gebhart/patrepeval huggingface dataset:
Isolation and characterization of a cDNA clone encoding a cognate 70-kDa heat shock protein of the chloroplast envelope. (1992)

The translocation of proteins into the endoplasmic reticulum, the mitochondrion, and the chloroplast has recently been shown to involve homologues of the highly conserved 70-kDa heat shock protein (HSP70) family. In this study, we have isolated and sequenced a full-length cDNA clone encoding a cognate 70-kDa heat shock protein of the spinach chloroplast envelope (SCE70). The cDNA insert is 2,535 base pairs long and codes for 653 amino acid residues of a protein with a predicted molecular mass of 71,731 daltons. The deduced amino acid sequence shows a high degree of homology with HSP70 proteins from other organisms. Southern genomic and RNA analyses reveal different hybridization patterns than that observed for a heat-inducible 70-kDa protein gene. The protein synthesized from the SCE70 cDNA insert co-migrates with a 70-kDa polypeptide of the chloroplast envelope following sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Western blot analysis and import studies indicate that SCE70 is associated with the chloroplast outer envelope. The import data suggest that SCE70 is targeted to the envelope membrane via a pathway different from other plastidic precursors but similar to that recently reported for outer envelope proteins SOE1 and OM14.
The retinitis pigmentosa GTPase regulator (RPGR) interacts with novel transport-like proteins in the outer segments of rod photoreceptors (2000)

Mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene cause X-linked retinitis pigmentosa type 3 (RP3), a severe, progressive and degenerative retinal dystrophy eventually leading to complete blindness. RPGR is ubiquitously expressed, yet mutations in the RPGR gene lead to a retina-restricted phenotype. To date, all RP3 associated missense mutations that have been identified are located in the RCC1-homologous domain (RHD) of RPGR. To investigate the molecular pathogenesis of RP3, we screened retinal yeast two-hybrid libraries with the RHD of RPGR. We identified several alternatively spliced gene products, some with retina-restricted expression, that interact specifically with RPGR in vivo and in vitro. Thus, these proteins were named RPGR-interacting protein 1 (RPGRIP1) isoforms. They contain a C-terminal RPGR-interacting domain and stretches of variable coiled-coil domains homologous to proteins involved in vesicular trafficking. The interaction between RPGR and RPGRIP1 isoforms was impaired in vivo by RP3-associated mutations in RPGR. Moreover, RPGR and RPGRIP1 co-localize in the outer segment of rod photoreceptors, which is in full agreement with the retinitis pigmentosa phenotype observed in RP3 patients. The localization of RPGRIP1 at 14q11 makes it a strong candidate gene for RP16. These results provide a clue for the retina-specific pathogenesis in RP3, and hint towards the involvement of RPGR and RPGRIP1 in mediating vesicular transport-associated processes.
Sequencing Genomes: From Individuals to Populations (2009)

The whole genome sequences of Jim Watson and Craig Venter are early examples of personalized genomics, which promises to change how we approach healthcare in the future. Before personal sequencing can have practical medical benefits, however, and before it should be advocated for implementation at the population-scale, there needs to be a better understanding of which genetic variants influence which traits and how their effects are modified by epigenetic factors. Nonetheless, for forging links between DNA sequence and phenotype, efforts to sequence the genomes of individuals need to continue; this includes sequencing sub-populations for association studies which analyse the difference in sequence between disease affected and unaffected individuals. Such studies can only be applied on a large enough scale to be effective if the massive strides in sequencing technology that have recently occurred also continue.
Mutational analysis of the helical hairpin region of diphtheria toxin transmembrane domain. (1994)

