treated at the time of meniscal surgery except for an ACL reconstruction. All tears were longitudinal and positioned mainly in the posterior horn of the medial meniscus. A total of 70 T-Fixes were used with an average of 3 per patient (range 2-7). Only 4 T-Fixes (6%) were unsuccessfully placed, and this occurred early on in the series in 4 patients. In 90% of the patients, the postoperative activity levels returned to preoperative levels, and the clinical symptoms had either resolved or were experienced at a higher level of activity. The T-Fix device was relatively easy to use and could be reliably placed in the meniscus. Postoperatively, there were no complications directly associated with the device. However, further studies are needed to confirmed these results in a long-term follow-up in a larger patient population.
A Survey of Noninteractive Zero Knowledge Proof System and Its Applications (2014)

Zero knowledge proof system which has received extensive attention since it was proposed is an important branch of cryptography and computational complexity theory. Thereinto, noninteractive zero knowledge proof system contains only one message sent by the prover to the verifier. It is widely used in the construction of various types of cryptographic protocols and cryptographic algorithms because of its good privacy, authentication, and lower interactive complexity. This paper reviews and analyzes the basic principles of noninteractive zero knowledge proof system, and summarizes the research progress achieved by noninteractive zero knowledge proof system on the following aspects: the definition and related models of noninteractive zero knowledge proof system, noninteractive zero knowledge proof system of NP problems, noninteractive statistical and perfect zero knowledge, the connection between noninteractive zero knowledge proof system, interactive zero knowledge proof system, and zap, and the specific applications of noninteractive zero knowledge proof system. This paper also points out the future research directions.
Bacterial microcompartment assembly: The key role of encapsulation peptides (2015)

Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (∼17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N- or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. Here, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.
Coupling between the N- and C-Terminal Domains Influences Transducin-α Intrinsic GDP/GTP Exchange (2000)

The N-terminal regions of the heterotrimeric G-protein alpha-subunits represent one of the major Gbetagamma contact sites and have been implicated in an interaction with G-protein-coupled receptors. To probe the role of the N-terminal domain of transducin-alpha in G-protein function, a chimeric Gtialpha subunit with the 31 N-terminal Gtalpha residues replaced by the corresponding 42 residues of Gsalpha (Ns-Gtialpha) has been examined for the interaction with light-activated rhodopsin (R). Gtialpha displayed a somewhat higher R-stimulated rate of GTPgammaS binding relative to Ns-Gtialpha, suggesting modest involvement of the Gtalpha N-terminal sequence in recognition of the receptor. However, the intrinsic rate of nucleotide exchange in Ns-Gtialpha was significantly faster (k(app) = 0.014 min(-)(1)) than that in Gtialpha (k(app) = 0.0013 min(-1)) as judged by the GTPgammaS binding rates. Substitution of 42 N-terminal residues of Gsalpha by the Gtalpha residues in a reciprocal chimera, Nt-Gsalpha, had an opposite effect-notable reduction in the intrinsic GTPgammaS-binding rate (k(app) = 0.0075 min(-)(1)) in comparison with Gsalpha (k(app) = 0.028 min(-)(1)). Residue Val30 (His41 in Gsalpha) within the N-terminal region of Gtalpha interacts with the C-terminal residue, Ile339. To test the hypothesis that observed changes in the intrinsic nucleotide exchange rate in chimeric Galpha subunits might be attributed to this interaction, GtialphaVal30His, GtialphaIle339Ala, and Ns-GtialphaHis41Val mutants have been made and analyzed for basal GTPgammaS binding. GtialphaVal30His and GtialphaIle339Ala had increased GTPgammaS binding rates (k(app) = 0. 010 and 0.009 min(-)(1), respectively), whereas Ns-GtialphaHis41Val had a decreased GTPgammaS binding rate (k(app) = 0.0011 min(-)(1)) relative to their parent proteins. These results suggest that the coupling between the N-terminal and C-terminal domains of Gtalpha is important for maintaining a low nucleotide exchange rate in unstimulated transducin.
Stable Isotope Labeled Target Compounds: Preparation and Use as Internal Standards in Quantitative Mass Spectrometry (1998)

&lt;p&gt;In this contribution we wish to address some routes to stable isotope labeled compounds, preferrably starting with the intact target molecule, and their use as internal standards in quantitative mass spectrometry. The methods surveyed include, besides others, HID-exchange reactions and reductive deuteration procedures. Oxygen-18 exchange of carboxylic oxygen and phenolic hydroxyls with various catalysts is also covered. Partial and total synthesis is also discussed, predominantly for the incorporation of carbon-13, nitrogen-15, and selected deuterated functionalities. Special attention is paid to the stability of the obtained label to back-exchange, which would preclude the compounds from using them as internal standards. &lt;/p&gt; &lt;p&gt; This review is dedicated to Professor Helmut Gleispach on the occasion of his 6oth birthday and in recognition of his many contributions to the field of analytical mass spectrometry. &lt;/p&gt;
The effect of anti-intercellular adhesion molecule-1 on phorbol-ester-induced rabbit lung inflammation. (1989)

