gebhart/patrepeval huggingface dataset:
Identification of the antigenic constituents of Ehrlichia chaffeensis. (1994)

Ehrlichia chaffeensis, the novel etiologic agent of human ehrlichiosis in the United States, was first isolated in 1990 and reported in 1991. To analyze the antigenic components of E. chaffeensis, we cultivated these obligate intracellular bacteria in DH82 cells, purified the ehrlichiae by renografin density gradient centrifugation, and examined the antigens by Western immunoblotting. Rabbit and human antisera to E. chaffeensis revealed more than 20 bands ranging from 20 to 200 kD. The distinct 22-kD protein was heat labile. The rest of the major immunoreactive components were heat stable. The immunoblots of E. chaffeensis were highly similar when probed with antisera to E. chaffeensis, E. canis, and E. ewingii, indicating the close antigenic relationships among the three species. The 22-kD protein cross-reacted only with anti-E. canis serum. The antibody against E. sennetsu reacted strongly with the 66-, 64-, 55-, and 44-kD antigens of E. chaffeensis. The E. risticii antisera reacted strongly with the 55- and 44-kD bands but only faintly with the 66-kD band. The major immunoreactive antigens of E. chaffeensis (66, 55, and 44 kD) showed cross-reactions with all the different antisera tested. The results indicated that E. chaffeensis is antigenically most closely related to E. canis, is less closely related to E. ewingii, and is only distantly related to E. sennetsu and E. risticii.
Gastrulation and Early Mesodermal Patterning in Vertebrates (2003)

The process of gastrulation occurs during the early embryogenesis of vertebrates, immediately following the phase of cleavage and when the embryo is at the blastula stage. Gastrulation results in the formation of the primitive gut or archenteron. With the initial formation of the archenteron, the embryo reaches the gastrula stage. As more broadly defined, gastrulation is the phase of development in which the three primary germ layers are established: the inner endoderm (i.e., the layer closest to the yolk and the layer that forms the archenteron), the outer ectoderm (i.e., the layer on the surface of the egg), and the mesoderm (i.e., the layer interposed between the endoderm and ectoderm).
Cellular Uptake of Antisense Morpholino Oligomers Conjugated to Arginine-Rich Peptides (2004)

Although the sequence specificity, biostability, and low toxicity of PMO (phosphorodiamidate morpholino oligomers) make them good antisense agents to study gene function, their limited ability to cross cell membranes limits their use in cell culture. In this paper we show that conjugation to arginine-rich peptides significantly enhanced the cellular uptake of PMO. The factors that affect the conjugate's cellular uptake and its antisense activity toward a targeted mRNA were investigated. Factors studied include the number of arginines in the peptide, the choice of cross-linker, the peptide conjugation position, the length of the PMO, and the cell culture conditions. Delivery of PMO to the cell nucleus and cytosol required conjugation rather than complexation of peptides to PMO. R(9)F(2)C was best suited to deliver a PMO to its target RNA resulting in the strongest antisense effect. By simply adding the R(9)F(2)C-PMO conjugate into the cell culture medium at low microM concentration, missplicing of pre-mRNA was corrected. This particular peptide-conjugated PMO was more effective than the PMO conjugated to the transmembrane transport peptides of HIV-1 Tat protein, Drosophila antennapedia protein, or to peptides with fewer arginines. Length of PMO did not affect a peptide's delivery efficacy, but all other factors were important. R(9)F(2)C peptide provided a simple and efficient delivery of PMO to a RNA target. Conjugation of peptide to PMO enhances the opportunities to evaluate gene functions in cell cultures.
Novel Biodegradable Poly(disulfide amine)s for Gene Delivery with High Efficiency and Low Cytotoxicity (2008)

