gebhart/patrepeval huggingface dataset:
High-Level Expression and Mutagenesis of Recombinant Human Phosphatidylcholine Transfer Protein Using a Synthetic Gene:  Evidence for a C-Terminal Membrane Binding Domain (2000)

Phosphatidylcholine transfer protein (PC-TP) is a 214-amino acid cytosolic protein that promotes intermembrane transfer of phosphatidylcholines, but no other phospholipid class. To probe mechanisms for membrane interactions and phosphatidylcholine binding, we expressed recombinant human PC-TP in Escherichia coli using a synthetic gene. Optimization of codon usage for bacterial protein translation increased expression of PC-TP from trace levels to >10% of the E. coli cytosolic protein mass. On the basis of secondary structure predictions of an amphipathic alpha-helix (residues 198-212) in proximity to a hydrophobic alpha-helix (residues 184-193), we explored whether the C-terminus might interact with membranes and promote binding of phosphatidylcholines. Consistent with this possibility, truncation of five residues from the C-terminus shortened the predicted amphipathic alpha-helix and decreased PC-TP activity by 50%, whereas removal of 10 residues eliminated the alpha-helix, abolished activity, and markedly decreased the level of membrane binding. Circular dichroic spectra of synthetic peptides containing one ((196-214)PC-TP) or both ((183-214)PC-TP) predicted C-terminal alpha-helices in aqueous buffer were most consistent with random coil structures. However, both peptides adopted alpha-helical configurations in the presence of trifluoroethanol or phosphatidylcholine/phosphatidylserine small unilamellar vesicles. The helical content of (196-214)PC-TP increased in proportion to vesicle phosphatidylserine content, consistent with stabilization of the alpha-helix at the membrane surface. In contrast, the helical content of (183-214)PC-TP was not influenced by vesicle composition, implying that the more hydrophobic of the alpha-helices penetrated into the membrane bilayer. These studies suggest that tandem alpha-helices located near the C-terminus of PC-TP facilitate membrane binding and extraction of phosphatidylcholines.
RNA Interference as a Tool to Reduce the Risk of Rejection in Cell-Based Therapies (2016)

Remarkable progress in the experimental and clinical applications of cell-based therapies has identified stem cells and their derived products as potential candidates for regenerative therapies for many disorders. The use of autologous stem cells as source for regenerative therapeutic products is strongly limited by their low availability. Therefore, the future applications of in vitro pharmed therapeutic cell products will most likely occur in an allogeneic manner. However, the high variability of the human leukocyte antigen (HLA) represents a major obstacle to the application of off-the-shelf products. We have developed a strategy to decrease the immunogenicity of in vitro generated cell products by silencing HLA expression using RNAi. HLA expression was permanently silenced in CD34+ hematopoietic stem and progenitor cells and induced the pluripotent stem cells to generate HLA-universal cells sources, which were then used for the differentiation of low immunogenic cell products. In this chapter, we will provide an overview about an RNAi-based strategy to reduce the immunogenicity of cell-based therapies, and in particular in the generation of HLA-universal platelets and tissues.
Bosentan Improves Exercise Capacity in Adolescents and Adults After Fontan Operation (2014)

http://www.clinicaltrials.gov. Unique identifier: NCT01292551.
Human Immunodeficiency Virus Type 1 p24 Concentration Measured by Boosted ELISA of Heat‐Denatured Plasma Correlates with Decline in CD4 Cells, Progression to AIDS, and Survival: Comparison with Viral RNA Measurement (2000)