The role of the CD18 complex of leukocyte glycoproteins in adhesion-dependent functions of human leukocytes in vitro has been well documented. A ligand, intercellular adhesion molecule-1 (ICAM-1), for at least one member of the CD18 complex has been identified. This molecule is inducible on many cell types including vascular endothelium and keratinocytes by inflammatory mediators such as IL-1, TNF, and IFN-gamma. ICAM-1 has been shown to mediate, in part, the in vitro adhesion of lymphocytes and neutrophils to endothelial cells expressing ICAM-1. In the present study we have shown that mAb's to the human CD18 complex and to human ICAM-1 cross react with rabbit cells and that both anti-CD18 and anti-CD11b but neither anti-CD11a nor anti-ICAM-1 mAb's inhibit neutrophil migration, an adhesion-dependent function, in vitro. Pretreatment of rabbits with anti-CD18 and anti-ICAM-1 but not anti-CD11a mAb inhibited by greater than 60% neutrophil migration into PMA-induced inflamed rabbit lungs. This effect of anti-ICAM-1 mAb on pulmonary neutrophil influx after PMA injection has important implications. Specifically, that ICAM-1 can function as a ligand for CD18 and can mediate, at least in part, the migration of neutrophils to inflammatory sites.
An analytical method for the detection of methylation differences at specific chromosomal loci using primer extension and ion pair reverse phase HPLC (2002)

We have developed a rapid, accurate, and quantitative method for the detection of methylation differences at specific CpG sites based on bisulfite treatment of DNA followed by primer extension and ion-pair reversed-phase high performance liquid chromatography (IP RP HPLC). The application of the method is illustrated by analysis of differentially imprinted alleles arising from Prader-Willi and Angelman syndromes. In order to convert unmethylated cytosines to uracil, plasmid and genomic DNA samples were treated with sodium bisulfite and the targeted sequence was then amplified using oligodeoxynucleotide primers specific for the bisulfite-deaminated DNA. The PCR product(s) from this step was used as a template for a primer extension reaction and the products were subsequently analyzed chromatographically using IP RP HPLC. This method eliminates the need to use restriction enzymes to determine the methylation status of the amplicon and circumvents the need for radio labeling for the quantitative measurements. Finally, this method removes the need for nucleotide sequencing because it is not solely reliant on the presence or absence of one or more PCR products, as is the case with related methods.
Infectious Bronchitis Virus S2 Expressed from Recombinant Virus Confers Broad Protection Against Challenge (2014)

We developed a recombinant Newcastle disease virus (NDV) LaSota (rLS) expressing the infectious bronchitis virus (IBV) S2 gene (rLS/IBV.S2). The recombinant virus showed somewhat-reduced pathogenicity compared to the parental lentogenic LaSota strain but effectively elicited hemagglutination inhibition antibodies against NDV and protected chickens against lethal challenge with virulent NDV/CA02. IBV heterotypic protection was assessed using a prime-boost approach with a commercially available attenuated IBV Massachusetts (Mass)-type vaccine. Specific-pathogen-free chickens primed ocularly with rLS/IBV.S2 at 4 days of age and boosted with Mass at 18 days of age were completely protected against challenge at 41 days of age with a virulent Ark-type strain. In a second experiment, we compared protection conferred by priming with rLS/IBV.S2 and boosting with Mass (rLS/IBV.S2+Mass) versus priming and boosting with Mass (Mass+Mass). We also modified the timing of vaccination to prime at 1 day of age and boost at 12 days of age. Challenge with virulent Ark was performed at 21 days of age. Based on clinical signs, both vaccinated groups appeared equally protected against challenge compared to unvaccinated challenged chickens. Viral loads in lachrymal fluids of birds receiving rLS/IBV.S2+Mass showed a clear tendency of improved protection compared to Mass+Mass; however, the difference did not achieve statistical significance. A significant difference (P < 0.05) was determined between these groups regarding incidence of detection of challenge IBV RNA in the trachea; viral RNA was detected in 50% of rLS/IBV.S2+Mass-vaccinated chickens while chickens vaccinated with Mass+Mass and unvaccinated challenged controls showed 84 and 90% incidence of IBV RNA detection in the trachea, respectively. These results demonstrate that overexposing the IBV S2 to the chicken immune system by means of a vectored vaccine, followed by boost with whole virus, protects chickens against IBV showing dissimilar S1.
A two years open-label prospective study of OnabotulinumtoxinA 195 U in medication overuse headache: a real-world experience (2015)

This study represents the largest and longest post-marketing studies of doses comparison with OnabotulinumtoxinA in a real-life clinical setting. Here, we demonstrate the superior efficacy of OnabotulinumtoxinA 195 U compared to 155 U in CM patients with MOH during a 2-year treatment period with similar safety and tolerability profile.
Pulmonary Surfactant Subfractions in Patients With the Acute Respiratory Distress Syndrome (1995)

