gebhart/patrepeval huggingface dataset:
Safety of single-dose administration of an adeno-associated virus (AAV)-CFTR vector in the primate lung. (1996)

Gene therapy for cystic fibrosis (CF) would ideally be accomplished with a vector capable of long-term expression of the cystic fibrosis transmembrane conductance regulator (CFTR) in the absence of a host inflammatory response. Recombinant adeno-associated virus (AAV)-CFTR vectors possess these characteristics in rabbits. Because the utility of AAV vectors as gene transfer agents has only been recognized recently, AAV vector-mediated transduction has never been modeled in a primate host, which is an important step before its use in humans. In order to test the safety and biological activity of AAV-CFTR, single doses of AAV-CFTR vector were administered by fiberoptic bronchoscopy to the posterior basal segment of the right lower lobe (RLL) of the lungs of 10 rhesus macaques with four matched vehicle-treated controls. Animals were followed for 10, 21, 90 or 180 days following vector instillation. Vector DNA transfer occurred in bronchial epithelial cells in the RLL of each animal that received vector as assessed by in situ DNA PCR. Vector mRNA was detectable for 180 days after administration as detected by RT-PCR and by RNase protection assay. Safety of vector administration was determined by measurements of pulmonary mechanics, arterial blood gas analysis, chest radiographs, and bronchoalveolar lavage (BAL) fluid analysis including cell count and quantification of inflammatory cytokines. Gross and microscopic pathologic examination were also performed. There was no evidence of inflammation or other toxicity, although vector DNA was found in extrapulmonary organs of some animals. These results indicate that transduction of the primate airway epithelium with the AAV-CFTR mediates long-term CFTR cDNA transfer and is relatively safe.
The ZnuABC high‐affinity zinc uptake system and its regulator Zur in Escherichia coli (1998)

In Escherichia coli, lacZ operon fusions were isolated that were derepressed under iron repletion and repressed under iron depletion. Two fusions were localized in genes that formed an operon whose gene products had characteristics of a binding protein-dependent transport system. The growth defect of these mutants on TY medium containing 5mM EGTA was compensated for by the addition of Zn2+. In the presence of 0.5mM EGTA, only the parental strain was able to take up 65Zn2+. This high-affinity transport was energized by ATP. The genes were named znuACB (for zinc uptake; former name yebLMI) and localized at 42 min on the genetic map of E. coli. At high Zn2+ concentrations, the znu mutants took up more 65Zn2+ than the parental strain. The high-affinity 65Zn2+ uptake was repressed by growth in the presence of 10 microM Zn2+. A znuA-lacZ operon fusion was repressed by 5 microM Zn2+ and showed a more than 20-fold increase in beta-galactosidase activity when Zn2+ was bound to 1.5 microM TPEN [tetrakis-(2-pyridylmethyl) ethylenediamine]. To identify the Zn2+-dependent regulator, constitutive mutants were isolated and tested for complementation by a gene bank of E. coli. A complementing gene, yjbK of the E. coli genome, was identified and named zur (for zinc uptake regulation). The Zur protein showed 27% sequence identity with the iron regulator Fur. High-affinity 65Zn2+ transport of the constitutive zur mutant was 10-fold higher than that of the uninduced parental strain. An in vivo titration assay suggested that Zur binds to the bidirectional promoter region of znuA and znuCB.
Improved Radiolabeling of PEGylated Protein: PEGylated Annexin V for Noninvasive Imaging of Tumor Apoptosis (2003)

We have developed a one-step procedure to introduce both polyethylene glycol (PEG) and the metal chelator diethylenetriaminepentaacetic acid (DTPA) to proteins through a heterofunctional PEG precursor. The PEG precursor contains DTPA at one end and an amine-reactive isothiocyanate (SCN-) functional group at the other end. It was obtained as lyophilized powder and could be stored at 4 degrees C for several months. Protein conjugation was achieved by simply mixing the proteins and the PEG precursor SCN-PEG-DTPA in an aqueous solution. As exemplified by the PEGylation and radiolabeling of annexin V, the resulting conjugate 111In-DTPA-PEG-annexin V showed selective binding to apoptotic cells in vitro and increased blood half-life in vivo. The PEGylated, radiolabeled annexin V may be useful in the noninvasive imaging of apoptosis.
Optimal immunoreactivity of keratin proteins in formalin-fixed, paraffin-embedded tissue requires preliminary trypsinization. An immunoperoxidase study of various tumours using polyclonal and monoclonal antibodies. (1985)

