gebhart/patrepeval huggingface dataset:
The Human‐Specific Action of Intermedilysin, a Homolog of Streptolysin O, Is Dictated by Domain 4 of the Protein (2004)

Intermedilysin is a pore-forming cytolysin belonging to the streptolysin O gene family known as the 'Cholesterol-binding/dependent cytolysins' and is unique within the family in that it is highly humanspecific. This specificity suggests interaction with a component of human cells other than cholesterol, the proposed receptor for the other toxins of the gene family. Indeed, intermedilysin showed no significant degree of affinity to free or liposome-embedded cholesterol. Characterization of intermedilysin undecapeptide mutants revealed that this lack of affinity to cholesterol was a result of the substitutions of intermedilysin in this region. Absorption assays with erythrocyte membranes from various animals, competitive inhibition with domain 4 of intermedilysin and liposome-binding assays of streptolysin O and intermedilysin indicated that cell membrane binding is the human-specific step of intermedilysin action, that the host cell membrane-binding site is located within domain 4 in common with other members of the family and that the receptor for this toxin is not cholesterol. The species specificity of undecapeptide mutants of intermedilysin and streptolysin O and chimeric mutants between intermedilysin and streptolysin O, and intermedilysin and pneumolysin indicated that domain 4 of intermedilysin determines the human-specific action step and the cell-binding site of domain 4 lies within the 56 amino acids of the C-terminal, excluding the undecapeptide region.
1.8 and 1.9 Å resolution structures of thePenicillium amagasakienseandAspergillus nigerglucose oxidases as a basis for modelling substrate complexes (1999)

Glucose oxidase is a flavin-dependent enzyme which catalyses the oxidation of beta-D-glucose by molecular oxygen to delta-gluconolactone and hydrogen peroxide. The structure of the enzyme from Aspergillus niger, previously refined at 2.3 A resolution, has been refined at 1.9 A resolution to an R value of 19.0%, and the structure of the enzyme from Penicillium amagasakiense, which has 65% sequence identity, has been determined by molecular replacement and refined at 1.8 A resolution to an R value of 16.4%. The structures of the partially deglycosylated enzymes have an r.m.s. deviation of 0.7 A for main-chain atoms and show four N-glycosylation sites, with an extended carbohydrate moiety at Asn89. Substrate complexes of the enzyme from A. niger were modelled by force-field methods. The resulting model is consistent with results from site-directed mutagenesis experiments and shows the beta-D-glucose molecule in the active site of glucose oxidase, stabilized by 12 hydrogen bonds and by hydrophobic contacts to three neighbouring aromatic residues and to flavin adenine dinucleotide. Other hexoses, such as alpha-D-glucose, mannose and galactose, which are poor substrates for the enzyme, and 2-deoxy-D-glucose, form either fewer bonds or unfavourable contacts with neighbouring amino acids. Simulation of the complex between the reduced enzyme and the product, delta-gluconolactone, has provided an explanation for the lack of product inhibition by the lactone.
Kinetics of intracellular transport and sorting of lysosomal membrane and plasma membrane proteins. (1987)

We have used monospecific antisera to two lysosomal membrane glycoproteins, lgp120 and a similar protein, lgp110, to compare the biosynthesis and intracellular transport of lysosomal membrane components, plasma membrane proteins, and lysosomal enzymes. In J774 cells and NRK cells, newly synthesized lysosomal membrane and plasma membrane proteins (the IgG1/IgG2b Fc receptor or influenza virus hemagglutinin) were transported through the Golgi apparatus (defined by acquisition of resistance to endo-beta-N-acetylglucosaminidase H) with the same kinetics (t1/2 = 11-14 min). In addition, immunoelectron microscopy of normal rat kidney cells showed that lgp120 and vesicular stomatitis virus G-protein were present in the same Golgi cisternae demonstrating that lysosomal and plasma membrane proteins were not sorted either before or during transport through the Golgi apparatus. To define the site at which sorting occurred, we compared the kinetics of transport of lysosomal and plasma membrane proteins and a lysosomal enzyme to their respective destinations. Newly synthesized proteins were detected in dense lysosomes (lgp's and beta-glucuronidase) or on the cell surface (Fc receptor or hemagglutinin) after the same lag period (20-25 min), and accumulated at their final destinations with similar kinetics (t1/2 = 30-45 min), suggesting that these two lgp's are not transported to the plasma membrane before reaching lysosomes. This was further supported by measurements of the transport of membrane-bound endocytic markers from the cell surface to lysosomes, which exhibited additional lag periods of 5-15 min and half-times of 1.5-2 h. The time required for transport of newly synthesized plasma membrane proteins to the cell surface, and for the transport of plasma membrane markers from the cell surface to lysosomes would appear too long to account for the rapid transport of lgp's from the Golgi apparatus to lysosomes. Thus, the observed kinetics suggest that lysosomal membrane proteins are sorted from plasma membrane proteins at a post-Golgi intracellular site, possibly the trans Golgi network, before their delivery to lysosomes.
Supercooling of Peltier cooler using a current pulse (2002)