Novel biodegradable poly(disulfide amine)s with defined structure, high transfection efficiency, and low cytotoxicity were designed and synthesized as nonviral gene delivery carriers. Michael addition between N, N'-cystaminebisacrylamide (CBA) and three N-Boc protected diamines ( N-Boc-1,2-diaminoethane, N-Boc-1,4-diaminobutane, and N-Boc-1,6-diaminohexane) followed by N-Boc deprotection under acidic condition resulted in final cationic polymers with disulfide bonds, tertiary amine groups in main chains, and pendant primary amine groups in side chains. Polymer structures were confirmed by 1H NMR, and their molecular weights were in the range 3.3-4.7 kDa with narrow polydispersity (1.12-1.17) as determined by size exclusion chromatography (SEC). Acid-base titration assay showed that the poly(disulfide amine)s possessed superior buffering capacity to branched PEI 25 kDa in the pH range 7.4-5.1, which may facilitate the escape of DNA from the endosomal compartment. Gel retardation assay demonstrated that significant polyplex dissociation was observed in the presence of 5.0 mM DTT within 1 h, suggesting rapid DNA release in the reduction condition such as cytoplasm due to the cleavage of disulfide bonds. Genetic transfections mediated by these poly(disulfide amine)s were side-chain spacer length dependent. The poly(disulfide amine) with a hexaethylene spacer, poly(CBA-DAH), had comparable transfection efficiency to bPEI 25 kDa in the tested cell lines, i.e., 293T cells, Hela cells, and NIH3T3 cells. This same poly(disulfide amine) mediated 7-fold higher luciferase expression than bPEI 25 kDa in C2C12 cells (mouse myoblast cell line), a cell line difficult to transfect with many cationic polymers. Furthermore, MTT assay indicated that all three poly(disulfide amine)s/pDNA polyplexes were significantly less toxic than bPEI/pDNA complexes.
Spectral Graph Analyses of Water Hydrogen-Bonding Network and Osmolyte Aggregate Structures in Osmolyte–Water Solutions (2015)

Recently, it was shown that the spectral graph theory is exceptionally useful for understanding not only morphological structural differences in ion aggregates but also similarities between an ion network and a water H-bonding network in highly concentrated salt solutions. Here, we present spectral graph analysis results on osmolyte aggregates and water H-bonding network structures in aqueous renal osmolyte solutions. The quantitative analyses of the adjacency matrices that are graph-theoretical representations of aggregates of osmolyte molecules and water H-bond structures provide the ensemble average eigenvalue spectra and degree distribution. We show that urea molecules form quite different morphological structures compared to other protecting renal osmolyte molecules in water, particularly sorbitol and trimethylglycine, which are well-known protecting osmolytes, and at high concentrations exhibit a strong propensity to form morphological structures that are graph-theoretically similar to that of the water H-bond network. Conversely, urea molecules, even at similarly high concentrations, form separated clusters instead of extended osmolyte-osmolyte networks. This difference in morphological structure of osmolyte-osmolyte aggregates between protecting and destabilizing osmolytes is considered to be an important observation that led us to propose a hypothesis on the osmolyte aggregate growth mechanism via either osmolyte network formation or segregated osmolyte cluster formation. We anticipate that the present spectral graph analyses of osmolyte aggregate structures and their interplay with the water H-bond network structure in highly concentrated renal osmolyte solutions could provide important information on the osmolyte effects of not only water structures but also protein stability in biologically relevant osmolyte solutions.
SF 36 health survey questionnaire: I. Reliability in two patient based studies. (1994)

All eight scales of the SF 36 questionnaire show high reliability when used to monitor health in groups of patients, and at least four scales possess adequate reliability for use in managing individual patients. Further studies are required to test the feasibility of implementing the SF 36 and other outcome measures in routine clinical practice within the health service.
Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins (2017)

Easi-CRISPR solves the major problem of animal genome engineering, namely the inefficiency of targeted DNA cassette insertion. The approach is robust, succeeding for all tested loci. It is versatile, generating both conditional and targeted insertion alleles. Finally, it is highly efficient, as treating an average of only 50 zygotes is sufficient to produce a correctly targeted allele in up to 100% of live offspring. Thus, Easi-CRISPR offers a comprehensive means of building large-scale Cre-LoxP animal resources.
Synthesis of High Density, Size-Controlled Si Nanowire Arrays via Porous Anodic Alumina Mask (2006)

