gebhart/patrepeval huggingface dataset:
Mutational analysis of hydrophobic domain interactions in γB‐crystallin from bovine eye lens (1997)

gamma B-crystallin is a monomeric member of the beta gamma-superfamily of vertebrate eye lens proteins. It consists of two similar domains with all-beta Greek key topology associating about an approximate two-fold axis. At pH 2, with urea as the denaturant, the domains show independent equilibrium unfolding transitions, suggesting different intrinsic stabilities. Denaturation experiments using recombinant one- or two-domain proteins showed that the N-terminal domain on its own exhibits unaltered intrinsic stability but contributes significantly to the stability of its C-terminal partner. It has been suggested that docking of the domains is determined by a hydrophobic interface that includes phenylalanine at position 56 of the N-terminal domain. In order to test this hypothesis, F56 was substituted by site-directed mutagenesis in both complete gamma B-crystallin and its isolated N-terminal domain. All mutations destabilize the N-terminal domain to about the same extent but affect the C-terminal domain in a different way. Replacement by the small alanine side chain or the charged aspartic acid residue results in a significant destabilization of the C-terminal domain, whereas the more bulky tryptophan residue causes only a moderate decrease in stability. In the mutants F56A and F56D, equilibrium unfolding transitions obtained by circular dichroism and intrinsic fluorescence differ, suggesting a more complex denaturation behavior than the one observed for gamma B wild type. These results confirm how mutations in one crystallin domain can affect the stability of another when they occur at the interface. The results strongly suggest that size, hydrophobicity, and optimal packing of amino acids involved in these interactions are critical for the stability of gamma B-crystallin.
Further studies on oligoribonucleotide synthesis. (1980)

Recent results concerning the synthesis of oligoribonucleotides via the phosphotriester method, such as functionalization of ribonucleosides, new phosphorylating agents, 5'-O-sulfonylation and chromatography on Sephadex LH-20 for monitoring the removal of internucleotide phosphotriester groups, are presented. To show that efficiency of a new approach to the synthesis of oligoribonucleotides the pentamer /Up/4U was obtained.
Astrocyte expression of a dominant-negative interferon-γ receptor (2005)

Interferon-gamma (IFN-gamma) is a major proinflammatory cytokine, and binding to its nearly ubiquitous receptor induces a wide variety of biological functions. To explore the role(s) of IFN-gamma signaling in astrocytes, transgenic mice (GFAP/IFN-gammaR1DeltaIC) expressing a dominant-negative IFN-gamma receptor alpha chain under control of the astrocyte-specific glial fibrillary acid protein (GFAP) promoter were generated. Transgenic mice developed normally, had normal astrocyte numbers and distribution, and exhibited no clinically overt phenotype. Transgene mRNA expression was detected only in the CNS, and the transgene-encoded IFN-gamma receptor 1 colocalized with GFAP, which is consistent with astrocyte expression. Astrocytes from transgenic mice exhibited reduced IFN-gamma-induced signaling as measured by major histocompatibility class II induction. Neither CNS inflammation nor perforin-mediated clearance of a neurotropic mouse hepatitis virus from astrocytes was impaired following infection. Transgenic mice with impaired astrocyte responsiveness to IFN-gamma provide a model for studying the selective astrocyte-dependent effects of this critical cytokine in CNS immunopathology.
Thermostabilisation of an Agonist-Bound Conformation of the Human Adenosine A2A Receptor (2011)

The adenosine A(2A) receptor (A(2A)R) is a G-protein-coupled receptor that plays a key role in transmembrane signalling mediated by the agonist adenosine. The structure of A(2A)R was determined recently in an antagonist-bound conformation, which was facilitated by the T4 lysozyme fusion in cytoplasmic loop 3 and the considerable stabilisation conferred on the receptor by the bound inverse agonist ZM241385. Unfortunately, the natural agonist adenosine does not sufficiently stabilise the receptor for the formation of diffraction-quality crystals. As a first step towards determining the structure of A(2A)R bound to an agonist, the receptor was thermostabilised by systematic mutagenesis in the presence of the bound agonist [(3)H]5'-N-ethylcarboxamidoadenosine (NECA). Four thermostabilising mutations were identified that when combined to give mutant A(2A)R-GL26, conferred a greater than 200-fold decrease in its rate of unfolding compared to the wild-type receptor. Pharmacological analysis suggested that A(2A)R-GL26 is stabilised in an agonist-bound conformation because antagonists bind with up to 320-fold decreased affinity. None of the thermostabilising mutations are in the ZM241385 binding pocket, suggesting that the mutations affect ligand binding by altering the conformation of the receptor rather than through direct interactions with ligands. A(2A)R-GL26 shows considerable stability in short-chain detergents, which has allowed its purification and crystallisation.
Gene and Protein Sequence Optimization for High-Level Production of Fully Active and Aglycosylated Lysostaphin in Pichia pastoris (2014)

