gebhart/patrepeval huggingface dataset:
Purification of Bovine Lysosomal α‐Mannosidase, Characterization of its Gene and Determination of two Mutations that Cause α‐Mannosidosis (1997)

Bovine kidney lysosomal alpha-mannosidase was purified to homogeneity and the gene was cloned. The gene was organized in 24 exons that spanned 16 kb and its corresponding cDNA contained an open reading frame of 2997 bp beginning from a putative ATG start codon. The deduced amino acid sequence contained a signal peptide of 50 amino acids adjacent to a protein sequence of 949 amino acids that was cleaved into five peptides in the mature enzyme; starting with the peptide derived from the N-terminal part of this precursor, their molecular masses were 35/38 (peptide a), 11/13 (peptide b), 22 (peptide c), 38 (peptide d) and 13/15 kDa (peptide e). Variation in the degree of N-glycosylation accounts for molecular mass heterogeneities of peptides a, b and e. Peptides a, b and c were disulphide-linked. A T961-->C transition, resulting in Phe321-->Leu substitution, was identified in the cDNA of alpha-mannosidosis-affected Angus cattle. In affected Galloway cattle, a G662-->A transition that causes Arg221-->His substitution was identified. Phe321 and Arg221 are conserved among the alpha-mannosidase class-2 family, indicating that the substitutions resulted from disease-causing mutations in these breeds.
The pixel machine: a parallel image computer (1989)

We describe the system architecture and the programming environment of the Pixel Machine - a parallel image computer with a distributed frame buffer.The architecture of the computer is based on an array of asynchronous MIMD nodes with parallel access to a large frame buffer. The machine consists of a pipeline of pipe nodes which execute sequential algorithms and an array of m &amp;times; n pixel nodes which execute parallel algorithms. A pixel node directly accesses every m -th pixel on every n -th scan line of an interleaved frame buffer. Each processing node is based on a high-speed, floating-point programmable processor.The programmability of the computer allows all algorithms to be implemented in software. We present the mappings of a number of geometry and image-computing algorithms onto the machine and analyze their performance.
Effect of rfaH (sfrB) and temperature on expression of rfa genes of Escherichia coli K-12 (1991)

In order to study the regulation of a large block of contiguous genes at the rfa locus of Escherichia coli K-12 which are involved in synthesis and modification of the lipopolysaccharide core, the transposon TnlacZ was used to generate in-frame lacZ fusions to the coding regions of five genes (rfaQ, -G, -P, -B and -J) within this block. The beta-galactosidase activity of strains in which these fusions had been crossed into the chromosomal rfa locus was significantly decreased when the rfaH11 (sfrB11) allele was introduced and was restored to wild-type levels when these strains were lysogenized with a lambda phage carrying wild-type rfaH. This indicates that the positive regulatory function encoded by rfaH is required throughout this block of genes. In addition, expression of the lacZ fusion to rfaJ was reduced by growth at 42 degrees C, and this correlated with a temperature-induced change in the electrophoretic profile of the core lipopolysaccharide.
Chemical Management for Colorful, Efficient, and Stable Inorganic–Organic Hybrid Nanostructured Solar Cells (2013)

Chemically tuned inorganic-organic hybrid materials, based on CH3NH3(═MA)Pb(I(1-x)Br(x))3 perovskites, have been studied using UV-vis absorption and X-ray diffraction patterns and applied to nanostructured solar cells. The band gap engineering brought about by the chemical management of MAPb(I(1-x)Br(x))3 perovskites can be controllably tuned to cover almost the entire visible spectrum, enabling the realization of colorful solar cells. We demonstrate highly efficient solar cells exhibiting 12.3% in a power conversion efficiency of under standard AM 1.5, for the most efficient device, as a result of tunable composition for the light harvester in conjunction with a mesoporous TiO2 film and a hole conducting polymer. We believe that the works highlighted in this paper represent one step toward the realization of low-cost, high-efficiency, and long-term stability with colorful solar cells.
Sub-10 nm Nanofabrication via Nanoimprint Directed Self-Assembly of Block Copolymers (2011)

