gebhart/patrepeval huggingface dataset:
Probing the Proximity of the Core Domain of an HIV-1 Tat Fragment in a Tat−TAR Complex by Affinity Cleaving (1997)

Transactivation of human immunodeficiency virus (HIV) gene expression depends upon the interaction of the viral regulatory protein Tat with the transactivation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all mRNAs. We have used a site-directed RNA-cleaving strategy to determine the neighborhood of the core domain of a Tat fragment in the Tat-TAR complex. We synthesized a 35-amino acid fragment containing arginine-rich RNA-binding domain of Tat(38-72) and attached an EDTA analog to its amino terminus. A derivative of (p-aminobenzyl)-EDTA tetra-tert-butyl ester was synthesized and attached to the amino terminus of the Tat peptide by standard peptide coupling methods. Cleavage from the resin and deprotection of the peptide were carried out in trifluoroacetic acid which also generated unprotected metal binding EDTA moieties. We used this EDTA-Tat conjugate to form a specific complex with TAR RNA. This sequence-specific RNA-binding peptide was converted into a sequence-specific RNA-cleaving peptide by the addition of Fe(II) salt, ascorbate, and H2O2. Hydroxyl radicals generated from the tethered Fe(II) cleaved the TAR RNA backbone in two localized regions. Site-specific cleavage of TAR RNA was observed at the bulge residues (U23, C24, and U25), in the loop region (G34 and A35), and at the strand opposite the bulge (U40 and C41). These results demonstrate that, in the three-dimensional structure of the Tat-TAR complex, the Phe38 of Tat(38-72) is located in the proximity of the bulge region and two nucleotides from the loop sequence.
The epidermal growth factor. (1995)

Epidermal growth factor (EGF) is a single polypeptide of 53 amino acid residues which is involved in the regulation of cell proliferation. Egf exerts its effects in the target cells by binding to the plasma membrane located EGF receptor. The EGF receptor is a transmembrane protein tyrosine kinase. Binding of EGF to the receptor causes activation of the kinase and subsequently receptor autophosphorylation. The autophosphorylation is essential for the interaction of the receptor with its substrates. These bind to the receptor by the so-called SH2 domains. The signal transduction pathways activated by EGF include the phosphatidylinositol pathway, leading to activation of protein kinase C and to increase in the intracellular Ca2+ concentration, and to the ras pathway leading to MAP kinase activation. Recently the cytoplasm has been implicated as playing an important role in EGF induced signal transduction. The EGF receptor has been demonstrated to be an actin-binding protein. In addition EGF causes a rapid actin depolymerisation and the formation of membrane ruffles. In particular these membrane ruffles have been shown to act as the first site of signal transduction after EGF binding, and thus may be considered as signal transduction structures. Finally evidence has been presented suggesting a positive role for EGF and/or the receptor in the nucleus.
HLA Class I Depleted hESC as a Source of Hypoimmunogenic Cells for Tissue Engineering Applications (2015)

HLA-I depletion does not preclude hESC differentiation into cardiac or hepatic lineages. This methodology can be used to engineer tissue from nonautologous hESC sources with improved immunocompatibility.
Genetic Causes of Generalized Epilepsies (2015)

Generalized epilepsies, particularly the idiopathic or genetic generalized epilepsies (GGEs), represent some of the most common epilepsies. Clinical genetic data including family studies and twin studies provide compelling evidence for a prominent genetic impact. The first decade of the 21st century was marked by progress in understanding the basic biology of generalized epilepsies including generalized/genetic epilepsies with febrile seizures plus (GEFS+) and GGE through studies of large families, discovering causative mutations in SCN1A, SCN1B, GABRG2, and GABRA1. Subsequently, recurrent microdeletions at 15q13.3, 16p13.11, and 15q11.2 were found to be relevant risk factors for nonfamilial GGE. Genes for epileptic encephalopathies such as SLC2A1 were rediscovered in GGE, highlighting the biological continuum between different epilepsies. Genome-wide studies examining common genetic risk factors identified common variants in SCN1A, indicating a convergence of shared pathophysiological pathways in various types of epilepsies. In the era of next-generation sequencing, however, the GGEs appear more complex than expected, and small or moderately sized studies give only a limited genetic perspective. Thus, there is a strong impetus for large collaborative investigations on an international level.
Immortalization and controlledin vitro differentiation of murine multipotent neural crest stem cells (1997)