Changes in the surfactant system have been observed in patients with acute respiratory distress syndrome (ARDS). These alterations in surfactant are thought to contribute to lung dysfunction in this disease. In this report we describe the changes in surfactant subfractions in bronchoalveolar wash obtained from five patients with established ARDS compared with five non-ARDS patients. Our results show that, in addition to the changes in surfactant composition and yield reported previously, the ratio of small to large surfactant aggregates is significantly increased in patients with ARDS compared with non-ARDS patients (0.48 +/- 0.09 versus 0.20 +/- 0.05 respectively [p < 0.05]). This increased ratio was associated with a decreased level of SP-A in the large aggregate fraction. We suggest that this increased ratio represents a marker for surfactant alterations in ARDS that is independent of lavage technique and can be measured in a very small surfactant sample.
Evolution of a Highly Selective and Potent 2-(Pyridin-2-yl)-1,3,5-triazine Tie-2 Kinase Inhibitor (2007)

Inhibition of angiogenesis is a promising and clinically validated approach for limiting tumor growth and survival. The receptor tyrosine kinase Tie-2 is expressed almost exclusively in the vascular endothelium and is required for developmental angiogenesis and vessel maturation. However, the significance of Tie-2 signaling in tumor angiogenesis is not well understood. In order to evaluate the therapeutic utility of inhibiting Tie-2 signaling, we developed a series of potent and orally bioavailable small molecule Tie-2 kinase inhibitors with selectivity over other kinases, especially those that are believed to be important for tumor angiogenesis. Our earlier work provided pyridinyl pyrimidine 6 as a potent, nonselective Tie-2 inhibitor that was designed on the basis of X-ray cocrystal structures of KDR inhibitors 34 (triazine) and 35 (nicotinamide). Lead optimization resulted in pyridinyl triazine 63, which exhibited >30-fold selectivity over a panel of kinases, good oral exposure, and in vivo inhibition of Tie-2 phosphorylation.
A general pattern for substrate recognition by P‐glycoprotein (1998)

P-glycoprotein actively transports a wide variety of chemically diverse compounds out of the cell. Based on a comparison of a hundred compounds previously tested as P-glycoprotein substrates, we suggest that a set of well-defined structural elements is required for an interaction with P-glycoprotein. The recognition elements are formed by two (type I unit) or three electron donor groups (type II unit) with a fixed spatial separation. Type I units consist of two electron donor groups with a spatial separation of 2.5 +/- 0.3 A. Type II units contain either two electron donor groups with a spatial separation of 4.6 +/- 0.6 A or three electron donor groups with a spatial separation of the outer two groups of 4.6 +/- 0.6 A. All molecules that contain at least one type I or one type II unit are predicted to be P-glycoprotein substrates. The binding to P-glycoprotein increases with the strength and the number of electron donor or hydrogen bonding acceptor groups forming the type I and type II units. Correspondingly, a high percentage of amino acids with hydrogen bonding donor side chains is found in the transmembrane sequences of P-glycoprotein relevant for substrate interaction. Molecules that minimally contain one type II unit are predicted to be inducers of P-glycoprotein over-expression.
Citrate can effectively replace bicarbonate in oral rehydration salts for cholera and infantile diarrhoea. (1986)

This study investigated the therapeutic effectiveness of oral rehydration salt (ORS) solutions containing trisodium citrate (ORS-citrate) in place of sodium bicarbonate (ORS-bicarbonate). 74 children with cholera and 34 infants and children under 2 years of age with infantile diarrhea, all of whom had moderate to severe dehydration, were randomly assigned to 1 of the 2 treatment solution groups. Children with severe dehydration were 1st rehydrated with intravenous fluid followed by maintenance therapy with ORS solution (bicarbonate or citrate), while those with moderate dehydration received either ORS-bicarbonate or ORS-citrate during both the initial and the maintenance phases of therapy. Treatment effectiveness was assessed by comparing the success rates, stool output, ORS intake, gain in body weight, changes in erythrocyte volume fraction and plasma specific gravity, correction of acidosis, and maintenance of electrolyte balance. Of the children with cholera, 92% of those who received ORS-citrate and 86% of those who received ORS-bicarbonate were successfully treated. Of the children under 2 years of age with infantile diarrhea, 100% of those who received ORS-citrate and 94% of those who received ORS-bicarbonate were treated successfully. The results indicated that treatment with ORS-citrate is as successful as that with ORS-bicarbonate in terms of its ability to rehydrate, correct the acidosis, and maintain electrolyte concentrations. Thus, trisodium citrate dihydrate, which has the a advantage of a longer shelf-life in hot and humid climates, can effectively replace sodium bicarbonate in the standard ORS solution if used as an adjunct to standard hydration and antibiotic therapy in children with severe cholera or as the only treatment in children with infantile diarrhea assocated with less severe dehydration.