Porous anodic alumina (PAA) masks are employed for the template synthesis of high density silicon nanowire (SiNW) arrays on a silicon substrate by the vapor−liquid−solid method. The uniform-sized ordered arrays of nanopores in the PAA mask anchored to Si(111) substrate are shown to enable the realization of vertically aligned epitaxial SiNWs with uniform diameter and spacing. The average diameter of the wires is 72 nm while the density is 60 wires/μm2. The high packing density and tightly controlled dimensions of SiNWs obtained by this nonlithographic method allow their effective integration into nanodevices for mass production.
Chicken CD4, CD8alphabeta, and CD8alphaalpha T cell co-receptor molecules (1998)

New knowledge has recently been obtained about the evolutionary conservation of CD4, CD8alphaalpha, and CD8alphabeta T cell receptor (TCR) co-receptor molecules between chicken and mammals. This conservation extends from biochemical structure and tissue distribution to function. Panels of monoclonal antibodies and polyclonal antisera against different epitopes of chicken CD8 and CD4 molecules have proven their value in several recent studies. Chicken CD8 allotypes and homozygous strains carrying these allotypes have been established and these strains provide excellent models for further studies. The extensive polymorphism of CD8alpha in chickens has not been observed in any other species, suggesting that CD8alpha and CD8beta have evolved under different selective pressure in the chicken. A large peripheral blood CD4+CD8+ T cell population in chicken resembles that observed in some human individuals but the inheritance of peripheral blood CD4CD8alphaalpha T cells in the chicken is a unique observation, which suggests the presence of a single gene responsible for CD8alpha, but not CD8beta, specific expression. Despite these unique findings in chicken, the data on CD4, CD8alphaalpha, and CD8alphabeta molecules show that they have evolved before the divergence of mammalian and avian branches from their reptilian ancestors.
Towards molecular farming in the future: moving from diagnostic protein and antibody production in microbes to plants (1999)

Molecular farming of pharmaceuticals in plants has the potential to provide almost unlimited amounts of recombinant proteins for use in disease diagnosis and therapy. Transgenic plants are attracting interest as bioreactors for the inexpensive production of large amounts of safe, functional, recombinant macromolecules, such as blood substitutes, vaccines and antibodies. In some cases, the function of expressed recombinant proteins can be rapidly analysed by expression in microbes or by transient expression in intact or virally infected plants. Protein production can be increased by upscaling production in fermenters, using yeast- or plant-suspension cells or by using transient-expression systems. Stable transgenic plants can be used to produce leaves or seeds rich in the recombinant protein for long-term storage or direct processing. This demonstrates the promise for using plants as bioreactors for the molecular farming of recombinant therapeutics, diagnostics, blood substitutes and antibodies. We anticipate that this technology has the potential to greatly benefit human health by making safe recombinant pharmaceuticals widely available.
Cleavage of members of the synaptobrevin/VAMP family by types D and F botulinal neurotoxins and tetanus toxin. (1994)

Tetanus toxin (TeTx) and the various forms of botulinal neurotoxins (BoNT/A to BoNT/G) potently inhibit neurotransmission by means of their L chains which selectively proteolyze synaptic proteins such as synaptobrevin (TeTx, BoNT/B, BoNT/F), SNAP-25 (BoNT/A), and syntaxin (BoNT/C1). Here we show that BoNT/D cleaves rat synaptobrevin 1 and 2 in toxified synaptosomes and in isolated vesicles. In contrast, synaptobrevin 1, as generated by in vitro translation, is only a poor substrate for BoNT/D, whereas this species is cleaved by BoNT/F with similar potency. Cleavage by BoNT/D occurs at the peptide bond Lys59-Leu60 which is adjacent to the BoNT/F cleavage site (Gln58-Lys59) and again differs from the site hydrolyzed by TeTx and BoNT/B (Gln76-Phe77). Cellubrevin, a recently discovered isoform expressed outside the nervous system, is efficiently cleaved by all three toxins examined. For further characterization of the substrate requirements of BoNT/D, we tested amino- and carboxyl-terminal deletion mutants of synaptobrevin 2 as well as synthetic peptides. Shorter peptides containing up to 15 amino acids on either side of the cleavage site were not cleaved, and a peptide extending from Arg47 to Thr116 was a poor substrate for all three toxins tested. However, cleavability was restored when the peptide is further extended at the NH2 terminus (Thr27-Thr116) demonstrating that NH2 terminally located sequences of synaptobrevin which are distal from the respective cleavage sites are required for proteolysis. To further examine the isoform specificity, several mutants of rat synaptobrevin 2 were generated in which individual amino acids were replaced with those found in rat synaptobrevin 1. We show that a Met46 to Ile46 substitution drastically diminishes cleavability by BoNT/D and that the presence of Val76 instead of Gln76 dictates the reduced cleavability of synaptobrevin isoforms by TeTx.
A human 200-kDa protein binds selectively to DNA fragments containing G.T mismatches. (1988)