To isolate mouse neural crest stem cells, we have generated a rat monoclonal antibody to murine neurotrophin receptor (p75). We have immortalized p75+ murine neural crest cells by expression of v-myc, and have isolated several clonal cell lines. These lines can be maintained in an undifferentiated state, or induced to differentiate by changing the culture conditions. One of these cell lines, MONC-1, is capable of generating peripheral neurons, glia, and melanocytic cells. Importantly, most individual MONC-1 cells are multipotent when analyzed at clonal density. The neurons that differentiate under standard conditions have an autonomic-like phenotype, but under different conditions can express markers of other peripheral neuronal lineages. These lines therefore exhibit a similar differentiation potential as their normal counterparts. Furthermore, they can be genetically modified or generated from mice of different genetic backgrounds, providing a useful tool for molecular studies of neural crest development.
Direct isolation and identification of promoters in the human genome (2005)

Transcriptional regulatory elements play essential roles in gene expression during animal development and cellular response to environmental signals, but our knowledge of these regions in the human genome is limited despite the availability of the complete genome sequence. Promoters mark the start of every transcript and are an important class of regulatory elements. A large, complex protein structure known as the pre-initiation complex (PIC) is assembled on all active promoters, and the presence of these proteins distinguishes promoters from other sequences in the genome. Using components of the PIC as tags, we isolated promoters directly from human cells as protein-DNA complexes and identified the resulting DNA sequences using genomic tiling microarrays. Our experiments in four human cell lines uncovered 252 PIC-binding sites in 44 semirandomly selected human genomic regions comprising 1% (30 megabase pairs) of the human genome. Nearly 72% of the identified fragments overlap or immediately flank 5' ends of known cDNA sequences, while the remainder is found in other genomic regions that likely harbor putative promoters of unannotated transcripts. Indeed, molecular analysis of the RNA isolated from one cell line uncovered transcripts initiated from over half of the putative promoter fragments, and transient transfection assays revealed promoter activity for a significant proportion of fragments when they were fused to a luciferase reporter gene. These results demonstrate the specificity of a genome-wide analysis method for mapping transcriptional regulatory elements and also indicate that a small, yet significant number of human genes remains to be discovered.
Quantitative PET studies in pretreated melanoma patients: a comparison of 6-[18F]fluoro-L-dopa with 18F-FDG and (15)O-water using compartment and noncompartment analysis. (2001)

In patients with negative FDG findings, FDOPA can help to identify viable melanoma metastases and thus may help to select patients who would benefit from further treatment.
Cloning and expression in Escherichia coli of the streptolysin O determinant from Streptococcus pyogenes: characterization of the cloned streptolysin O determinant and demonstration of the absence of substantial homology with determinants of other thiol-activated toxins (1984)

A gene bank of Streptococcus pyogenes Richards was constructed in Escherichia coli by using the bacteriophage replacement vector lambda L47.1, and hybrid phage expressing streptolysin O (SLO) were identified among the recombinants. DNA sequences encoding SLO were subcloned from an slo+ hybrid phage into a low-copy-number vector plasmid to yield an slo+ hybrid plasmid, pMK157. This plasmid contains 5.6 kilobase pairs of cloned streptococcal DNA sequences, is stable, and expresses SLO at easily detectable levels in E. coli. Transposon gamma delta insertion mutants and in vitro-generated deletion mutants of pMK157 were isolated and analyzed. This analysis showed that a single gene is sufficient for production of SLO in E. coli and allowed this slo gene to be mapped to within +/- 100 base pairs. Two forms of the slo gene product, with molecular weights of 68,000 and 61,000, were detected in E. coli minicells harboring slo+ plasmids and by immunoblotting of E. coli whole cells harboring slo+ plasmids. Southern blotting hybridization experiments with the cloned SLO DNA sequences as probes failed to demonstrate homology between the cloned SLO determinant and DNA isolated from bacteria expressing thiol-activated cytolysins related to SLO.
Isolation and characterization of Borrelia burgdorferi from Illinois Ixodes dammini (1991)