The effect of preliminary trypsinization on the immunoreactivity of keratin proteins in formalin-fixed, paraffin-embedded tissues of a variety of tumors (squamous cell carcinomas, adenocarcinomas, mesotheliomas, and transitional cell carcinomas) was evaluated. Three types of trypsin (Type II and Type IX porcine trypsin and Type III bovine trypsin) and varying concentrations of trypsin were assessed. Immunoreactivity of keratin proteins was determined using rabbit anti-keratin antibodies and monoclonal antibodies (combination of AE1 and AE3) and immunoperoxidase techniques. Preliminary trypsinization was mandatory for optimal immunoreactivity of keratin proteins using either polyclonal or monoclonal antibodies. Excellent results were obtained using Type II porcine trypsin at concentrations of 25 mg/dl for 30-45 min or 50 mg/dl for 20 min, at 37 degrees C. Trypsin treatment with excessive concentrations of enzyme and/or extended incubation times promoted tissue digestion and in some cases, yielded decreased immunoreactivity and altered staining patterns.
New fluoro‐modified thermoplastic polyurethanes (2003)

Abstract New fluoro‐modified thermoplastic polyurethanes containing perfluoropolyether (PFPE) blocks were synthesized by the reaction of a fluorinated macrodiol with a hydrogenated prepolymer based on poly(tetramethylene glycol) and 4,4′‐methylene‐ bis ‐phenylisocyanate, followed by subsequent chain extension with 1,4‐ n ‐butanediol. This multistep bulk process opened the way for a new family of polymeric materials whose tensile properties appear to be excellent and unchanged in comparison with the corresponding unmodified hydrogenated polymers. Dynamic mechanical analysis and differential scanning calorimetry revealed peculiar characteristics. These polymers showed an unusual multiphase structure in which not only the hard and the hydrogenated soft segments were self‐organized, but also a second soft phase, constituted by the PFPE segments, was present. Moreover, an easier hard‐phase segregation and self‐organization were observed, as was evidenced by the higher melting temperatures of the semicrystalline phase. This unique characteristic combined with a selective enrichment of PFPE segments to the surface, as indicated by the unusually low coefficient of friction data and superior chemical resistance. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 87: 2279–2294, 2003
Negative association of antibiotics on clinical activity of immune checkpoint inhibitors in patients with advanced renal cell and non-small-cell lung cancer (2018)

ATB were associated with reduced clinical benefit from ICI in RCC and NSCLC. Modulatation of ATB-related dysbiosis and gut microbiota composition may be a strategy to improve clinical outcomes with ICI.
Expression, purification, and characterization of recombinant gamma-carboxylated factor IX synthesized in Chinese hamster ovary cells. (1986)

Factor IX has been expressed to high levels within a recombinant host cell and the biologically active fraction subsequently purified to homogeneity for characterization. The coding sequence for Factor IX was inserted into a mammalian cell expression vector and transfected into dihydrofolate reductase-deficient Chinese hamster ovary cells. The integrated DNA was amplified to a high copy number by selection for increasingly higher expression levels of the marker gene, dihydrofolate reductase, contained within a co-transfected plasmid. Cloned cell lines secreting over 100 micrograms/ml Factor IX antigen and up to 1.5 microgram/ml native Factor IX antigen have been obtained. Expression of biologically active Factor IX was dependent on the presence of vitamin K in the culture media. The gamma-carboxylated Factor IX was isolated from cell culture fluid by immunoaffinity chromatography using antibodies conformation-specific for the metal-stabilized conformer of Factor IX. This conformation is dependent upon metal ions and gamma-carboxyglutamic acid. Purified recombinant Factor IX migrated as a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with an electrophoretic mobility equivalent to plasma-derived Factor IX. The purified recombinant Factor IX demonstrated Factor IX coagulant activity, measured in Factor IX-deficient plasma, of 35-75 units/mg. Amino acid analysis of the alkaline hydrolysate of recombinant Factor IX demonstrated an average of 6-7 mol of gamma-carboxyglutamic acid per mol of Factor IX. NH2-terminal sequence analysis of the first 17 residues revealed equivalent amino acid sequences for both purified recombinant and plasma-derived Factor IX. The results represent the first purification and characterization of a biologically active, gamma-carboxylated vitamin K-dependent protein expressed in a recombinant DNA system.
LOCAL ANESTHESIA IN OTOLARYNGOLOGY A RE-EVALUATION (1976)