Human immunodeficiency virus type 1 (HIV-1) RNA and p24 antigen concentrations were determined in plasma samples from 169 chronically infected patients (median CD4 cell count, 140 cells/microL; range, 0-1500 cells/microL). p24 quantification involved heat-mediated immune complex dissociation and tyramide signal amplification-boosted ELISA, which has a diagnostic sensitivity similar to that of RNA quantification by a commercial polymerase chain reaction kit. In Cox's proportional hazard models adjusted for CD4 cell count, both RNA (P<.005) and p24 (P=.043) levels were significant predictors of progression to AIDS. Measurement of p24 was superior to measurement of RNA in the model for survival (P=.032 vs. P=.19). p24 level was a significant predictor of CD4 cell decline in models adjusted for CD4 cell counts and was superior or equivalent to RNA level, depending on the group analyzed. Stratification by CD4 cell counts at baseline showed that the superiority of p24 measurement was more pronounced at lower levels of CD4 cells (<200/microL). p24 level may be of interest as a simple and inexpensive predictive marker of disease progression.
Highly Versatile and Robust Materials for Soft Imprint Lithography Based on Thiol‐ene Click Chemistry (2008)

As easy as “shake and bake”, the mixing and photocuring of poly-functional thiols with alkene-functional cross-linkers, via thiol-ene click chemistry, leads to materials with outstanding and tunable characteristics for soft imprint lithography. The materials are cured within 2 minutes at ambient conditions allowing stamps with high aspect ratio and sub-100 nm features to be fabricated.
Further Development and Use of a Molecular Serotype Identification Test for Infectious Bronchitis Virus (1997)

Previously, we developed a rapid serotype identification test for infectious bronchitis virus (IBV) that utilizes the reverse transcriptase-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism analysis. The RT-PCR is used to amplify the S1 gene from RNA extracted from the virus grown in eggs. Restriction enzyme digestion and electrophoresis of that PCR product is used to determine the serotype of the virus. The purpose of this study was threefold. First, using a modified 5' PCR primer, we altered the procedures of our rapid serotype identification test and amplified the S1 gene of IBV in tracheal swabs collected from specific-pathogen-free leghorn chickens experimentally inoculated with the Arkansas or Mass 41 serotypes of IBV. Direct amplification of IBV in tracheal swabs eliminates the need to isolate the virus in eggs. Second, we attempted to amplify inactivated IBV in allantoic fluid, possibly allowing us to obtain and determine the serotype of isolates originating from outside the U.S.A. Virus inactivated by formalin (0.1% final concentration) could not be amplified by the RT-PCR procedure, but heat-inactivated IBV (56 C for 15 min) was successfully amplified. Third, we developed an internal control for the RT-PCR test by synthesizing RNA runoff transcripts of a cloned truncated S1 gene. The truncated S1 RNA transcripts were added to the RT-PCR reaction and a 1031-bp product was amplified, which could be distinguished from the coamplified S1 gene from viral RNA. The internal RNA control reduces the possibility of obtaining false-negative results in the RT-PCR test.
Production of capsular material by Streptococcus suis serotype 2 under different growth conditions. (1993)

The procedure currently used for the production of Streptococcus suis antigen is very long and includes several subcultures. The aim of the present work was to study the in vitro production of capsular material by S. suis serotype 2 after each of these subcultures. The amount of capsular material produced was evaluated by electron microscopy using bacterial cells grown on blood-agar plates and in Todd-Hewitt broth (THB) or THB supplemented with serum. In addition, the production of antibodies in rabbits with antigens produced using different growth conditions was compared. Antigens produced after only three subcultures possessed as much capsular material as cells obtained after the complete procedure and induced a similar antibody response. The use of serum as a supplement to the broth did not assure a higher production of capsule; in addition, antibody titers obtained with antigens produced in THB were as high as those obtained with antigens produced in THB supplemented with serum. We recommend the use of three subcultures in nonsupplemented broth for the production of immunogens. This revised protocol offers two main advantages: it is less time-consuming because of the limited number of subcultures and is also less expensive since nonsupplemented broths are used.
Impact of Carotid Atherosclerosis on the Risk of Adverse Cardiac Events in Patients With and Without Coronary Disease (2014)

CA and carotid artery stenosis are independent predictors of major adverse cardiovascular event in patients undergoing coronary angiography. The prognostic implications of carotid disease are imparted predominantly in patients without pre-existent CAD.
Dissecting the maize genome by using chromosome addition and radiation hybrid lines (2004)