Directed self-assembly (DSA) of block copolymers (BCPs), either by selective wetting of surface chemical prepatterns or by graphoepitaxial alignment with surface topography, has ushered in a new era for high-resolution nanopatterning. These pioneering approaches, while effective, require expensive and time-consuming lithographic patterning of each substrate to direct the assembly. To overcome this shortcoming, nanoimprint molds--attainable via low-cost optical lithography--were investigated for their potential to be reusable and efficiently template the assembly of block copolymers (BCPs) while under complete confinement. Nanoimprint directed self-assembly conveniently avoids repetitive and expensive chemical or topographical prepatterning of substrates. To demonstrate this technique for high-resolution nanofabrication, we aligned sub-10 nm resolution nanopatterns using a cylinder-forming, organic-inorganic hybrid block copolymer, polystyrene-block-polydimethylsiloxane (PS-b-PDMS). Nanopatterns derived from oxidized PDMS microdomains were successfully transferred into the underlying substrate using plasma etching. In the development phase of this procedure, we investigated the role of mold treatments and pattern geometries as DSA of BCPs are driven by interfacial chemistry and physics. In the optimized route, silicon molds treated with PDMS surface brushes promoted rapid BCP alignment and reliable mold release while appropriate mold geometries provided a single layer of cylinders and negligible residual layers as required for pattern transfer. Molds thus produced were reusable to the same efficacy between nanoimprints. We also demonstrated that shear flow during the nanoimprint process enhanced the alignment of the BCP near open edges, which may be engineered in future schemes to control the BCP microdomain alignment kinetics during DSA.
Histidine Patch Thioredoxins (1996)

A cluster of surface amino acid residues on Escherichia coli thioredoxin were systematically mutated in order to provide the molecule with an ability to chelate metal ions. The combined effect of two histidine mutants, E30H and Q62H, gave thioredoxin the capacity to bind to nickel ions immobilized on iminodiacetic acid- and nitrilotriacetic acid-Sepharose resins. Even though these two histidines were more than 30 residues apart in thioredoxin's primary sequence, they were found to satisfy the geometric constraints for metal ion coordination as a result of the thioredoxin tertiary fold. A third histidine mutation, S1H, provided additional metal ion chelation affinity, but the native histidine at position 6 of thioredoxin was found not to participate in binding. All of the histidine mutants exhibited decreased thermal stability as compared with wild-type thioredoxin; however, the introduction of an additional mutation, D26A, increased their melting temperatures beyond that of wild-type thioredoxin. The metal chelating abilities of these histidine mutants of thioredoxin were successfully utilized for convenient purifications of human interleukin-8 and -11 expressed in E. coli as soluble thioredoxin fusion proteins.
Hyperfibrinolysis, physiologic fibrinolysis, and fibrinolysis shutdown (2014)

Prognostic study, level III.
Methods to measure sensory function in humans versus animals (2003)

Sensation is perhaps one of the most complex senses. It allows us to experience our environment, and it provides ongoing feedback for the performance of accurate motor tasks. The present methods used for clinical testing of sensation in patients with spinal cord injury (SCI) rely on traditional techniques developed many years ago. This type of testing has been incorporated into the ASIA (American Spinal Injury Association) score, which has become the principal instrument for measuring the recovery of sensory function in humans. Unfortunately, the ASIA score lacks sophistication and is not quantitative. Similar shortcomings are found in the testing of sensation in experimental animal models of SCI. Although highly refined methods have been developed for the study of sensation and pain perception in animals, these methods have not been incorporated for measuring recovery of function in experimental SCI. A review of the available literature suggests that further refined and quantifiable tests need to be developed in this area.
IgG Antibody to Pneumococcal Capsular Polysaccharide in Human Immunodeficiency Virus-Infected Subjects: Persistence of Antibody in Responders, Revaccination in Nonresponders, and Relationship of Immunoglobulin Allotype to Response (1996)