Almost a half century following attempts to ban its use, cocaine remains at the pinnacle of topical anesthesia in otolaryngology. To understand how nonaddicting synthetic substitutes such as procaine, dibucaine, tetracaine and lidocaine have not totally supplanted cocaine, requires an in-depth analysis of its unique pharmological properties, untoward effects and potential substitutes. Almost all of the reported cocaine deaths occurred after subcutaneous injection; when used topically, cocaine's toxicity has been confined to an occasional reaction. Certain variables under physician control may be manipulated to reduce the chance of reaction to a minimum. For example, intermittent application of a particular dosage results in lower blood levels, and allowing sufficient time between doses reduces the amount necessary to obtain the desired anesthesia. If total dosage is kept below 200 mg there are few reactions. A singular advantage of cocaine over other topical anesthetics is its inherent ability to cause vasoconstriction, thus retarding its own absorption. The addition of a topical vasoconstrictor such as epinephrine is thus redundant, and may actually be harmful as cocaine sensitizes the patient to exogenous epinephrine. Finally, the usual preoperative dosages of barbiturates are entirely inadequate to prevent or treat cocaine reactions. Why, then, have synthetic local anesthetics not replaced cocaine? Inherent differences in topical effectiveness, duration of anesthesia and toxicity provide the answer. Of other local anesthetics possessing topical effectiveness tetracaine is about six times more toxic than cocaine. Dibucaine is as toxic as tetracaine, and lidocaine, while relatively nontoxic, provides only a 15 minute duration of topical anesthesia. A review of cocaine and its potential substitutes thus leads to the conclusion that cocaine is still a vital and necessary instrument in the otolaryngologist's armamentarium, singularly providing excellent topical anesthesia of usable duration, vasoconstriction, and shrinkage of mucous membranes, all with a quite acceptable margin of safety.
Differential Solvation and Tautomer Stability of a Model Base Pair within the Minor and Major Grooves of DNA (2005)

2-(2'-Hydroxyphenyl)benzoxazole (HBO) may be used as a model base pair to study solvation, duplex environment, and tautomerization within the major and minor groves of DNA duplexes. In its ground state, HBO possesses an enol moiety which may be oriented syn or anti relative to the imino nitrogen of the benzoxazole ring. In the absence of external hydrogen-bond donors and acceptors HBO exists as the internally hydrogen-bonded syn-enol, a mimic of the rare base pair tautomer found in DNA, which may be photoinduced to tautomerize and form the keto tautomer, a mimic of the dominant base pair tautomer. Previously, we demonstrated that when incorporated into DNA such that the enol moiety is positioned in the major groove, HBO is not solvated, exists exclusively as the internally hydrogen-bonded syn-enol which is efficiently photoinduced to tautomerize, and the corresponding keto tautomer is preferentially stabilized. In stark contrast, we now show that when HBO is incorporated in DNA such that the enol moiety is positioned in the minor groove, the enol tautomer is preferentially stabilized. Molecular dynamics simulations suggest that this results from the formation of a stable hydrogen-bond between the HBO enol and the O4' atom of an adjacent nucleotide, an H-bond acceptor that is only available in the minor groove. The differential stabilization of the enol and keto tautomers in the major and minor grooves may reflect the functions for which these environments evolved, including duplex replication, stability, and recognition.
DNA fingerprinting using non-radioactive oligonucleotide probes specific for simple repeats (1988)

Journal Article DNA fingerprinting using non-radioactive oligonucleotide probes specific for simple repeats Get access Renate Schäfer, Renate Schäfer Max-Planck-Institute für PsychiatrieAm Klopferspitz 18a, D-8033 Martinsried, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Hans Zischler, Hans Zischler Max-Planck-Institute für PsychiatrieAm Klopferspitz 18a, D-8033 Martinsried, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Jörg T. Epplen Jörg T. Epplen Max-Planck-Institute für PsychiatrieAm Klopferspitz 18a, D-8033 Martinsried, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 19, 11 October 1988, Page 9344, https://doi.org/10.1093/nar/16.19.9344 Published: 11 October 1988 Article history Received: 05 September 1988 Published: 11 October 1988
The geometry of positive real functions with applications to the rational covariance extension problem (2002)