Lysostaphin represents a promising therapeutic agent for the treatment of staphylococcal infections, in particular those of methicillin-resistant Staphylococcus aureus (MRSA). However, conventional expression systems for the enzyme suffer from various limitations, and there remains a need for an efficient and cost-effective production process to facilitate clinical translation and the development of nonmedical applications. While Pichia pastoris is widely used for high-level production of recombinant proteins, there are two major barriers to the production of lysostaphin in this industrially relevant host: lack of expression from the wild-type lysostaphin gene and aberrant glycosylation of the wild-type protein sequence. The first barrier can be overcome with a synthetic gene incorporating improved codon usage and balanced A+T/G+C content, and the second barrier can be overcome by disrupting an N-linked glycosylation sequon using a broadened choice of mutations that yield aglyscosylated and fully active lysostaphin. The optimized lysostaphin variants could be produced at approximately 500 mg/liter in a small-scale bioreactor, and 50% of that material could be recovered at high purity with a simple 2-step purification. It is anticipated that this novel high-level expression system will bring down one of the major barriers to future development of biomedical, veterinary, and research applications of lysostaphin and its engineered variants.
Transfusion‐induced autoantibodies and differential immunogenicity of blood group antigens: a novel hypothesis (2007)

Blood bank serology has identified hundreds of red blood cell (RBC) antigens contained within numerous blood group systems. Although most blood group antigens are defined by amino acid polymorphisms in the extracellular domain of membrane proteins, it is also possible that additional nonexofacial polymorphisms (NEPs) may exist within cytoplasmic or transmembrane domains. To assess this possibility, we analyzed several blood group molecules by searching the SNPper database for nonsynonymous single‐nucleotide polymorphisms. We report the identification of a number of NEPs in the Kell, Kidd, and Duffy molecules. Because the identified NEPs are not exposed on the surface of intact RBCs and are, thus, not accessible to recipient antibodies, they would neither be detected by blood bank serology in vitro, nor would they be recognized targets in hemolytic transfusion reactions in vivo. The presentation of peptides containing NEPs by recipient MHC Class II molecules, however, would nevertheless produce helper T‐cell epitopes. In addition to identifying NEPs in human blood group molecules, we explore a novel hypothesis that the presence of NEPs contributes to the immunogenicity of blood group antigens. We further hypothesize that NEPs provide a mechanism by which transfusion can lead to anti‐RBC autoantibodies, which are known to occur in humans after transfusion. The scientific basis, existing evidence, approaches to testing, and predicted biology of this hypothesis are presented.
Protein-calorie malnutrition in a community hospital (1980)

An assessment of protein-calorie status was performed on 200 consecutive adult nonobstetric admissions to a private hospital from two group family practices. Anthropometric measurements, serum albumin level, and total lymphocyte count were determined at admission and weekly if the patient remained in the hospital. Nonnutritional factors affecting muscle protein stores and serum albumin level were taken into account. A total of 63 patients (31.5%) were found to be malnourished. The most common conditions associated with decreased protein stores were hypoxic cardiopulmonary disease, gastrointestinal disease, neuromuscular or arthritic impairment, organic brain syndrome, and febrile illness. Although nonnutritional factors accounted for many instances of protein depletion, especially milder degrees of depletion, nevertheless protein calorie malnutrition was highly prevalent in this population. (<i>JAMA</i>243:1720-1722, 1980)
NVIDIA Tesla: A Unified Graphics and Computing Architecture (2008)

To enable flexible, programmable graphics and high-performance computing, NVIDIA has developed the Tesla scalable unified graphics and parallel computing architecture. Its scalable parallel array of processors is massively multithreaded and programmable in C or via graphics APIs.
Efficacy of a Novel Class of RNA Interference Therapeutic Agents (2012)

