gebhart/patrepeval huggingface dataset:
Equine Chorionic Gonadotrophin purification, from pregnant mare plasma, by affinity chromatography. (2009)

A Gonadotrofina Coriônica Eqüina (eCG) é produzida pela égua prenhe e tem ação folículo estimulante e luteinizante em animais domésticos não eqüídeos. Um pool formado por plasma de 4 éguas prenhes, com média de 69 dias de gestação, foi purificado em coluna cromatográfica com resina de afinidade Blue Sepharose FF (BS). As frações que adsorveram à resina BS foram purificadas em coluna cromatográfica com resina de afinidade Concanavalina A 4B (ConA). As frações que não adsorveram à resina BS também foram purificadas em coluna cromatográfica com resina de afinidade ConA. O mesmo pool de palsma foi diafiltrado, em cartucho de hemodiálise. O diafiltrado foi aplicado em coluna cromatográfica com resina de afinidade ConA. Atividade biológica (UI/mL) do plasma, do diafiltrado e das frações purificadas foram quantificadas por ensaio biológico com ratas impúbres. As atividades biológicas encontradas no plasma e no plasma diafiltrado foram de 3,63 e 5,14UI/mL, respectivamente. A atividade biológica encontrada nas frações que adsorveram à BS foi de 3,50UI/mL. Não foi encontrarda atividade biológica nas frações que não adsorveram à BS. A atividade biológica contida nas frações que adsorveram à BS e que também adsorveram a ConA foi de 3,65UI/mL. O rendimento do processo cromatográfico onde o plasma foi adsorvido pela BS e pela ConA, foi de 69,52%. Não foi encontrada atividade biológica nas frações obtidas da aplicação do plasma diafiltrado em coluna de ConA. O processo cromatográfico com uso de BS seguido de ConA mostou-se eficaz em purificar a eCG do plasma de éguas prenhes.
Myasthenia gravis. Residues of the alpha and gamma subunits of muscle acetylcholine receptor involved in formation of immunodominant CD4+ epitopes. (1994)

We propagated from myasthenia gravis (MG) patients by stimulation in vitro with synthetic sequences (alpha 48-67, alpha 304-322, gamma 75-94 and gamma 321-340) of the human muscle acetylcholine receptor (AChR), CD4+ lines against four 20-residue sequence regions of the AChR alpha and gamma subunits that are recognized by Th cells of most MG patients. Most lines secreted IL-2 and not IL-4, suggesting that they comprise Th1 cells. For three lines we verified that, as reported previously, AChR epitopes are presented by DR molecules: their response to the relevant peptide was abolished by anti-DR Abs. The DR molecules presenting AChR epitopes were identified by testing the response of the lines to the relevant peptide, using APC from donors homozygous for the different DR alleles of the line. We tested the lines with single residue-substituted analogues of the epitope sequence. The results of these experiments indicated that the lines were polyclonal and recognized overlapping epitopes. Their response was abolished by some substitutions, identifying residues common to all epitopes within a given region, whereas other substitutions reduced but did not obliterate the response, indicating residues included in some but not all epitopes recognized by the line. Comparison of the residues involved in epitope formation for different lines supported the conclusion that within the 20-residue immunodominant regions investigated here, the same sequence segment is involved in formation of epitopes, even in DR-discordant patients.
Hydroactive dressings and serum proteins: an in vitro study (1996)

An in vitro approach was used to obtain information about the compatibility of hydroactive dressing materials with the serum proteins which are thought to be relevant to wound healing. Artificial wound fluid was incubated with different hydroactive dressings (Cutinova hydro, Varihesive E, Comfeel Ulcer Dressing and Allevyn), and concentrations of total protein, albumin, immunoglobulin and growth factors were measured after one day of incubation. Cutinova hydro and Allevyn absorbed considerable amounts of fluid. Fluid uptake was lower for the hydrocolloid dressings. An unexpected finding was that Cutinova hydro showed an approximately two-fold increase over control values in the concentration of all proteins tested, indicating a selective absorption of water by this dressing. For the other dressings tested, zero or very low absorption of proteins was found, indicating a basically satisfactory protein compatibility.
Light Modulation of Ferredoxin mRNA Abundance Requires an Open Reading Frame (1994)