Ixodes dammini ticks from two northwestern Illinois sites were found to be infected with Borrelia burgdorferi at rates of 19 and 32%. B. burgdorferi isolates, one from each site, had protein and antigenic patterns similar to those of the B-31 strain. An indirect immunofluorescence method proved to be more sensitive than dark-field microscopy in detection of these spirochetes. A modified BSK medium containing rifampin was found to be more efficient for spirochete isolation than unsupplemented BSK medium.
Molecular basis for a familial defect in phagocyte expression of IgG receptor I (CD64). (1995)

Four individuals have been identified, within a single family, who lack phagocyte expression of the high affinity type I IgG receptor (CD64). As a result, their monocytes are unable to support mouse IgG2a anti-CD3-induced T cell mitogenesis (nonresponder individuals). Southern blotting proved all three human Fc gamma receptor I (hFc gamma RI) genes to be present in nonresponders without major structural changes. Nucleotide sequencing showed identical hFc gamma RIA promoter regions in all individuals. At the message level, a distinct difference was noted between monocytes from control (responder) donors and from nonresponders. Both a 1.7- and 1.6-kb message were found in responders, whereas in nonresponders only the 1.6-kb species was detectable. Reverse transcriptase-PCR analyses showed the hFc gamma RIa transcript (encoding a receptor with three extracellular Ig-like domains) to be present at a approximately 15- to 20-fold lower level in nonresponder monocytes. Importantly, we found a single nucleotide difference (C --> T) within the extracellular domain exon 1-encoding region of hFc gamma RIA in nonresponders, resulting in the change of codon 92 (encoding an arginine) into a termination codon. This change likely affects mRNA stability and, thereby, leads to undetectable expression of phagocyte-hFc gamma RIa. Despite this defect, these individuals are apparently healthy, suggesting that hFc gamma RIa is dispensable for phagocyte functioning.
Development of ceramic and ceramic composite devices for maxillofacial applications (1972)

Abstract Ceramic and ceramic composite materials and devices were developed for specific maxillofacial applications. These applications included: ( 1 ) Replacement of hard tissue voids in low stress areas with a phosphate‐bonded alumina‐foamed ceramic and a calcium aluminate‐bonded alumina foam; ( 2 ) development of porous ceramic‐coated metallic devices for stabilization of mandibles with avulsed segments; ( 3 ) development of implantable ceramic tooth roots onto which more or less conventional crowns may be mounted. Efforts to date have been rewarding. Using the rhesus monkey for all experimental implant work, incorporation of porous ceramic foam prostheses to eliminate maxillary defects has been accomplished. Also, we have succeeded in stabilizing the mandible where segments of from 3 to 8 mm were removed. Bridging of the gap with new bone occurred within 6 weeks resulting in a total regeneration of the resected area with restoration of normal mandibular function. Finally, implantable tooth roots were developed. Three different surface treatment techniques have been used on a basic high‐density alumina core. The first is a high‐density matt finish which can only permit a fibrous tissue attachment or bony approximation but no ingrowth. The second is a porous alumina coating intended to permit bone ingrowth. The third is a rough surface consisting of particles of alumina sintered to the surface to maximize the bone/ceramic interface shear strength potential. Implantations of both anterior and posterior tooth roots with all three surface configurations have been successful for periods of up to six months.
A Small Interfering RNA Targeting Vascular Endothelial Growth Factor as Cancer Therapeutics (2004)

Vascular endothelial growth factor (VEGF) plays a critical role during normal embryonic angiogenesis and also in the pathological angiogenesis that occurs in a number of diseases, including cancer. We developed a novel VEGF blockade system using RNA interference. The small interfering RNA (siRNA) targeting human VEGF almost completely inhibited the secretion of VEGF in a human prostate cancer cell line, PC-3, whereas the control scramble siRNA showed no effects. The VEGF siRNA with atelocollagen dramatically suppressed tumor angiogenesis and tumor growth in a PC-3 s.c. xenograft model. Atelocollagen provided a beneficial delivering means by which stabilization and efficient transfection of the siRNA injected into the tumors were achieved.
Presence of active and latent type 1 plasminogen activator inhibitor associated with porcine platelets (1992)