RNA interference (RNAi) is being widely used in functional gene research and is an important tool for drug discovery. However, canonical double-stranded short interfering RNAs are unstable and induce undesirable adverse effects, and thus there is no currently RNAi-based therapy in the clinic. We have developed a novel class of RNAi agents, and evaluated their effectiveness in vitro and in mouse models of acute lung injury (ALI) and pulmonary fibrosis. The novel class of RNAi agents (nkRNA®, PnkRNA™) were synthesized on solid phase as single-stranded RNAs that, following synthesis, self-anneal into a unique helical structure containing a central stem and two loops. They are resistant to degradation and suppress their target genes. nkRNA and PnkRNA directed against TGF-β1mRNA ameliorate outcomes and induce no off-target effects in three animal models of lung disease. The results of this study support the pathological relevance of TGF-β1 in lung diseases, and suggest the potential usefulness of these novel RNAi agents for therapeutic application.
Regulation of interleukin 1 gene expression by adherence and lipopolysaccharide. (1987)

Murine peritoneal exudate cells (PEC), analyzed immediately after isolation, did not express detectable IL 1 activity or IL 1-specific mRNA. Stimulation of these cells by adherence induced the expression of intracellular, membrane, and extracellular IL 1 activities within 4 hr. Analysis of mRNA from these cells showed a concurrent induction of both IL 1 alpha and IL 1 beta mRNA within 1 hr. However, this stimulation of IL 1 expression was transient, since PEC cultured for 5 days no longer expressed IL 1 bioactivity or specific mRNA. Stimulation of these quiescent cells with bacterial lipopolysaccharide induced the re-expression of intracellular, membrane, and extracellular IL 1 activities as well as IL 1 alpha and IL 1 beta mRNA. We found no qualitative difference in the degree or rate of induction of IL 1 alpha compared with IL 1 beta mRNA. These results indicate that resting macrophages are IL 1 negative, and that the IL 1 inducing stimuli used in this study act transiently to increase the levels of IL 1 alpha and IL 1 beta mRNA.
The Antibiotic Bead Pouch Technique (1993)

In a consecutive series of 704 compound fractures, 227 open fractures in 204 patients were managed with the antibiotic bead pouch technique. There were 16 Grade I compound fractures, 83 Grade II fractures, and 128 Grade III open fractures. The mean patient age was 35.25 years (range, 14-87). The Injury Severity Score (ISS) ranged from 9 to 57, with a mean of 15. Porous plastic film is placed over the soft-tissue defect to establish a "closed" bead-hematoma-fracture environment containing high local levels of antibiotic at the fracture site. All patients had serial wound debridements and parenteral systemic antibiotics (cefazolin, tobramycin, penicillin). Bead pouch changes ranged from one to seven per patient (mean, two). During these changes, 1248 cultures were taken, 78 (6.25%) of which were positive in 34 patients. Seventeen patients developed clinical signs consistent with an infection. The wound infection rate was 0% in Grade I open fractures, 1.2% in Grade II compound fractures, and 8.6% in Grade III open fractures. The osteomyelitis rate was 0% in Grade I compound fractures, 2.4% in Grade II open fractures, and 5.5% in Grade III compound fractures. Wound closure was obtained in 134 fractures with delayed primary closure of the skin, in 53 fractures with flap coverage, and in 23 fractures with split-thickness skin graft. Coverage was not completed in 17 wounds, at which time an amputation was performed or death occurred. Time of closure ranged from one to 32 days (mean, 7.1 days).(ABSTRACT TRUNCATED AT 250 WORDS)
Comparison of 24-month outcomes in chelated and non-chelated lower-risk patients with myelodysplastic syndromes in a prospective registry (2013)

This 5-year, prospective registry enrolled 600 lower-risk MDS patients (pts) with transfusional iron overload. Clinical outcomes were compared between chelated and nonchelated pts. At baseline, cardiovascular comorbidities were more common in non-chelated pts, and MDS therapy was more common in chelated pts. At 24 months, chelation was associated with longer median overall survival (52.2 months vs. 104.4 months; p<.0001) and a trend toward longer leukemia-free survival and fewer cardiac events. No differences in safety were apparent between groups. Limitations of this analysis included, varying time from diagnosis and duration of chelation, and the fact that the decision to chelate may have been influenced by pt clinical status.
Fabrication of microfluidic hydrogels using molded gelatin as a sacrificial element (2007)