Lynn F. Dickey, Thanh-Tuyen Nguyen, George C. Allen, William F. Thompson, Light Modulation of Ferredoxin mRNA Abundance Requires an Open Reading Frame, The Plant Cell, Vol. 6, No. 8 (Aug., 1994), pp. 1171-1176
Changes in cytochrome content and electron transport patterns in Pseudomonas putida as a function of growth phase (1978)

Optical absorbance difference spectra of membrane vesicles prepared from aerobically grown Pseudomonas putida indicated that, when harvested in logarithmic phase, the cells contained one c-type cytochrome and two or three b-type cytochromes, one of which was cytochrome o. As the cells grew into stationary phase and the oxygen concentration of the medium dropped to essentially zero, an additional component believed to be cytochrome d was produced. Both the o- and d-type cytochromes might function as terminal oxidases. No a-type cytochromes could be detected at any stage of growth. Polarographic measurement of oxygen utilization revealed that cyanide and azide are effective inhibitors of the oxidation of ascorbate coupled with 2,6-dichlorophenolindophenol or N,N,N',N'-tetramethyl-p-phenylenediamine in respiratory particles from either log-phase or stationary-phase cells. Reduced nicotinamide adenine dinucleotide- or succinate-dependent oxygen utilization, however, was sensitive to these inhibitors only in log-phase particles. These results indicate that an alternate terminal oxidase may be synthesized by this organism in response to restricted oxygen availability and that branching of the respiratory system may result.
In vivo inhibition of lipopolysaccharide-induced lethality and tumor necrosis factor synthesis by Rhodobacter sphaeroides diphosphoryl lipid A is dependent on corticosterone induction (1992)

Diphosphoryl lipid A from the lipopolysaccharide (LPS) of Rhodobacter sphaeroides (Rs-DPLA) has been demonstrated to block in mice and guinea pigs the increase in the serum tumor necrosis factor (TNF) response induced by highly purified deep rough chemotype LPS from Escherichia coli D31m4 (ReLPS). The present study was designed to determine the role of corticosterone induction by Rs-DPLA and its effect on TNF regulation and survival in lethal endotoxin shock models and to evaluate the ability of Rs-DPLA to induce endotoxin tolerance. Administration of a 100-fold excess of Rs-DPLA 1 h prior to ReLPS administration inhibited the characteristic peak in serum TNF levels induced by LPS. Inhibition was apparent in normal and D-galactosamine (GalN)-sensitized mice and occurred at the pretranslational level, as splenic TNF and interleukin-1 beta mRNAs were present in lower amounts in LPS-stimulated mice pretreated with Rs-DPLA. Consistent with its effects in reducing serum TNF levels, Rs-DPLA pretreatment protected GalN-sensitized mice from a lethal ReLPS challenge. In contrast, Rs-DPLA did not inhibit the increase in the serum TNF response or protect against a lethal ReLPS challenge in parallel experiments with adrenalectomized (Adrex) mice, for which the 50% lethal dose of ReLPS was comparable to that for GalN-sensitized mice. Furthermore, Rs-DPLA appeared to prime Adrex animals and increase the magnitude of the serum TNF response to a suboptimal LPS stimulus. Priming by Rs-DPLA, however, was not observed in normal or GalN-sensitized mice. Although Rs-DPLA by itself was nontoxic and unable to elevate serum TNF levels in any of the models investigated, it did induce a significant increase in the serum corticosterone response and was capable of inducing endotoxin tolerance in normal mice. The inability of Rs-DPLA to protect Adrex mice from a lethal ReLPS stimulus or to inhibit the increase in the serum TNF response suggests that the protective effect of Rs-DPLA in normal or GalN-sensitized animals occurs through corticosterone induction. These results support the concept that endogenous glucocorticoids can modulate the endotoxic effects of LPS by inhibiting the synthesis of inflammatory cytokines.
Parkin and Parkinsonʼs disease (2001)