G.T mispairs, the sole mismatch type that can arise in "resting" mammalian DNA (through spontaneous hydrolytic deamination of 5-methylcytosine), are corrected in vivo with high efficiency and mostly to a G.C. We identified a protein factor, present in HeLa cell extracts, that binds selectively to DNA substrates containing this mismatch. The partially purified protein was shown by gel-filtration chromatography and UV cross-linking experiments to have an apparent molecular mass of 200 kDa. Its binding to G.T mispairs was not influenced by sequences flanking the mismatch, but methylation of guanines either within the mismatch itself or in its immediate vicinity abolished the formation of the protein-DNA complex. The protein appears to lack both endo- and exonuclease activities and requires neither magnesium nor zinc nor ATP for binding. We discuss the possible role of this protein in a repair pathway, which helps mammalian cells counter the mutagenic effect of the hydrolytic deamination of 5-methylcytosine.
Quantum Computation using Vortices and Majorana Zero Modes of apx+ipySuperfluid of Fermionic Cold Atoms (2007)

We propose to use the recently predicted two-dimensional "weak-pairing" px + ipy superfluid state of fermionic cold atoms as a platform for topological quantum computation. In the core of a vortex, this state supports a zero-energy Majorana mode, which moves to finite energy in the corresponding topologically trivial "strong-pairing" state. By braiding vortices in the "weak-pairing" state, unitary quantum gates can be applied to the Hilbert space of Majorana zero modes. For readout of the topological qubits, we propose realistic schemes suitable for atomic superfluids.
Basic fibroblast growth factor mediates transduction of mechanical signals when articular cartilage is loaded (2004)

Cyclical loading of articular cartilage causes bFGF-dependent activation of ERK and synthesis of TIMP-1.
The SYNTAX Score: an angiographic tool grading the complexity of coronary artery disease. (2005)

1. Department of Interventional Cardiology, Erasmus Medical Center, Thoraxcenter Rotterdam, The Netherlands 2. Cardialysis BV, Rotterdam, The Netherlands 3. Department of Cardiothoracic Surgery, Erasmus Medical Center, Thoraxcenter, Rotterdam, The Netherlands 4. Institut Cardiovasculaire Paris Sud, Massy, France 5. San Raffaele Hospital, Milano, Italy 6. Southampton General Hospital, Southampton, UK 7. Ouderkerk aan den ijssel, The Netherlands 8. Boston Scientific Corporation, Maastricht, The Netherlands 9. Boston Scientific Corporation, Natick Massachusetts, USA 10. Herzzentrum, Leipzig, Germany
Computer-based remote programming and control of stimulation units (2011)

This paper describes the architecture of the functional electrical stimulation systems developed in the context of the TIME European project. Contributions are the definition of a generic FES architecture and the specialization of this architecture, depending on the applicative context, by the deployment, the programming and the control of hardware units, notably stimulation ones. This specialization process is managed by a dedicated software environment, named SENIS Manager.
High-performance intraoperative cone-beam CT on a mobile C-arm: an integrated system for guidance of head and neck surgery (2009)