Data from a number of laboratories indicate that human platelets contain type I plasminogen activator inhibitor (PAI-1) primarily in a latent form; however, one report (Biochemistry 28:5773, 1989) indicated that it is predominantly the active form of PAI-1 that is present in and can be purified from an ammonium sulfate precipitate of porcine platelets. To clarify this situation, we investigated and compared the status of PAI-1 in porcine and human platelets. Immunologic analysis of the ability of PAI-1 to form complexes with immobilized t-PA indicated that porcine and human platelets contained 3.7 +/- 0.4 and 1.7 +/- 0.3 U of PAI activity per 10(8) platelets (n = 6; +/- SD), respectively; sodium dodecyl sulfate (SDS)-activation of the lysates increased PAI-1 activity to 10.8 +/- 3.0 and 3.8 +/- 0.5 U per 10(8) platelets. Platelet lysates were also treated with an excess of soluble t-PA, which formed complexes with active PAI-1, whereas the latent form was detected by SDS-polyacrylamide gel electrophoresis and reverse fibrin autography. Furthermore, immobilized t-PA was able to deplete active PAI-1 from the platelet extracts, and the latent form remaining in the absorbed extract could be quantitated by activation with 4 mol/L guanidine. To investigate the differences between our observations and the published data, porcine platelets were extracted, and PAI-1 was partially purified as described in the literature. For quantitative analysis, porcine platelet PAI-1 was also purified to homogeneity using standard chromatographic procedures optimized in our laboratory for endothelial PAI-1, and the purified protein was used to develop an enzyme-linked immunoabsorbent assay for porcine PAI-1 antigen. Our results indicate that: (1) latent PAI-1 in concentrated ammonium sulfate precipitates of porcine platelet lysates cannot be detected unless the precipitates are diluted before treatment with denaturants; and (2) active and latent porcine platelet PAI-1 can be separated by gel filtration over molecular sieving columns. In summary, this report documents that PAI-1 in porcine platelets is present in both an active and a latent form.
SMART: An Efficient, Scalable, and Robust Streaming Video System (2004)

SMART, the acronym of scalable media adaptation and robust transport, is a suite of compression and transmission technologies for efficient, scalable, adaptive, and robust video streaming over the best-effort Internet. It consists of two indispensable parts: SMART video coding and SMART video streaming. The SMART video coding part is an efficient DCT-based universal fine granularity scalable coding scheme. Since the SMART video coding scheme adopts multiple-loop prediction and drifting reduction techniques at the macroblock level, it can achieve high coding efficiency at a wide range of bit rates. More importantly, it provides all sorts of scalabilities, that is, quality, temporal, spatial, and complexity scalabilities, in order to accommodate heterogeneous time-variant networks and different devices. The SMART video streaming part is a transport scheme that fully takes advantages of the special features of the scalable bit streams. An accurate bandwidth estimation method is first discussed as the prerequisite of network adaptation. Then, flexible error resilience technique and unequal error protection strategy are investigated to enhance the robustness of streaming SMART bit stream. The SMART system shows excellent performances with regard to high coding efficiency, flexible channel bandwidth adaptation, smooth playback, and superior error robustness in static and dynamic experiments.
Targeting hyaluronan (HA) in tumor stroma: A phase I study to evaluate the safety, pharmacokinetics (PK), and pharmacodynamics (PD) of pegylated hyaluronidase (PEGPH20) in patients with solid tumors. (2012)