Human immunodeficiency virus (HIV)-infected persons are less likely than are noninfected persons to respond to vaccination with pneumococcal polysaccharides (PPS). Among those who respond, however, similar IgG levels may be achieved. HIV-infected men immunized with pneumococcal vaccine were classified as high- or low-level responders (IgG > or = 1 microgram/mL for > or = 3 of 5 PPS [high] or for < or = 1 PPS [low]). One and 2 years after immunization, geometric mean IgG levels and the percentages of subjects with IgG levels > or = 1 microgram/mL were similar for HIV-infected and for healthy high-level responders (controls) for all PPS except for serotype 8. Among HIV-infected low-level responders, revaccination with a double dose of pneumococcal vaccine did not stimulate IgG responses. Responsiveness of HIV-infected white patients was significantly associated with the Km(1)- negative allotype. These findings support current general recommended guidelines for administering pneumococcal vaccine to HIV-infected persons. Nonresponders will not benefit from revaccination.
Pyroelectric effects in PVDF and P(VDF-TrFE) (2002)

The pyroelectric effects of PVDF and of the 50/50 P(VDF-TrFE) (polyvinylidene fluoride-trifluoroethylene) copolymers have been investigated. A novel experimental method is described which enables the simultaneous measurement of the static and dynamic pyroelectric coefficient on the same sample within one single temperature scan. Static measurements with partially clamped samples showed a significant piezoelectric contribution to the pyroelectric coefficient.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Susceptibility to Friend helper virus leukemias in CXB recombinant inbred mice. (1983)

The seven CXB recombinant inbred strains were tested for susceptibility to Friend helper virus (F-MuLV) hematopoietic neoplasms. BALB/c and CXB-H mice develop erythroblastosis after neonatal inoculation with F-MuLV, while C57BL/6 and the six other RI strains develop lymphoma and myelogenous leukemia. This strain distribution pattern is different from that for H-2, Gpd-1 (linked to Fv-1), Fv-2, Rfv-3, and Cv (linked to Rmcf) but the same as that for Bv, the endogenous ecotropic virus of C57BL/6. However, analysis of crosses segregating Bv show that resistance to F-MuLV erythroblastosis is not linked to Bv. Disease-free survival is shortest for BALB/c mice, intermediate for CXB-H and CXB-J, and longest for C57BL/6 and the other RI strains. We conclude: (a) the major C57BL/6 gene for resistance to F-MuLV erythroblastosis is different from previously identified Friend virus restriction loci; (b) latency for F-MuLV leukemias is controlled by more than one gene; and (c) latency and susceptibility to F-MuLV erythroblastosis are not inherited concordantly in the CXB-RI strains.
Posttranslational protein knockdown coupled to receptor tyrosine kinase activation with phosphoPROTACs (2013)

Posttranslational knockdown of a specific protein is an attractive approach for examining its function within a system. Here we introduce phospho-dependent proteolysis targeting chimeras (phosphoPROTACs), a method to couple the conditional degradation of targeted proteins to the activation state of particular kinase-signaling pathways. We generated two phosphoPROTACs that couple the tyrosine phosphorylation sequences of either the nerve growth factor receptor, TrkA (tropomyosin receptor kinase A), or the neuregulin receptor, ErbB3 (erythroblastosis oncogene B3), with a peptide ligand for the E3 ubiquitin ligase von Hippel Lindau protein. These phosphoPROTACs recruit either the neurotrophic signaling effector fibroblast growth factor receptor substrate 2α or the survival-promoting phosphatidylinositol-3-kinase, respectively, to be ubiquitinated and degraded upon activation of specific receptor tyrosine kinases and phosphorylation of the phosphoPROTACs. We demonstrate the ability of these phosphoPROTACs to suppress the short- and long-term effects of their respective activating receptor tyrosine kinase pathways both in vitro and in vivo. In addition, we show that activation of phosphoPROTACs is entirely dependent on their kinase-mediated phosphorylation, as phenylalanine-containing null variants are inactive. Furthermore, stimulation of unrelated growth factor receptors does not induce target protein knockdown. Although comparable in efficiency to RNAi, this approach has the added advantage of providing a degree of temporal and dosing control as well as cell-type selectivity unavailable using nucleic acid-based strategies. By varying the autophosphorylation sequence of a phosphoPROTAC, it is conceivable that other receptor tyrosine kinase/effector pairings could be similarly exploited to achieve other biological effects.
ChemInform Abstract: The retro‐Diels—Alder Reaction. Part 2. Dienophiles with One or More Heteroatom (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Image inpainting (2000)