In this paper we provide a characterization of all positive rational extensions of a given partial covariance sequence. Indeed, motivated by its application to signal processing, speech processing and stochastic realization theory, this characterization is in terms of a complete bianalytic parameterization using familiar objects from systems theory. In particular, this proves a long-standing conjecture by Georgiou. The methodology is based on global analysis of the dynamics of certain fast algorithms for Kalman filtering.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High Affinity Ca2+-binding Site in the Serine Protease Domain of Human Factor VIIa and Its Role in Tissue Factor Binding and Development of Catalytic Activity (1995)

Factor VIIa, in the presence of Ca2+ and tissue factor (TF), initiates the extrinsic pathway of blood coagulation. The light chain (amino acids 1-152) of factor VIIa consists of an N-terminal gamma-carboxyglutamic acid (Gla) domain followed by two epidermal growth factor-like domains, whereas the heavy chain (amino acids 153-406) contains the serine protease domain. In this study, both recombinant factor VIIa (rVIIa) and factor VIIa lacking the Gla domain were found to contain two high-affinity (Kd approximately 150 microM) Ca2+ binding sites. The rVIIa also contained approximately 6-7 low-affinity (Kd approximately 1 mM) Ca(2+)-binding sites. By analogy to other serine proteases, one of the two high affinity Ca(2+)-binding sites in factor VIIa may be formed involving Glu-210 and Glu-220 of the protease domain. In support of this, a synthetic peptide composed of residues 206-242 of factor VIIa bound one Ca2+ with Kd approximately 230 microM; however, Ca2+ binding was observed only in Tris buffer (pH 7.5) containing 1 M NaCl and not in buffer containing 0.1 M NaCl. In both low or high salt +/- Ca2+, the peptide existed as a monomer as determined by sedimentation equilibrium measurements and had no detectable secondary structure as determined by CD measurements. This indicates that subtle changes undetectable by CD may occur in the conformation of the peptide that favor calcium binding in high salt. In the presence of recombinant TF and 5 mM Ca2+, the peptide inhibited the amidolytic activity of rVIIa toward the synthetic substrate, S-2288. The concentration of the peptide required for half-maximal inhibition was approximately 5-fold higher in the low salt buffer than that in the high salt buffer. From direct binding and competitive inhibition assays of active site-blocked 125I-rVIIa binding to TF, the Kd for peptide-TF interaction was calculated to be approximately 15 microM in the high salt and approximately 55 microM in the low salt buffer containing 5 mM Ca2+. Moreover, as inferred from S-2288 hydrolysis, the Kd for VIIa.TF interaction was approximately 1.5 microM in the absence of Ca2+, and, as inferred from factor X activation studies, it was approximately 10 pM in the presence of Ca2+. Thus, Ca2+ decreases the functional Kd of VIIa.TF interaction approximately 150,000-fold.(ABSTRACT TRUNCATED AT 400 WORDS)
Electrophysiological Effects of Remodeling Cardiac Gap Junctions and Cell Size (2000)

The increased incidence of arrhythmias in structural heart disease is accompanied by remodeling of the cellular distribution of gap junctions to a diffuse pattern like that of neonatal cardiomyocytes. Accordingly, it has become important to know how remodeling of gap junctions due to normal growth hypertrophy alters anisotropic propagation at a cellular level (V(max)) in relation to conduction velocities measured at a macroscopic level. To this end, morphological studies of gap junctions (connexin43) and in vitro electrical measurements were performed in neonatal and adult canine ventricular muscle. When cells enlarged, gap junctions shifted from the sides to the ends of ventricular myocytes. Electrically, normal growth produced different patterns of change at a macroscopic and microscopic level. Although the longitudinal and transverse conduction velocities were greater in adult than neonatal muscle, the anisotropic velocity ratios were the same. In the neonate, mean V(max) was not different during longitudinal (LP) and transverse (TP) propagation. However, growth hypertrophy produced a selective increase in mean TP V(max) (P<0.001), with no significant change in mean LP V(max). Two-dimensional neonatal and adult cellular computational models show that the observed increases in cell size and changes in the distribution of gap junctions are sufficient to account for the experimental results. Unexpectedly, the results show that cellular scaling (cell size) is as important (or more so) as changes in gap junction distribution in determining TP properties. As the cells enlarged, both mean TP V(max) and lateral cell-to-cell delay increased. V(max) increased because increases in cell-to-cell delay reduced the electric current flowing downstream up to the time of V(max), thus enhancing V(max). The results suggest that in pathological substrates that are arrhythmogenic, maintaining cell size during remodeling of gap junctions is important in sustaining a maximum rate of depolarization.
Nanofiltration extends the range of membrane filtration (1988)