We have developed from crosses of oat (Avena sativa L.) and maize (Zea mays L.) 50 fertile lines that are disomic additions of individual maize chromosomes 1-9 and chromosome 10 as a short-arm telosome. The whole chromosome 10 addition is available only in haploid oat background. Most of the maize chromosome disomic addition lines have regular transmission; however, chromosome 5 showed diminished paternal transmission, and chromosome 10 is transmitted to offspring only as a short-arm telosome. To further dissect the maize genome, we irradiated monosomic additions with gamma rays and recovered radiation hybrid (RH) lines providing low- to medium-resolution mapping for most of the maize chromosomes. For maize chromosome 1, mapping 45 simple-sequence repeat markers delineated 10 groups of RH plants reflecting different chromosome breaks. The present chromosome 1 RH panel dissects this chromosome into eight physical segments defined by the 10 groups of RH lines. Genomic in situ hybridization revealed the physical size of a distal region, which is represented by six of the eight physical segments, as being approximately 20% of the length of the short arm, representing approximately one-third of the genetic chromosome 1 map. The distal approximately 20% of the physical length of the long arm of maize chromosome 1 is represented by a single group of RH lines that spans >23% of the total genetic map. These oat-maize RH lines provide valuable tools for physical mapping of the complex highly duplicated maize genome and for unique studies of inter-specific gene interactions.
ChemInform Abstract: A NEW SELECTIVE SYNTHESIS OF RACEMIC DISPARLURE, THE SEX PHEROMONE OF GYPSY MOTH (PORTHETRIA DISPAR L.) (1978)

Abstract Aus 1,5‐Cyclooctadien (I) erhält man bei der selektiven Ozonolyse das Diol (IIa), aus dem mit Phosphortribromid das Dibromid (IIb) hergestellt wird.
Testing a degradable topical varnish of cetylpyridinium chloride in an experimental dental biofilm model (2001)

Dental biofilms are highly associated with the development of dental caries. Novel drug delivery systems are being developed in order to eliminate cariogenic bacteria from the dental biofilms. We formulated two degradable sustained release varnishes, based on acrylic resin, with cetylpyridinium chloride (CPC) as the active agent. These formulations were tested in a dental biofilm model. The retention of CPC in the biofilm was dependent upon the pharmaceutical additives of the varnish. Both varnishes decreased bacterial adhesion, while also demonstrating marked antibacterial properties against the bacteria in the biofilm.
Steroid Hormones Regulate Gene Expression Posttranscriptionally by Altering the Stabilities of Messenger RNAs (2005)

Hormones exert powerful effects on reproductive physiology by regulating gene expression. Recent discoveries in hormone action emphasize that regulation of gene expression is not restricted to their alterations of the rate of gene transcription. On the contrary, hormonal effects on the stability of a specific mRNA can profoundly alter its steady-state concentration. The mRNAs encoding hormone receptors are commonly regulated by their own hormones to create autoregulatory feedback loops. Negative and positive autoregulatory feedback loops serve to limit or augment hormonal responses, respectively. After introducing the topics of mRNA degradation and regulated stability, this review focuses on steroid hormone effects on mRNA stabilities. Autoregulation of the mRNAs encoding estrogen, progesterone, androgen, and glucocorticoid receptors by the steroid hormones in reproductive tissues is discussed. In addition, steroid hormone effects on the stabilities of many other mRNAs that are important to reproductive biology are reviewed. These include mRNAs that encode gonadotropin hormones, integrins, growth factors, and inflammatory response proteins. Through these posttranscriptional effects, steroid hormones impact the expression of a large population of genes. Studies of the molecular mechanisms of hormonally regulated mRNA stabilities continue to identify critical mRNA sequence elements and their interactions with proteins. Increased understanding of how hormones affect mRNA stability may yield novel approaches to the therapeutic control of hormone effects, including those essential to reproductive physiology in animals.
Free radicals and antioxidants in sepsis (1993)