This paper describes a general procedure for the formation of hydrogels that contain microfluidic networks. In this procedure, micromolded meshes of gelatin served as sacrificial materials. Encapsulation of gelatin meshes in a hydrogel and subsequent melting and flushing of the gelatin left behind interconnected channels in the hydrogel. The channels were as narrow as approximately 6 microm, and faithfully replicated the features in the original gelatin mesh. Fifty micrometre wide microfluidic networks in collagen and fibrin readily enabled delivery of macromolecules and particles into the channels and transport of macromolecules from channels into the bulk of the gels. Microfluidic gels were also suitable as scaffolds for cell culture, and could be seeded by human microvascular endothelial cells to form rudimentary endothelial networks for potential use in tissue engineering.
Purification of two distinct growth factors from bovine neural tissue by heparin affinity chromatography (1984)

Two growth factors have been purified to homogeneity from either bovine hypothalamus or brain by heparin affinity chromatography. Both stimulate the growth of murine 3T3 fibroblasts and bovine capillary endothelial cells. One heparin-binding growth factor (HGF alpha), purified from either tissue by elution from heparin with 1.0 M sodium chloride, is obtained in a yield of 0.4 mg/kg of tissue. Its apparent molecular weight is 16 000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and its amino acid composition is identical with that of the acidic fibroblast growth factor recently isolated from bovine brain by a multistep chromatographic procedure [Thomas, K. A., Rios-Candelore, M., & Fitzpatrick M. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 357-361]. A second growth factor (HGF beta), isolated from either tissue by elution from heparin with 2.0 M sodium chloride, is obtained in a yield of 0.02 mg/kg of tissue. Its apparent molecular weight is 18 000 by SDS-PAGE, and its amino acid composition differs from that of HGF alpha. These results confirm the existence of two distinct growth factors in bovine neural tissue and establish that the acidic endothelial cell growth factor from hypothalamus and the acidic brain fibroblast growth factor are identical.
Molecular cytogenetic study of supernumerary marker chromosomes in an unselected group children (1995)

We report on an unselected group of 24 children with small supernumerary marker chromosomes, found in a large sample of 34,910 consecutive newborns karyotyped at birth. Sixteen of these were available for reexamination. With the use of in situ hybridization with alpha-satellite centromere probes and satellite III, ribosomal and beta-satellite DNA probes, we have characterized these markers. In 14 of the 16 cases we have been able to determine the chromosomal origin of the marker. Twelve of the markers are derived from the acrocentric chromosomes. Of these 12 markers, 4 are derived from chromosome 14, 4 from chromosome 22, 3 from chromosome 15 and one is from either chromosome 13 or 21. Ten of these markers were initially ascertained with the satellite III DNA probe, taking advantage of the fact that satellite III DNA is found in the centromeric region of the following chromosomes: 1, 5, 9, 13, 14, 15, 16, 20, 21, 22, and Y. Two markers were derived from chromosomes 4 and 8. The origin of the last 2 markers could not be determined with the techniques employed. Only one of these children is psychometrically retarded and has a peculiar appearance. Unfortunately we were not able to determine the origin of the marker in her case. All other children developed normally.
SEROLOGIC DEMONSTRATION OF DUAL SPECIFICITY OF RABBIT BIVALENT HYBRID ANTIBODY (1964)

Hybrid, bivalent antibody molecules bearing specific combining sites for both ovalbumin and bovine gamma globulin were produced by reoxidation of a mixture of the 3.5S fragments of the two specifically purified antibodies. The dual specificity and the properties of the hybrid antibody were demonstrated by mixed agglutination and two stage agglutination experiments, and by test systems utilizing inhibition of agglutination or dispersal of agglutinates followed by antiglobulin reactions.
Rheological and Thermal Properties of Elastomeric Polypropylene (1998)

The properties of elastomeric polypropylene synthesized from an unbridged metallocene catalyst are investigated by mechanical rheometry, differential scanning calorimetry, and optical depolarization. The material is compositionally heterogeneous in tacticity, and its behavior is compared to that of its solvent fractions. The behavior of elastomeric polypropylene is also compared with tacticity-matched atactic/isotactic homopolymer blends. For T below Tm, mechanical rheometry shows that elastomeric polypropylene forms a more constrained network than tacticity-matched homopolymer blends. Differential scanning calorimetry reveals that the elastomeric samples crystallize at a lower temperature than blends composed of the same isotactic content. Depolarization studies show similar transitions but reveal the presence of an additional slower time scale involved with crystallizing the elastomeric sample. Data are consistent with the presumed atactic/isotactic multiblock microstructure of elastomeric polypropylene.
Evaluation of filtering mechanisms for MPEG video communications (2002)