The operation of a Peltier cooler can be temporarily enhanced by utilizing the transient response of a current pulse. The performance of such a device, using (Bi,Sb)2Te3-based thermoelectric elements, was examined from −70 to 55 °C. We establish both theoretically and experimentally the essential parameters that describe the pulse cooling effect, such as the minimum temperature achieved, maximum temperature overshoot, time to reach minimum temperature, time while cooled, and time between pulses. Using simple theoretical and semiempirical relationships the dependence of these parameters on the current pulse amplitude, temperature, thermoelectric element length, thermoelectric figure of merit and thermal diffusivity is established. At large pulse amplitudes the amount of pulse supercooling is proportional to the maximum steady-state difference in temperature. This proportionality factor is about half that expected theoretically. This suggests that the thermoelectric figure of merit is the key materials parameter for pulse cooling. For this cooler, the practical optimum pulse amplitude was found to be about three times the optimum steady-state current. A pulse cooler was integrated into a small commercial thermoelectric three-stage cooler and it provided several degrees of additional cooling for a period long enough to operate a laser sensor. The improvement due to pulse cooling is about the equivalent of two additional stages in a multistage thermoelectric cooler.
ANTIGEN-SPECIFIC MEMORY B CELL DEVELOPMENT (2004)

Helper T (Th) cell-regulated B cell immunity progresses in an ordered cascade of cellular development that culminates in the production of antigen-specific memory B cells. The recognition of peptide MHC class II complexes on activated antigen-presenting cells is critical for effective Th cell selection, clonal expansion, and effector Th cell function development (Phase I). Cognate effector Th cell-B cell interactions then promote the development of either short-lived plasma cells (PCs) or germinal centers (GCs) (Phase II). These GCs expand, diversify, and select high-affinity variants of antigen-specific B cells for entry into the long-lived memory B cell compartment (Phase III). Upon antigen rechallenge, memory B cells rapidly expand and differentiate into PCs under the cognate control of memory Th cells (Phase IV). We review the cellular and molecular regulators of this dynamic process with emphasis on the multiple memory B cell fates that develop in vivo.
Restoring Savanna Using Fire: Impact on the Breeding Bird Community (2000)

Abstract Restoration of many terrestrial plant communities involves the reintroduction of fire. However, there have been few studies of the effects of fire on the avifauna during the restoration process. To study the effects of oak savanna restoration on avian communities, breeding birds were censused and the vegetation structure documented in seven experimental burn units (8–18 ha) that had experienced different frequencies of controlled burns during the past 31 years (0–26 burns). Data were analyzed with both direct and indirect gradient analyses using multivariate techniques. The results showed that, as savanna restoration proceeded, there was a general decline in predominantly insectivorous species, particularly those that feed in the upper canopy region (leaves and air space), and a general increase in omnivorous species, particularly those that feed on the ground and in the lower canopy. Insectivorous bark gleaners (woodpeckers) also increased during restoration and were correlated with the increase in standing dead trees resulting from the fires. Overall, savanna restoration resulted in increases in the abundance of many open country bird species, including many species that have been declining in central and eastern North America, including red‐headed woodpecker, Baltimore oriole, eastern kingbird, vesper sparrow, field sparrow, lark sparrow, brown thrasher, American goldfinch, and brown‐headed cowbird. The shifts in species and guilds were correlated with changes in burn frequency and the macro vegetation structure—tree and shrub density, leaf area index, and relative proportion of standing dead trees. The findings show that savanna restoration can increase bird diversity and provide important habitat for uncommon or declining bird species. These birds are most likely attracted to one or more of the distinctive habitat features of the restored savanna environments, including scattered mature trees, standing dead trees and snags, and presence of both shrubby and grassland vegetation. The findings also suggest that restoration ecologists and wildlife biologists will need to work together to achieve desired goals, since different types of savanna restoration efforts may produce different effects on the breeding bird community.
Diffusion Distance for Histogram Comparison (2006)