Objectives: The clinical condition of sepsis is caused by the release of numerous mediators from many cells. The purpose of this review is to describe the results of studies in which the role of free radicals and/or the potential therapeutic value of antioxidants are assessed. Data Sources: The studies described in this review come from a variety of sources, including Med-Line CD-ROM computerized database, Index Medicus, and references identified from the bibliographies of pertinent articles and books. Reports were confined to English language articles from 1966 to 1992. Study Selection: All retrieved references in which free-radical activity was assessed or antioxidants were measured or administered in sepsis or endotoxemia were included. This selection process encompassed clinical, animal and in vitro cell culture work. Data Extraction: Cited literature was found in reputable peer-reviewed clinical or basic science journals. Data Synthesis: Any contradictions in the results of studies are discussed. Conclusions: There is evidence that free radicals play an important role in the pathogenesis of sepsis. Antioxidant therapy has the potential to protect against such injury. It is suggested that combination therapy, which augments the endogenous antioxidant defenses, is likely to be the best approach. (Crit Care Med 1993; 21:1770–1776)
Comparative Genomics and Structure Prediction of Dental Matrix Proteins (2003)

Non-collagenous matrix proteins secreted by the ameloblasts (amelogenin) and odontoblasts (osteocalcin) play important roles in the mineralization of enamel and dentin. In this study, comparative genomics approaches were used to identify the functional domains and model the three-dimensional structure of amelogenin and osteocalcin, respectively. Multiple sequence analysis of amelogenin in different species showed a high degree of sequence conservation at the nucleotide and protein levels. At the protein level, motifs (a sequence pattern that occurs repeatedly in a group of related proteins or genes), conserved domains, secondary structural characteristics, and functional sites of amelogenin from lower phyla were similar to those of the higher-level mammals, reflecting the high degree of sequence conservation during vertebrate evolution. Osteocalcin, produced by both odontoblasts and osetoblasts, also showed sequence similarity between species. Three-dimensional structure predictions developed by modeling of conserved domains of osteocalcin supported a role for glutamic acid residues in the calcium mineralization process.
Testing of Lipoxygenase Inhibitors, Cyclooxygenase Inhibitors, Drugs with Immunomodulating Properties and Some Reference Antipsoriatic Drugs in the Modified Mouse Tail Test, an Animal Model of Psoriasis (1994)

Topical administration of lipoxygenase and cyclooxygenase inhibitors, antipsoriatic drugs and some immunomodulating drugs on adult mouse tail scales showed variable induction of of orthokeratosis. Dithranol and retinoic acid showed ED50 concentrations of 0.5% and 0.23%, respectively. The lipoxygenase inhibitors catechol and octyl gallate showed ED50 of 2.5 and 13.4%. 10% lonapalene showed 20% activity, curcumin, linoleic acid, primrose oil and AA673 10-15% activity, methyl and ethyl gallate 5% activity, nordihydroguaiaretic acid, diethylcarbamazine, ebselen, esculetin, quercetin, AA861, gallic acid, dodecyl gallate and 15-hydroxyeicosatetraenoic acid no activity. The cyclooxygenase inhibitors indomethacin, acetylsalicylic acid and bufexamac were inactive, benoxaprofen showed 14% activity. The immunomodulating drugs fluorouracil and triamcinolone showed > 10% activity, cyclosporin A and thalidomide no activity. Fumaric acid showed 5% activity. The results show that this model could be proposed for screening antipsoriatic drugs.
COMPLEMENT AS A FACTOR IN ARTERIOSCLEROSIS (1970)

Massive doses of vitamin‐D in a few days provoke heavy clinical symptoms and histologically significant vascular changes, particularly in the aorta, coronary arteries and renal vessels of rats. Intravenous administration of zymosan completely cuts out these effects. Our conclusion is, therefore, that inactivation of circulating complement inhibits the vitamin‐D produced arterial lesions. We suggest that complement not only is an important factor in arteriosclerosis produced by vitamin‐D poisoning, but find it conceivable that it may play a similar key role in human aortic and coronary sclerosis.
A goal-oriented web browser (2006)