Inpainting, the technique of modifying an image in an undetectable form, is as ancient as art itself. The goals and applications of inpainting are numerous, from the restoration of damaged paintings and photographs to the removal/replacement of selected objects. In this paper, we introduce a novel algorithm for digital inpainting of still images that attempts to replicate the basic techniques used by professional restorators. After the user selects the regions to be restored, the algorithm automatically fills-in these regions with information surrounding them. The fill-in is done in such a way that isophote lines arriving at the regions' boundaries are completed inside. In contrast with previous approaches, the technique here introduced does not require the user to specify where the novel information comes from. This is automatically done (and in a fast way), thereby allowing to simultaneously fill-in numerous regions containing completely different structures and surrounding backgrounds. In addition, no limitations are imposed on the topology of the region to be inpainted. Applications of this technique include the restoration of old photographs and damaged film; removal of superimposed text like dates, subtitles, or publicity; and the removal of entire objects from the image like microphones or wires in special effects.
Results of the CEO Project - WWW Management (1996)

This report contains the result of a ‘proof of concept’ study that was performed by the CTIT of the University of Twente, together with ESYS Limited (Guildford, UK) for the Institute of Remote Sensing Applications of the Joint Research Centre (JRC) of the EC (Ispra, Italy). The study is part of the ‘Centre of Earth Observation’ (CEO) programme. The subject of the study was the design and implementation of tools that allow status and utilisation monitoring of networks and distributed information servers. In the specific case of the CEO programme, these information servers are accessible via the WWW and contain large amounts of earth observation data (e.g. satellite pictures). The work division within the project was that ESYS investigated the management applications, which had to run on top of HP-Openview, and the CTIT designed and implemented the management agents. These agents had to include the following Management Information Bases (MIBs): • A HTTP-MIB, with detailed information concerning the WWW document transfer protocol. • A Retrieval Service (RS) MIB, with high level information concerning the WWW document transfer service. • An Information Store (IS) MIB, with information concerning the WWW server and the documents provided by that server. The specifications of these MIBs were presented to the IETF and provided a good starting point for subsequent standardization activities. The agents were implemented as sub-agents of the EMANATE extensible agent package and are currently being tested in a number of field trials.
Current Landscape for T-Cell Targeting in Autoimmunity and Transplantation (2011)

In recent years, substantial advances in T-cell immunosuppressive strategies and their translation to routine clinical practice have revolutionized management and outcomes in autoimmune disease and solid organ transplantation. More than 80 diseases have been considered to have an autoimmune etiology, such that autoimmune-associated morbidity and mortality rank as third highest in developed countries, after cardiovascular diseases and cancer. Solid organ transplantation has become the therapy of choice for many end-stage organ diseases. Short-term outcomes such as patient and allograft survival at 1 year, acute rejection rates, as well as time course of disease progression and symptom control have steadily improved. However, despite the use of newer immunosuppressive drug combinations, improvements in long-term allograft survival and complete resolution of autoimmunity remain elusive. In addition, the chronic use of nonspecifically targeted immunosuppressive drugs is associated with significant adverse effects and increased morbidity and mortality. In this article, we discuss the current clinical tools for immune suppression and attempts to induce long-term T-cell tolerance induction as well as much-needed future approaches to produce more short-acting, antigen-specific agents, which may optimize outcomes in the clinic.
Intracellular disposition and metabolism of fluorescently-labled unmodified and modified oligouncleotides microijjected into mammalian cells (1993)