Parkin is the causative gene for an autosomal recessive form of Parkinson's disease. The gene was discovered in 1998. The parkin gene is a novel gene containing 12 exons spanning over 1.5 Mb and encodes a protein of 465 amino acids with a molecular mass of approximately 52,000 M(r). Various deletion mutations and point mutations have been discovered in patients with autosomal recessive Parkinson's disease. The substantia nigra and the locus coeruleus selectively undergo neurodegeneration without forming Lewy bodies. The parkin gene product, Parkin protein, has a unique structure with a ubiquitin-like domain in the amino-terminus and a RING finger motif in the carboxy terminus. The function of Parkin was not known until recently. During the year 2000, great progress was made in defining its function. First of all, Parkin was found to be a ubiquitin-protein ligase (E3), a component of the ubiquitin system, which is an important adenosine triphosphate-dependent protein degradation machinery. In addition, CDCrel-1, a synaptic vesicle associated protein, was found to be a substrate for Parkin as an E3. Although many studies still need to be performed to elucidate the molecular mechanism of the selective nigral neurodegeneration in this form of familial Parkinson's disease, it will not be too long before this is accomplished. In this review article, we evaluate the developments in this area published since 1 February 2000.
Monitor Alarm Fatigue (2010)

It is standard practice within an intensive care, progressive care, or telemetry unit to rely on physiologic monitor alarms to alert the nurse or other care providers when limits are exceeded or certain dysrhythmias occur. Given the sheer number of potential alarms on equipment within the clinical environment, there is a high risk of nurses becoming desensitized to the sound of patient alarms. Additionally, alarms may be disabled, silenced, or ignored. These practices create a patient safety concern. As Graham and Cvach note, “Physiologic monitors are only as reliable as the clinicians who use them.”1
A Mass Spectrometric Solution to the Address Problem of Combinatorial Libraries (1994)

The molecular weights of femtomole quantities of small peptides attached to polystyrene beads have been determined with imaging time-of-flight secondary ion mass spectrometry. The analysis is made possible by the selective clipping of the bond linking the peptide to a bead with trifluoroacetic acid vapor before the secondary ion mass spectrometry assay. The approach can be applied to large numbers of 30- to 60-micrometer polystyrene beads for the direct characterization of massive combinatorial libraries.
In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell–recognized tumor antigen T-cell epitopes (2017)

Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-specific T cells often are tumoricidal. However, identifying tumor-specific T-cell epitopes is a major challenge. A widely used strategy relies on initial prediction of human leukocyte antigen-binding peptides by <i>in silico</i> algorithms, but the predictive power of this approach is unclear. Here, we used the human tumor antigen NY-ESO-1 (ESO) and the human leukocyte antigen variant HLA-A*0201 (A2) as a model and predicted <i>in silico</i> the 41 highest-affinity, A2-binding 8-11-mer peptides and assessed their binding, kinetic complex stability, and immunogenicity in A2-transgenic mice and on peripheral blood mononuclear cells from ESO-vaccinated melanoma patients. We found that 19 of the peptides strongly bound to A2, 10 of which formed stable A2-peptide complexes and induced CD8<sup>+</sup> T cells in A2-transgenic mice. However, only 5 of the peptides induced cognate T cells in humans; these peptides exhibited strong binding and complex stability and contained multiple large hydrophobic and aromatic amino acids. These results were not predicted by <i>in silico</i> algorithms and provide new clues to improving T-cell epitope identification. In conclusion, our findings indicate that only a small fraction of <i>in silico</i>-predicted A2-binding ESO peptides are immunogenic in humans, namely those that have high peptide-binding strength and complex stability. This observation highlights the need for improving <i>in silico</i> predictions of peptide immunogenicity.
Infestation by Aquatic Weeds of the Fern GenusSalvinia: Its Status and Control (1986)

The paper starts with a report on the growing predominance of aquatic weeds of the genus Salvinia in the waterbodies of the world. The various ways in which Salvinia molesta , particularly, causes pollution and depletion water resources are then reviewed, as are the attempts made so far to control and eradicate Salvinia through chemical, biological, and mechanical, means. It is shown not only that these attempts have failed to achieve their purpose but also that there are possibilities of environmental backlashes being caused by the introduction of chemicals or bioagents into the environment. The importance developing environmentally safe methods of utilization Salvinia has been stressed, so that the cost of mechanical removal of the weed can be offset by the profits earned through its utilization.
The HNK-1 reactive sulfoglucuronyl glycolipids are ligands for L-selectin and P-selectin but not E-selectin. (1993)