Many users are familiar with the interesting but limited functionality of Data Detector interfaces like Microsoft's Smart Tags and Google's AutoLink. In this paper we significantly expand the breadth and functionality of this type of user interface through the use of large-scale knowledge bases of semantic information. The result is a Web browser that is able to generate personalized semantic hypertext, providing a goal-oriented browsing experience.We present (1) Creo, a Programming by Example system for the Web that allows users to create a general-purpose procedure with a single example, and (2) Miro, a Data Detector that matches the content of a page to high-level user goals.An evaluation with 34 subjects found that they were more efficient using our system, and that the subjects would use features like these if they were integrated into their Web browser.
High-efficiency AlGaAs-GaAs Cassegrainian concentrator cells (1985)

AlGaAs-GaAs heteroface space concentrator solar cells have been fabricated by metalorganic chemical vapor deposition. AMO efficiencies as high as 21.1% have been observed both for p-n and np structures under concentration (90 to 100X) at 25 C. Both cell structures are characterized by high quantum efficiencies and their performances are close to those predicted by a realistic computer model. In agreement with the computer model, the n-p cell exhibits a higher short-circuit current density.
Plasma Nucleic Acids in the Diagnosis and Management of Malignant Disease (2002)

Circulating nucleic acids are an emerging class of molecular tumor markers. Their wide applicability and clinical relationship with the malignant state will likely grant them increasing clinical importance in the near future.
Total Synthesis of (−)-Spirotryprostatin B:  Synthesis and Related Studies (2005)

The total synthesis of spirotryprostatin B, a cytostatic spiro[pyrrolidine-3,3'-oxindole] alkaloid, is described. The key step of the synthetic approach consists of the application of the MgI2-mediated ring-expansion reaction of a spiro[cyclopropane-1,3'-oxindole] with an aldimine, leading to rapid assembly of the spirotryprostatin core. The route documents the installation of the prenyl side chain by Julia-Kocieński olefination of a key aldehyde precursor, a transformation that ultimately allows for facile synthesis of analogues and facilitates structure-activity relationships studies.
A Genomic Analysis of Rat Proteases and Protease Inhibitors (2004)

Proteases perform important roles in multiple biological and pathological processes. The availability of the rat genome sequence has facilitated the analysis of the complete protease repertoire or degradome of this model organism. The rat degradome consists of at least 626 proteases and homologs, which are distributed into 24 aspartic, 160 cysteine, 192 metallo, 221 serine, and 29 threonine proteases. This distribution is similar to that of the mouse degradome but is more complex than that of the human degradome composed of 561 proteases and homologs. This increased complexity of rat proteases mainly derives from the expansion of several families, including placental cathepsins, testases, kallikreins, and hematopoietic serine proteases, involved in reproductive or immunological functions. These protease families have also evolved differently in rat and mouse and may contribute to explain some functional differences between these closely related species. Likewise, genomic analysis of rat protease inhibitors has shown some differences with mouse protease inhibitors and the expansion of families of cysteine and serine protease inhibitors in rodents with respect to human. These comparative analyses may provide new views on the functional diversity of proteases and inhibitors and contribute to the development of innovative strategies for treating proteolysis diseases.
Identifying fault activation during hydraulic stimulation in the Barnett shale: Source mechanisms, b values, and energy release analyses of microseismicity (2011)

Identification of fault planes that intersect horizontal wellbores is critical to optimizing formation stimulation, preventing waste of valuable time and materials, and avoiding the establishment of fluid flow pathways into non‐target formations, such as aquifers. We can detect and locate microseismic events accurately over a broad area using a large near surface seismic monitoring array. In addition, source mechanism inversion techniques can be used to determine the method of failure experienced by the rock formation, expanding our understanding of the dynamics involved in hydraulic fracturing. Events in this analysis are segregated into two populations based upon the distinct source mechanisms present. Spatial and temporal analysis of frequency magnitude distributions (FMD) allows us to characterize trends useful in assessing the hydraulic treatment efficiency. This information can assist in interpretation of faults in a 3D seismic volume to delineate faults in reservoirs, or when used alone, identify faults of subseismic displacement to further optimize future well placement. Also b values and source mechanisms can help to better define stimulated reservoir volumes (SRV) by indicating the effective level of stimulation.