The intracellular distribution and metabolism of microinjected fluorescently-labeled oligonucleotides (ODNs) have been evaluated using confocal fluorescence microscopy. Fluorescent phosphodiester ODNs, microinjected into the cytoplasm of mammalian cells, rapidly accumulate within the nucleus; the fluorescence disappears with a half-life of 15-20 minutes. Microinjected fluorescent phosphorothioate ODNs remain in the nucleus for more than 24 hours. The persistence of fluorescence depends on the length of the ODN. Modification of the 3' end of phosphodiester ODNs does not significantly slow the rapid disappearance of fluorescence, although certain 3' modifications localize ODNs into the cytoplasm. Using specially designed ODNs, endonuclease activity is demonstrated to exist in the cytoplasm and nucleus. Modification of the 2' position of the ribose rings of a fluorescent phosphodiester oligodeoxynucleotide with O-methyl or O-allyl does not alter its intracellular distribution; however, the 2'-O-allyl modification stabilizes the persistence of fluorescence more than 60-fold compared to the 2'-deoxy control. Thus, the experiments indicate that somatic cells contain nucleolytic activities which degrade microinjected ODNs; however, chemical modification can dramatically circumvent this process.
Rapid and reliable cloning of antibody variable regions and generation of recombinant single chain antibody fragments (1996)

Single chain antibody variable region fragments (sFv), by virtue of their size and method of construction are potentially useful as therapeutic reagents and as tools for exploring cell surface receptor function. sFv offer several advantages over the intact immunoglobulin molecule. For instance, they are expressed from a single transcript and can be molecularly linked to other proteins to generate bispecific sFv molecules or single-chain immunotoxins. The relatively small size of sFv is an advantage in allowing for easier penetrance into tissue spaces, and their clearance rate is exceedingly rapid. sFv are useful for gene therapy since they can be directed to a specific cellular localization and can be fused to retroviral env genes to control viral host range. To prepare sFv to murine and human leukocyte CD antigens, we devised a method for rapid cloning and expression that can yield functional protein within 2-3 weeks of RNA isolation from hybridoma cells. The variable regions were cloned by poly-G tailing the first strand cDNA followed by anchor PCR with a forward poly-C anchor primer and a reverse primer specific for constant region sequence. Both primers contain flanking restriction sites for insertion into PUC19. Sets of PCR primers for isolation of murine, hamster and rat VL and VH genes were generated. Following determination of consensus sequences for a specific VL and VH pair, the VL and VH genes were linked by DNA encoding an intervening peptide linker [usually (Gly4Ser)3] and the VL-link-VH gene cassettes were transferred into the pCDM8 mammalian expression vector. The constructs were transfected into COS cells and sFvs were recovered from spent culture supernatant. We have used this method to generate functional sFv to human CD2, CD3, CD4, CD8, CD28, CD40, CD45 and to murine CD3 and gp39, from hybridomas producing murine, rat, or hamster antibodies. Initially, the sFvs were expressed as fusion proteins with the hinge-CH2-CH3 domains of human IgG1 to facilitate rapid characterization and purification using goat anti-human IgG reagents or protein A. We also found that active sFv could be expressed with a small peptide > or = tag > or = or in a tail-less form. Expression of CD3 (G19-4) sFv tail-less or Ig tailed forms demonstrated increased cellular signalling activity and suggested that sFv have potential for activating receptors.
Identification of In-Gel Digested Proteins by Complementary Peptide Mass Fingerprinting and Tandem Mass Spectrometry Data Obtained on an Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometer (2000)

The present study reports a procedure developed for the identification of SDS-polyacrylamide gel electrophoretically separated proteins using an electrospray ionization quadrupole time-of-flight mass spectrometer (Q-TOF MS) equipped with pressurized sample introduction. It is based on in-gel digestion of the proteins without previous reduction/alkylation and on the capability of the Q-TOF MS to provide data suitable for peptide mass fingerprinting database searches and for tandem mass spectrometry (MS/MS) database searches (sequence tags). Omitting the reduction/alkylation step reduces sample contamination and sample loss, resulting in increased sensitivity. Omitting this step can leave disulfide-connected peptides in the analyte that can lead to misleading or ambiguous results from the peptide mass fingerprinting database search. This uncertainty, however, is overcome by MS/MS analysis of the peptides. Furthermore, the two complementary MS approaches increase the accuracy of the assignment of the unknown protein. This procedure is thus, highly sensitive, accurate, and rapid. In combination with pressurized nanospray sample introduction, it is suitable for automated sample handling. Here, we apply this approach to identify protein contaminants observed during the purification of the yeast DNA mismatch repair protein Mlh 1.