E-selectin, L-selectin, and P-selectin are related cell adhesion molecules that bind via their lectin domains to sialyl Lewis x and related carbohydrate determinants. Reports have indicated that sulfated glycolipids and polysaccharides also bind selectins. To extend these findings, we compared binding of selectin-IgG chimeras to immobilized sulfated and sialylated glycosphingolipids. E-, L-, and P-selectin chimeras all bound to surfaces absorbed with 2,3-sialyl Lewis x glycolipid or sulfatide (galactosylceramide I3-sulfate) but not to surfaces adsorbed with control sulfated lipids (octadecyl sulfate, sphingosine sulfate). Notably, the L- and P-selectin chimeras but not E-selectin chimera bound to surfaces adsorbed with sulfoglucuronyl glycosphingolipids (SGNL lipids; e.g., IV3 glucuronylneolactotetraosylceramide V3-sulfate). These unusual lipids have been reported as antigenic determinants for monoclonal IgM antibodies produced in patients with neuropathy associated with paraproteinemia and react with the mouse monoclonal antibody HNK-1. Binding of L- and P-selectin chimeras to SGNL lipids was specifically inhibited by appropriate anti-selectin antibodies. While binding of all three selectin chimeras to sialyl Lewis x was blocked by removal of calcium, binding to SGNL lipid was only modestly reduced by EDTA. Chemically desulfated SGNL lipid retained binding activity for L- and P-selectin chimeras, while methyl esterification of the glucuronic acid eliminated binding. We conclude that SGNL lipids, unlike sialyl Lewis x and sulfatides, selectively support L- and P-selectin but not E-selectin chimera binding. The presence of SGNL lipids on brain microvascular endothelium (and other endothelia) may implicate these molecules in leukocyte trafficking to the nervous system and elsewhere.
Vancomycin-Resistant Staphylococcus aureus Isolate from a Patient in Pennsylvania (2003)

A vancomycin-resistant Staphylococcus aureus (VRSA) isolate was obtained from a patient in Pennsylvania in September 2002. Species identification was confirmed by standard biochemical tests and analysis of 16S ribosomal DNA, gyrA, and gyrB sequences; all of the results were consistent with the S. aureus identification. The MICs of a variety of antimicrobial agents were determined by broth microdilution and macrodilution methods following National Committee for Clinical Laboratory Standards (NCCLS) guidelines. The isolate was resistant to vancomycin (MIC = 32 micro g/ml), aminoglycosides, beta-lactams, fluoroquinolones, macrolides, and tetracycline, but it was susceptible to linezolid, minocycline, quinupristin-dalfopristin, rifampin, teicoplanin, and trimethoprim-sulfamethoxazole. The isolate, which was originally detected by using disk diffusion and a vancomycin agar screen plate, was vancomycin susceptible by automated susceptibility testing methods. Pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA indicated that the isolate belonged to the USA100 lineage (also known as the New York/Japan clone), the most common staphylococcal PFGE type found in hospitals in the United States. The VRSA isolate contained two plasmids of 120 and 4 kb and was positive for mecA and vanA by PCR amplification. The vanA sequence was identical to the vanA sequence present in Tn1546. A DNA probe for vanA hybridized to the 120-kb plasmid. This is the second VRSA isolate reported in the United States.
GT-Scan: identifying unique genomic targets (2014)

GT-Scan can be run via the web at: http://gt-scan.braembl.org.au.
Removal of Viral Contaminants by Monoclonal Antibody Purification of Plasma Proteins (2015)

The transmittance of pathogenic viruses by the widespread administration of protein fractions such as F VIII prepared on a large scale from pooled human plasma has been of growing concern. We have now demonstrated that significant amounts of pathogenic viruses including LAV/HTLVIII may be removed by a new large scale fractionation process for the preparation of human F VIII (Monoclate) which employs immunoaffinity chromatography. Model viruses representative of different virus families and the LAV strain of HIV were added to cryoprecipitate and then the mixture was processed as for Monoclate manufacturing. Virus titers were determined at each step of the fractionation procedures. An overall reduction of at least 6 logs was obtained for the model viruses and the HIV due to the purification process. An added heating step further increased the safety margin for the product resulting in at least an overall reduction of 7-9 logs for HIV. Clinical experience with Monoclate in virgin hemophiliacs has confirmed its viral safety. Our laboratories are exploiting a similar strategy of immunoaffinity chromatography to ensure the viral safety of FIX and protein C preparations derived from plasma.
Self-Assembling Peptide Nanotubes (1996)