Entry of the catalytic domain of diphtheria toxin into the cytoplasma of eukaryotic cells depends on insertion of the T (transmembrane) domain into the endosomal membrane, a process triggered by low pH. To probe the mechanism of insertion, we mutated ionizable residues within the helical hairpin region of the T domain. Only three mutations caused significant effects on cytotoxicity, D295K, E349K, and D352K. Each of these represents a substitution of a basic for an acidic residue at the tip of a helical hairpin. Substitution of Lys for Glu349 or Asp352, in the TH8/9 hairpin, reduced toxicity for Vero cells > 100-fold, whereas a Lys substitution for Asp295, one of 3 acidic residues in the TH5/6/7 hairpin, caused a less marked reduction. All three mutations also altered the pH-dependent formation, and/or ion conductance, of channels formed by the toxin in artificial bilayers or the plasma membrane. E349K or D352K did not alter the pH dependence of conformational changes in the toxin occurring near pH 5. Our findings support the hypothesis that the TH8/9 hairpin inserts into the endosomal membrane after low pH-mediated partial unfolding of the T domain. A positive residue at the tip of this hairpin apparently inhibits insertion and blocks toxin action. The ion-conducting properties of channels formed by selected mutants, described elsewhere, are consistent with this model. The status of the TH5/6/7 hairpin in the integral membrane form of the T domain remains uncertain.
Influence of breathing pattern on oxygen exchange during hypoxia and exercise (1975)

During hypoxia, arterial oxygen saturation (SaO2) measured by ear oximeter shows cyclic fluctuations which are related to the pattern and rate of breathing. Continuous recordings of SaO2 may be corrected for distortion, due to circulatory transport, to yield approximate values for pulmonary end-capillary saturation (Sc'O2). This permits calculation of the corresponding end-capillary PO2 (Pc'O2). We have used this technique to study the effect of spontaneous and imposed breathing patterns on mean Pc'O2, amplitude of Pc'O2 (delta Pc'O2) and minute ventilation (VE). The studies were conducted during mild hypoxia, at rest and exercise. The amplitude of delta Pc'O2 is inversely related to breathing frequency. When frequency is constant, patterns with with prolonged expiration or end-expiratory pauses produce large delta Pc'O2 and greater VE. This effect is reversed with prolonged inspiration or end-inspiratory pauses. Spontaneous breathing patterns produced smaller delta Pc'O2, with lower VE than imposed patterns. These findings are compatible with animal studies which suggest the magnitude of PaO2 fluctuations produced by the breathing pattern may act as a feedback stimulus to ventilation. The breathing patterns, which are spontaneously chosen, produce the minimum delta Pc'O2 and VE.
Circulating Long-Chain ω-3 Fatty Acids and Incidence of Congestive Heart Failure in Older Adults: The Cardiovascular Health Study (2011)

National Institutes of Health.
Acute and Chronic Cardiovascular Effects of Doxorubicin in the Dog (1980)

We evaluated the acute hemodynamic effects of doxorubicin in the open-chest dog. Doxorubicin at doses of 1-4 mg/kg administered over 2 min produced profound hemodynamic changes that were similar to those produced by histamine. These changes persisted despite administering the drug as a slow infusion. Histamine release in peripheral tissues was documented by a marked increase in venous histamine levels following doxorubicin administration. The heart extracted histamine during a period when arterial levels were increased, as indicated by consistently low coronary sinus/aortic ratios. Secondary catecholamine release occurred in response to histamine and histamine-mediated hemodynamic effects. Immunoreactive prostaglandins E and F were increased in coronary sinus blood beginning 30 min after the initiation of a continuous infusion of doxorubicin, and increased slowly thereafter. H1- and H2-receptor blockade with diphenhydramine and cimetidine prevented the early (2-30 min postinfusion) effects of doxorubicin, and combined histaminergic and adrenergic blockade prevented the late effects. A dose of doxorubicin (1 mg/kg) that released histamine and catecholamines produced primary cardiac effects acutely and a cardiomyopathy when administered chronically. The release of vasoactive substances could be part of the pathogenetic mechanism of anthracycline cardiomyopathy.
Tunable dispersion compensation at 10 Gb/s and 40 Gb/s using multicavity all-pass etalons (2004)

Our tunable dispersion compensator devices based on multiple cavity all-pass etalons are designed to compensate all channels throughout the C- and L-bands and appropriate for 10 Gb/s and 40 Gb/s applications. Detailed characterization of devices and system experimental results will be presented.
Symmetry Controls the Face Geometry of DNA Polyhedra (2009)

Two complementary strategies have been developed to control the face geometry during the self-assembly of DNA polyhedra from branched DNA nanomotifs (tiles). In these approaches, any two interacting tiles are not equivalent in terms of either sequence or orientation; thus, each face must contain an even number of tiles. As a demonstration, DNA cubes, whose each face contains four tiles, have been assembled through these approaches.
microRNA‐directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems (2005)