A system for intraoperative cone-beam CT (CBCT) surgical guidance is under development and translation to trials in head and neck surgery. The system provides 3D image updates on demand with sub-millimeter spatial resolution and soft-tissue visibility at low radiation dose, thus overcoming conventional limitations associated with preoperative imaging alone. A prototype mobile C-arm provides the imaging platform, which has been integrated with several novel subsystems for streamlined implementation in the OR, including: real-time tracking of surgical instruments and endoscopy (with automatic registration of image and world reference frames); fast 3D deformable image registration (a newly developed multi-scale Demons algorithm); 3D planning and definition of target and normal structures; and registration / visualization of intraoperative CBCT with the surgical plan, preoperative images, and endoscopic video. Quantitative evaluation of surgical performance demonstrates a significant advantage in achieving complete tumor excision in challenging sinus and skull base ablation tasks. The ability to visualize the surgical plan in the context of intraoperative image data delineating residual tumor and neighboring critical structures presents a significant advantage to surgical performance and evaluation of the surgical product. The system has been translated to a prospective trial involving 12 patients undergoing head and neck surgery - the first implementation of the research prototype in the clinical setting. The trial demonstrates the value of high-performance intraoperative 3D imaging and provides a valuable basis for human factors analysis and workflow studies that will greatly augment streamlined implementation of such systems in complex OR environments.
Na+/Ca2+ exchange inhibition protects the rat heart from ischemia-reperfusion injury by blocking energy-wasting processes (2004)

We have recently reported that exposure of rat hearts to high Ca(2+) produces a Ca(2+) overload-induced contractile failure in rat hearts, which was associated with proteolysis of alpha-fodrin. We hypothesized that contractile failure after ischemia-reperfusion (I/R) is similar to that after high Ca(2+) infusion. To test this hypothesis, we investigated left ventricular (LV) mechanical work and energetics in the cross-circulated rat hearts, which were subjected to 15 min global ischemia and 60 min reperfusion. Sixty minutes after I/R, mean systolic pressure-volume area (PVA; a total mechanical energy per beat) at midrange LV volume (mLVV) (PVA(mLVV)) was significantly decreased from 5.89 +/- 1.55 to 3.83 +/- 1.16 mmHg.ml.beat(-1).g(-1) (n = 6). Mean myocardial oxygen consumption per beat (Vo(2)) intercept of (Vo(2)-PVA linear relation was significantly decreased from 0.21 +/- 0.05 to 0.15 +/- 0.03 microl O(2).beat(-1).g(-1) without change in its slope. Initial 30-min reperfusion with a Na(+)/Ca(2+) exchanger (NCX) inhibitor KB-R7943 (KBR; 10 micromol/l) significantly reduced the decrease in mean PVA(mLVV) and Vo(2) intercept (n = 6). Although Vo(2) for the Ca(2+) handling was finally decreased, it transiently but significantly increased from the control for 10-15 min after I/R. This increase in Vo(2) for the Ca(2+) handling was completely blocked by KBR, suggesting an inhibition of reverse-mode NCX by KBR. alpha-Fodrin proteolysis, which was significantly increased after I/R, was also significantly reduced by KBR. Our study shows that the contractile failure after I/R is similar to that after high Ca(2+) infusion, although the contribution of reverse-mode NCX to the contractile failure is different. An inhibition of reverse-mode NCX during initial reperfusion protects the heart against reperfusion injury.
Primary structure of the human follistatin precursor and its genomic organization. (1988)

Follistatin is a single-chain gonadal protein that specifically inhibits follicle-stimulating hormone release. By use of the recently characterized porcine follistatin cDNA as a probe to screen a human testis cDNA library and a genomic library, the structure of the complete human follistatin precursor as well as its genomic organization have been determined. Three of eight cDNA clones that were sequenced predicted a precursor with 344 amino acids, whereas the remaining five cDNA clones encoded a 317 amino acid precursor, resulting from alternative splicing of the precursor mRNA. Mature follistatins contain four contiguous domains that are encoded by precisely separated exons; three of the domains are highly similar to each other, as well as to human epidermal growth factor and human pancreatic secretory trypsin inhibitor. The genomic organization of the human follistatin is similar to that of the human epidermal growth factor gene and thus supports the notion of exon shuffling during evolution.