The general design criteria and synthesis of four new peptide-based solid-state tubular array structures are described. Peptide nanotubes, which are extended tubular β-sheet-like structures, are constructed by the self-assembly of flat, ring-shaped peptide subunits made up of alternating d- and l-amino acid residues. Peptide self-assembly is directed by the formation of an extensive network of intersubunit hydrogen bonds. In the crystal structures, nanotubes are stabilized by intertubular hydrophobic packing interactions. Peptide nanotubes exhibit good mechanical and thermal stabilities in water and are stable for long periods of times in most common organic solvents including DMF and DMSO. The remarkable stability of peptide nanotubes can be attributed to the highly cooperative nature of the noncovalent interactions throughout the crystal lattice. Nanotube structures were characterized by cryoelectron microscopy, electron diffraction, Fourier-transform infrared spectroscopy, and crystal structure modeling. This study also serves to exemplify the predictive structural aspects of the peptide self-assembly process.
Characterization of Humanized Anti-TAC, an Antibody Directed Against the Interleukin 2 Receptor, Using Electrospray Ionization Mass Spectrometry by Direct Infusion, LC/MS, and MS/MS (1994)

Characterization of a humanized monoclonal antibody (Hu-anti-TAC) directed against a surface protein expressed on T-lymphocytes was performed with an electrospray mass spectrometer. Capillary reversed-phase liquid chromatography (LC)/mass spectrometry (MS) and direct infusion MS were utilized along with tandem MS/MS analysis to confirm the sequence and to determine the sources of heterogeneity in Hu-anti-TAC. The MS analysis was performed on disulfide-reduced and trypsin-digested samples of the antibody. Two forms of diantennary carbohydrate structures were identified and found to be consistent with those reported for the human IgG1 framework. The analysis demonstrated that the N-terminus was modified by conversion of a glutamine residue to pyroglutamic acid. Another source of heterogeneity was the partial removal of the C-terminal lysine residue and was confirmed by mass calculations of tryptic peptides followed by MS/MS sequencing. This study demonstrates that the high sensitivity of electrospray mass spectrometry when combined with capillary chromatography can allow detailed characterization of microgram samples of high molecular weight proteins such as antibodies.
Multiview Geometry for Texture Mapping 2D Images Onto 3D Range Data (2006)

The photorealistic modeling of large-scale scenes, such as urban structures, requires a fusion of range sensing technology and traditional digital photography. This paper presents a system that integrates multiview geometry and automated 3D registration techniques for texture mapping 2D images onto 3D range data. The 3D range scans and the 2D photographs are respectively used to generate a pair of 3D models of the scene. The first model consists of a dense 3D point cloud, produced by using a 3D-to-3D registration method that matches 3D lines in the range images. The second model consists of a sparse 3D point cloud, produced by applying a multiview geometry (structure-from-motion) algorithm directly on a sequence of 2D photographs. This paper introduces a novel algorithm for automatically recovering the rotation, scale, and translation that best aligns the dense and sparse models. This alignment is necessary to enable the photographs to be optimally texture mapped onto the dense model. The contribution of this work is that it merges the benefits of multiview geometry with automated registration of 3D range scans to produce photorealistic models with minimal human interaction. We present results from experiments in large-scale urban scenes.
THE PATH OF CARBON IN PHOTOSYNTHESIS. XXVI. UPTAKE AND TRANSPORT OF METHYLGLUCOPYRANOSIDE THROUGHOUT PLANTS (2010)

14Carbon methyl-β-D-glucopyranoside (14C-MeG) was applied to roots and shoots of Beta vulgaris L. and the label was tracked as it was transported and assimilated, primarily as a plant nutrient. Foliar application resulted in 6.7% of the 14C-MeG absorbed within 15 min of the solution drying into leaves. Roots in liquid medium with dissolved 14C-MeG absorbed approximately 97% of the 14C-label in 22 h. Whether fed in the light or dark, 40% of the 14C-MeG that was applied appeared in the cellulose fraction, incorporated completely intact. Rapid incorporation of 14C-MeG into the insoluble fraction with few 14C-labeled metabolites found in the soluble fraction were observed. In contrast to roots, a higher percentage of 14C-MeG was incorporated into starch and lipids of shoots.