2579 Background: HA, a glycosaminoglycan, accumulates in ~25% of solid tumors and is associated with poor prognosis. Tumors that accumulate HA develop high interstitial fluid pressure (IFP) and become resistant to chemotherapy. In animal models, PEGPH20 reduced tumor-associated HA and increased efficacy of chemotherapy. Methods: This ongoing phase 1 study was designed to assess safety, tolerability, PK, PD, and the maximum tolerated dose (MTD) of PEGPH20 as a single agent in patients with treatment-refractory solid tumors. IV PEGPH20 was administered in a twice weekly or a once weekly dosing schedule with oral dexamethasone (dex) pre-and post dose. Biomarkers included tumor histochemistry to detect HA depletion, plasma HA catabolites, and DCE-MRI or FDG-PET. Results: Fifteen patients have been enrolled into the study. Dose administration ranged from 0.5 µg/kg to 5 µg/kg. Musculoskeletal events (MSEs) were the most common and dose limiting toxicities. To date, up to 3 µg/kg twice weekly IV infusions of PEGPH20 were well tolerated with manageable Grade 1 MSEs in most patients. MTD has not been reached. Plasma concentrations of PEGPH20 showed dose proportional exposure with a terminal half life of ~2 days. Enzymatic activity of PEGPH20 was reflected by dose-dependent HA catabolites in plasma. Pre- and post-dose tumor biopsies from 2 colon patients demonstrated 23-60% reduction in tumor HA after 4 weeks of dosing. Serial DCE-MRI and FDG-PET demonstrated increased tumor perfusion (K trans ) and decreased metabolic activity 8 and 24hrs post-PEGPH20 in one patient each. Doses of ≤3 µg/kg were tolerated with intermittent Grade 1-2 MSE. Enrollment at dose levels &gt; 3 µg/kg is ongoing. Conclusions: Repeated IV PEGPH20 infusion resulted in dose-dependent systemic exposure and is tolerated with concomitant dex treatment. HA catabolites in plasma demonstrated the in vivo enzymatic activity of PEGPH20. Reduced HA in tumor biopsies and serial DCE-MRI and FDG-PET images confirmed PD activity. Increased tumor perfusion by PEGPH20 may enhance drug delivery to tumor. Combination studies of PEGPH20 with cytotoxic chemotherapy are planned.
A smart surface with switchable wettability by an ionic liquid (2017)

Smart control of surface wettability by ionic liquids (ILs) is significant for designing IL-related intelligent materials and devices. Herein, we present mixed molecular brushes comprised of poly(phenylethyl methacrylate) and 1H,1H,2H,2H-perfluorodecyltrimethoxysilane (PPhEtMA-co-PFDMS) grafted surfaces that are capable of dynamically regulating 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIm][NTf<sub>2</sub>]) wettability. <sup>1</sup>H NMR and quartz crystal microbalance characterization demonstrate that the wettability changes result from a temperature-dominated cation-π interaction between [EMIm][NTf<sub>2</sub>] and PPhEtMA-co-PFDMS brushes.
Role of Type 1 Fimbria- and P Fimbria-Specific Adherence in Colonization of the Neurogenic Human Bladder by Escherichia coli (2002)

Recent clinical studies suggest that the deliberate colonization of the human bladder with a prototypic asymptomatic bacteriuria-associated bacterium, Escherichia coli 83972, may reduce the frequency of urinary tract infection in individuals with spinal cord injuries. However, the mechanism by which E. coli 83972 colonizes the bladder is unknown. We examined the role in bladder colonization of the E. coli 83972 genes papG and fimH, which respectively encode P and type 1 receptor-specific fimbrial adhesins. E. coli 83972 and isogenic papGDelta and papGDelta fimHDelta mutants of E. coli 83972 were compared for their capacities to colonize the neurogenic human bladder. Both strains were capable of stable colonization of the bladder. The results indicated that type 1 class-specific adherence and P class-specific adherence, while implicated as significant colonization factors in experiments that employed various animal model systems, were not required for colonization of the neurogenic bladder in human beings. The implications of these results with regard to the selection of potential vaccine antigens for the prevention of urinary tract infection are discussed.
Crystallization of human interleukin-8. A protein chemotactic for neutrophils and T-lymphocytes. (1990)

Interleukin-8 is a 72-residue peptide which is chemotactic for neutrophils and T-lymphocytes. It crystallizes in space group P3(1)21 or P3(2)21 with unit cell dimensions of a = b = 40.3 and c = 90.1 A. X-ray diffraction data have been measured to 1.6-A resolution.
Molecular cloning of DNA from specific chromosomal regions by microdissection and sequence-independent amplification of DNA (1990)

A method that permits the in vitro amplification and cloning of DNA dissected from specific regions of a chromosome and does not require prior knowledge of the DNA sequence is described. DNA from several different chromosomal loci in the Drosophila melanogaster genome has been isolated by this method. Although the procedure was developed to permit the isolation of DNA sequences from serial sections of a single microdissected polytene chromosome, it should be useful for obtaining DNA clones from specific regions of the nonpolytene chromosomes of other organisms as well.