Class III homeodomain-leucine zipper proteins regulate critical aspects of plant development, including lateral organ polarity, apical and lateral meristem formation, and vascular development. ATHB15, a member of this transcription factor family, is exclusively expressed in vascular tissues. Recently, a microRNA (miRNA) binding sequence has been identified in ATHB15 mRNA, suggesting that a molecular mechanism governed by miRNA binding may direct vascular development through ATHB15. Here, we show that miR166-mediated ATHB15 mRNA cleavage is a principal mechanism for the regulation of vascular development. In a gain-of-function MIR166a mutant, the decreased transcript level of ATHB15 was accompanied by an altered vascular system with expanded xylem tissue and interfascicular region, indicative of accelerated vascular cell differentiation from cambial/procambial cells. A similar phenotype was observed in Arabidopsis plants with reduced ATHB15 expression but reversed in transgenic plants overexpressing an miR166-resistant ATHB15. ATHB15 mRNA cleavage occurred in standard wheat germ extracts and in Arabidopsis and was mediated by miR166 in Nicotiana benthamiana cells. miR166-assisted ATHB15 repression is likely to be a conserved mechanism that regulates vascular development in all vascular plants.
Isolation and characterization of a full-length expressible cDNA for human hypoxanthine phosphoribosyl transferase. (1983)

We have cloned a full-length 1.6-kilobase cDNA of a human mRNA coding for hypoxanthine phosphoribosyltransferase (HPRT; IMP:pyrophosphate phosphoribosyltransferase, EC 2.4.2.8) into a simian virus 40-based expression vector and have determined its full nucleotide sequence. The inferred amino acid sequence agrees with a partial amino acid sequence determined for authentic human HPRT protein. Transfection of HPRT-deficient mouse LA9 cells with the purified plasmid leads to the expression of human HPRT enzyme activity in cells stably transfected and selected for enzyme activity in hypoxanthine/aminopterin/thymidine medium.
Fusion between immunoglobulin‐secreting and nonsecreting myeloma cell lines (1976)

The defects in two nonsecreting variant clones of the mouse plasmacytoma MOPC 21 (P3) were studied by tissue culture methods. The variants (NSI and NSIII) do not synthesize detectable heavy chains. NSI synthesizes, but does not secrete, light chains and NSIII does not synthesize light chain. A screening procedure was used allowing the detection of revertant cells secreting immunoglobulin. The method is based on a hemolytic plaque assay using anti-immunoglobulin-coated red cells. No revertants were detected among 2 x 10(7) cells. Both variant lines were fused to another myeloma line (PI) which secretes a complete immunoglobulin and excess light chains. Analysis of the products by isoelectric focusing showed that in the hybrids there was no reactivation of synthesis of the nonexpressed chains. The defects leading to loss of synthesis cannot therefore be complemented in the hybrid lines. The secretion of light chain in NSI, on the other hand, could be complemented in the hybrid but the light chain was only secreted as part of a new immunoglobulin hybrid molecule.
Polymorphisms in the human cysteine-rich secretory protein 2 (CRISP2) gene in Australian men (2008)

Although none of the many polymorphisms identified herein showed a significant association with male infertility, functional studies suggested that the C196R polymorphism may compromise CRISP2 function.
In Situ Cross-Linking of Elastin-like Polypeptide Block Copolymers for Tissue Repair (2007)

Rapid cross-linking of elastin-like polypeptides (ELPs) with hydroxymethylphosphines (HMPs) in aqueous solution is attractive for minimally invasive in vivo implantation of biomaterials and tissue engineering scaffolds. In order to examine the independent effect of the location and number of reactive sites on the chemical cross-linking kinetics of ELPs and the mechanical properties of the resulting hydrogels, we have designed ELP block copolymers comprised of cross-linkable, hydrophobic ELP blocks with periodic Lys residues (A block) and aliphatic, hydrophilic ELP blocks with no cross-linking sites (B block); three different block architectures, A, ABA, and BABA were synthesized in this study. All ELP block copolymers were rapidly cross-linked with HMPs within several minutes under physiological conditions. The inclusion of the un-cross-linked hydrophilic block, its length relative to the cross-linkable hydrophobic block, and the block copolymer architecture all had a significant effect on swelling ratios of the cross-linked hydrogels, their microstructure, and mechanical properties. Fibroblasts embedded in the ELP hydrogels survived the cross-linking process and remained viable for at least 3 days in vitro when the gels were formed from an equimolar ratio of HMPs and Lys residues of ELPs. DNA quantification of the embedded cells indicated that the cell viability within triblock ELP hydrogels was statistically greater than that in the monoblock gels at day 3. These results suggest that the mechanical properties of ELP hydrogels and the microenvironment that they present to cells can be tuned by the design of the block copolymer architecture.
Ultrasound-Assisted, Base-Catalyzed Oxidation of 4,6-Dimethyldibenzothiophene in a Biphasic Diesel−Acetonitrile System (2004)