Abstract Nanofiltration is a pressure driven membrane process between reverse osmosis and ultrafiltration. The rejection is low for salts with monovalent anion and nonionized organics with molecular weight below 150 while high for salts with di‐ and multivalent anions and organics with molecular weight above 300. Examples of applications are removal of color and TOC from Florida surface water, removal of hardness, radium, and sulfate from well water, removal of sulfate from seawater and simultaneous removal of sodium chloride and concentration of organics with molecular weight 300–1000 in the food and pharmaceutical industries. The investment cost for a nanofiltration plant is about the same as for a brackish water reverse osmosis plant, but the energy savings can be considerable by using nanofiltration instead of reverse osmosis.
DNA, RNA, and Protein Extraction: The Past and The Present (2009)

Extraction of DNA, RNA, and protein is the basic method used in molecular biology. These biomolecules can be isolated from any biological material for subsequent downstream processes, analytical, or preparative purposes. In the past, the process of extraction and purification of nucleic acids used to be complicated, time-consuming, labor-intensive, and limited in terms of overall throughput. Currently, there are many specialized methods that can be used to extract pure biomolecules, such as solution-based and column-based protocols. Manual method has certainly come a long way over time with various commercial offerings which included complete kits containing most of the components needed to isolate nucleic acid, but most of them require repeated centrifugation steps, followed by removal of supernatants depending on the type of specimen and additional mechanical treatment. Automated systems designed for medium-to-large laboratories have grown in demand over recent years. It is an alternative to labor-intensive manual methods. The technology should allow a high throughput of samples; the yield, purity, reproducibility, and scalability of the biomolecules as well as the speed, accuracy, and reliability of the assay should be maximal, while minimizing the risk of cross-contamination.
Synthesis and Photoreaction of 4′-Pivaloyl Guanosides (2001)

The synthesis of a 4’-pivaloylated guanosine and its incorporation into oligonucleotides is described. Photolysis of the modified nucleoside and DNA double strand leads in nearly quantitative yield to enol ethers. The decisive step in this reaction is a very fast electron transfer from guanine to an enol ether radical cation.
Characterization of fHbp , nhba ( gna2132 ), nadA , porA , and Sequence Type in Group B Meningococcal Case Isolates Collected in England and Wales during January 2008 and Potential Coverage of an Investigational Group B Meningococcal Vaccine (2010)

Invasive disease caused by meningococcal capsular groups A, C, W-135, and Y is now preventable by means of glycoconjugate vaccines that target their respective polysaccharide capsules. The capsule of group B meningococci (MenB) is poorly immunogenic and may induce autoimmunity. Vaccines based on the major immunodominant surface porin, PorA, are effective against clonal epidemics but, thus far, have a limited scope of coverage against the wider MenB population at large. In an alternative approach, the first-generation, investigational, recombinant MenB (rMenB) plus outer membrane vesicle (OMV) (rMenB-OMV) vaccine contains a number of relatively conserved surface proteins, fHBP, NHBA (previously GNA2132), and NadA, alongside PorA P1.4-containing OMVs from the New Zealand MeNZB vaccine. MenB currently accounts for approximately 90% of cases of meningococcal disease in England and Wales. To assess potential rMenB-OMV vaccine coverage of pathogenic MenB isolates within this region, all English and Welsh MenB case isolates from January 2008 (n = 87) were genetically characterized with respect to fHBP, NHBA, NadA, and PorA. Alleles for fHbp, nhba, and porA were identified in all of the isolates, of which 22% were also found to harbor nadA alleles. On the basis of genotypic data and predicted immunological cross-reactivity, the potential level of rMenB-OMV vaccine coverage in England and Wales ranges from 66% to 100%.