In this paper, we evaluate two video filtering mechanisms for MPEG-1 video, namely low-pass filtering and selective frame dropping. The evaluation provides tradeoffs between the reduction achieved in bandwidth requirements and the perceptual quality of the video sequences delivered to the client. Extensive experiments revealed that these filtering mechanisms result in a significant reduction in bandwidth requirements while maintaining acceptable perceptual quality.
Estimation of blood pressure using Photoplethysmography on the wrist (2009)

Blood pressure measuring method using PPG signal is the one of many non-invasive blood pressure methods. In this study, we have studied a new method that estimates the blood pressure using wrist cuff and wrist PPG (Photoplethysmograph) signal.
Selection and Characterization of Replicon Variants Dually Resistant to Thumb- and Palm-Binding Nonnucleoside Polymerase Inhibitors of the Hepatitis C Virus (2006)

Multiple nonnucleoside inhibitor binding sites have been identified within the hepatitis C virus (HCV) polymerase, including in the palm and thumb domains. After a single treatment with a thumb site inhibitor (thiophene-2-carboxylic acid NNI-1), resistant HCV replicon variants emerged that contained mutations at residues Leu419, Met423, and Ile482 in the polymerase thumb domain. Binding studies using wild-type (WT) and mutant enzymes and structure-based modeling showed that the mechanism of resistance is through the reduced binding of the inhibitor to the mutant enzymes. Combined treatment with a thumb- and a palm-binding polymerase inhibitor had a dramatic impact on the number of replicon colonies able to replicate in the presence of both inhibitors. A more exact characterization through molecular cloning showed that 97.7% of replicons contained amino acid substitutions that conferred resistance to either of the inhibitors. Of those, 65% contained simultaneously multiple amino acid substitutions that conferred resistance to both inhibitors. Double-mutant replicons Met414Leu and Met423Thr were predominantly selected, which showed reduced replication capacity compared to the WT replicon. These findings demonstrate the selection of replicon variants dually resistant to two NS5B polymerase inhibitors binding to different sites of the enzyme. Additionally, these findings provide initial insights into the in vitro mutational threshold of the HCV NS5B polymerase and the potential impact of viral fitness on the selection of multiple-resistant mutants.
DNA Synthesis and Mitotic Clonal Expansion Is Not a Required Step for 3T3-L1 Preadipocyte Differentiation into Adipocytes (2001)

Upon differentiation induction of 3T3-L1 preadipocytes by a hormone mixture containing 1-isobutyl-3-methylxanthine, dexamethasone, and insulin, the preadipocytes undergo approximately 2 rounds of mitotic clonal expansion, which just precedes the adipogenic gene expression program and has been thought to be an essential early step for differentiation initiation. By inducing 3T3-L1 preadipocytes with each individual hormone, it was determined that the mitotic clonal expansion was induced only by insulin and not by 1-isobutyl-3-methylxanthine or dexamethasone. Cell number counting and fluorescence-activated cell-sorting analysis indicated that a significant fraction of 3T3-L1 preadipocytes differentiated into adipocytes without mitotic clonal expansion when induced with the combination of 1-isobutyl-3-methylxanthine and dexamethasone. Furthermore, when normally induced 3T3-L1 preadipocytes were treated with PD98059 (an inhibitor of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase 1) to block the activation of extracellular signal-regulated kinase (Erk) 1 and Erk2, the mitotic clonal expansion was blocked, but adipocyte differentiation was not affected. These observations were confirmed by bromodeoxyuridine labeling. The differentiated adipocytes induced with 1-isobutyl-3-methylxanthine and dexamethasone or standard hormone mixture plus PD98059 were not labeled by bromodeoxyuridine. Thus, it is evident that 3T3-L1 preadipocytes could differentiate into adipocytes without DNA synthesis and mitotic clonal expansion. Our results also suggested that activation of Erk1 and Erk2 is essential to but not sufficient for induction of mitotic clonal expansion.