New stricter regulations are being imposed on diesel quality for sulfur content worldwide. Recalcitrant aromatic sulfur compounds such as 4,6-dimethyldibenzothiophene (4,6-DMDBT) are resistant to removal by hydrodesulfurization, because of their low reactivity and sterically hindering structure. Oxidative desulfurization is one of the alternatives that are being investigated for this purpose. In this study, an oxidative system composed of sodium carbonate and hydrogen peroxide was investigated in a biphasic system of diesel and acetonitrile. Ultrasonic methods were applied for the intensive mixing of the biphasic system. The effects of different operating conditionsincluding temperature, amount of oxidant, and the base concentrationwere investigated. Reduction of the DMDBT content by >90% was achieved in the diesel samples. The activation energy of pseudo-first-order reaction for DMDBT was determined to be 57 kJ/mol.
Kinematic analysis of generalized adaptive trusses (1991)

Adaptive trusses offer the greatest stiffness and strength for a given weight of any articulated structure or mechanism. Because of this, there are many potential extraterrestrial applications of these variable-geometry trusses, including serpentine manipulators, payload isolation, tracking, pointing and docking mechanisms, and gimbals. All of these applications will require the ability to precisely control the kinematic parameters of the mechanism, including position, velocity, and acceleration. This paper explores the fundamental nature of adaptive trusses by examining the basic truss elements or unit cells. A general method for analyzing forward and inverse motion of all the basic truss units is presented, followed by a more efficient formulation for the octahedral unit cell. Finally, general closed-form techniques are presented for finding velocity, acceleration, and all higher derivatives of truss motion.
Thiyl Radicals in Ribonucleotide Reductases (1996)

The ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii catalyzes adenosylcobalamin (AdoCbl)-dependent nucleotide reduction, as well as exchange of the 5' hydrogens of AdoCbl with solvent. A protein-based thiyl radical is proposed as an intermediate in both of these processes. In the presence of RTPR containing specifically deuterated cysteine residues, the electron paramagnetic resonance (EPR) spectrum of an intermediate in the exchange reaction and the reduction reaction, trapped by rapid freeze quench techniques, exhibits narrowed hyperfine features relative to the corresponding unlabeled RTPR. The spectrum was interpreted to represent a thiyl radical coupled to cob(II)alamin. Another proposed intermediate, 5'-deoxyadenosine, was detected by rapid acid quench techniques. Similarities in mechanism between RTPR and the Escherichia coli ribonucleotide reductase suggest that both enzymes require a thiyl radical for catalysis.
Chemical Transformations in Individual Ultrasmall Biomimetic Containers (1999)

Individual phospholipid vesicles, 1 to 5 micrometers in diameter, containing a single reagent or a complete reaction system, were immobilized with an infrared laser optical trap or by adhesion to modified borosilicate glass surfaces. Chemical transformations were initiated either by electroporation or by electrofusion, in each case through application of a short (10-microsecond), intense (20 to 50 kilovolts per centimeter) electric pulse delivered across ultramicroelectrodes. Product formation was monitored by far-field laser fluorescence microscopy. The ultrasmall characteristic of this reaction volume led to rapid diffusional mixing that permits the study of fast chemical kinetics. This technique is also well suited for the study of reaction dynamics of biological molecules within lipid-enclosed nanoenvironments that mimic cell membranes.
High power superluminescent diode source (1994)

A high power superluminescent tapered GaAlAs amplifier source is described which produces 165 mW of broadband, diffraction limited emission, and 470 mW when seeded by a conventional low power SLD. A maximum of 252 mW was transmitted through a singlemode fibre.
Automatic Location for Multi-Symbology and Multiple 1D and 2D Barcodes (2013)

Multi-symbology barcode location is a practical and challenging issue. Image-based barcode recognition techniques are robust and extendable approaches for reading versatile one-dimensional (1D) and two-dimensional (2D) barcodes. Most methods may work for a single 1D or 2D barcode or rely on a unique pattern to locate a single 1D or 2D barcode. This work proposes a general localization framework for extraction of real barcodes under complex backgrounds when multiple symbology types exist in the same snapshot for 1D barcodes, 2D barcodes, or both. There are five steps of the proposed algorithm: image grayscale conversion, adaptive thresholding, application of a modified run length smearing algorithm, connected-component labeling, and barcode verification. Experimental results indicate that the proposed approach can locate multiple barcodes and multi-symbology barcodes in complex backgrounds with acceptable accuracy.
Perfluorocarbons in the Twenty-First Century: Clinical Applications as Transfusion Alternatives (1995)

The risks of allogeneic transfusion are well known to physicians and have prompted a search for alternatives. Perfluorocarbons were introduced into clinical trials in the early 1980's with the hope that these products would develop into acceptable blood substitutes. Unfortunately, the limited potency, short half-life, and potential toxicity of these early formulations coupled with unrealistic expectations for efficacy prevented the perfluorocarbons from playing a significant role in transfusion medicine. Recent changes in formulation to improve efficacy and eliminate toxicity have stimulated renewed interest in perfluorocarbons as alternatives to allogeneic transfusion. Our recent work has focused on the role of perfluoroctylbromide (PFOB), a second generation perfluorocarbon, as an adjunct to autologous transfusion and acute normovolemic hemodilution (ANH), rather than as a total blood substitute. Initial animal experiments have shown the ability of small doses of PFOB to maintain oxygen delivery without the need for blood transfusion in the setting of hemodilution. Our presentation will focus on subsequent clinical work using PFOB as an alternative to both allogeneic and autologous blood transfusion during ANH. We believe that perfluorocarbons such as PFOB will have a significant role in the future as one of several, additive alternatives to blood transfusion.
Basic fibroblast growth factor inhibits mineralization but induces neuronal differentiation by human dental pulp stem cells through a FGFR and PLCγ signaling pathway (2011)

Basic fibroblast growth factor (basic FGF) has pivotal roles in the function of various cell types. Here, we report the effects of basic FGF in the regulation of dental pulp stem cell (DPSC) behaviors including maintaining stemness and directing differentiation. Cells isolated from human dental pulp tissues exhibited stem cell properties including the expression of mRNA markers for embryonic and mesenchymal stem cells, the expression of Stro-1, and the multipotential differentiation. Basic FGF stimulated colony-forming units of DPSCs and up-regulated the expression of the embryonic stem cell markers; Oct4, Rex-1, and Nanog. Moreover, osteogenic medium containing basic FGF inhibited alkaline phosphatase enzymatic activity and mineralization of DPSCs. On the contrary, basic FGF appeared to be an influential growth factor in the neurogenic differentiation of DPSCs. In the presence of basic FGF, increased DPSCs neurosphere size and the up-regulation of neurogenic markers were noted. Inhibitors of FGFR or PLCγ were able to ablate the basic FGF-induced neuronal differentiation of DPSCs. Taken together, these results suggest basic FGF may be involved in the mechanisms controlling DPSCs cell fate decisions.
A cucurbituril-based molecular switch (1990)

W. L. Mock and J. Pierpont, J. Chem. Soc., Chem. Commun., 1990, 1509 DOI: 10.1039/C39900001509
Abstract 16127: Effect of REGN727/SAR236553 Anti-Proprotein Convertase Subtilisin/Kexin Type 9 Fully Human Monoclonal Antibody in Patients with Elevated Triglycerides/Low High-Density Lipoprotein Cholesterol: Data from Three Phase 2 Studies (NCT:01266876; 01288469; 01288443) (2012)

Background: Low-density lipoprotein cholesterol (LDL-C) is regarded as the primary target for risk reduction in hypercholesterolemia. However, patients with associated high triglycerides (TGs) and ...