In this paper we propose diffusion distance, a new dissimilarity measure between histogram-based descriptors. We define the difference between two histograms to be a temperature field. We then study the relationship between histogram similarity and a diffusion process, showing how diffusion handles deformation as well as quantization effects. As a result, the diffusion distance is derived as the sum of dissimilarities over scales. Being a cross-bin histogram distance, the diffusion distance is robust to deformation, lighting change and noise in histogram-based local descriptors. In addition, it enjoys linear computational complexity which significantly improves previously proposed cross-bin distances with quadratic complexity or higher. We tested the proposed approach on both shape recognition and interest point matching tasks using several multi-dimensional histogram-based descriptors including shape context, SIFT, and spin images. In all experiments, the diffusion distance performs excellently in both accuracy and efficiency in comparison with other state-of-the-art distance measures. In particular, it performs as accurately as the Earth Mover’s Distance with much greater efficiency.
Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames. (1996)

An increasing amount of evidence has shown that epitopes restricted to MHC class I molecules and recognized by CTL need not be encoded in a primary open reading frame (ORF). Such epitopes have been demonstrated after stop codons, in alternative reading frames (RF) and within introns. We have used a series of frameshifts (FS) introduced into the Influenza A/PR/8 /34 nucleoprotein (NP) gene to confirm the previous in vitro observations of cryptic epitope expression, and show that they are sufficiently expressed to prime immune responses in vivo. This presentation is not due to sub-dominant epitopes, transcription from cryptic promoters beyond the point of the FS, or internal initiation of translation. By introducing additional mutations to the construct exhibiting the most potent presentation, we have identified initiation codon readthrough (termed scanthrough here, where the scanning ribosome bypasses the conventional initiation codon, initiating translation further downstream) as the likely mechanism of epitope production. Further mutational analysis demonstrated that, while it should operate during the expression of wild-type (WT) protein, scanthrough does not provide a major source of processing substrate in our system. These findings suggest (i) that the full array of self- and pathogen-derived epitopes available during thymic selection and infection has not been fully appreciated and (ii) that cryptic epitope expression should be considered when the specificity of a CTL response cannot be identified or in therapeutic situations when conventional CTL targets are limited, as may be the case with latent viral infections and transformed cells. Finally, initiation codon readthrough provides a plausible explanation for the presentation of exocytic proteins by MHC class I molecules.
Layered and homogeneous films of aluminum and aluminum/silicon with titanium, zirconium, and tungsten for multilevel interconnects (1984)

Layered structures and homogeneous alloy films synthesized by sputter deposition were investigated for use in a VLSI multilevel interconnect technology. Major areas studied include hillock formation, resistivity before and after annealing, film composition and structure reproducibility, interlevel shorts and dry etching. We have demonstrated in this work that aluminum alloyed with silicon and titanium and layered with titanium offers advantages over current technological materials for interconnections in integrated circuits. Measurements of surface roughness and electrical shorts between two levels of metal showed that the hillock densities in the films are, significantly reduced when small amounts (one to two atomic percent) of titanium and silicon are present However, the resistivity of such homogeneous films is 4.5 to 6 µΩ-cm which is higher than standard metallization alloys. When Al/Si was layered with Ti, no hillocks were, observed and the resistivity of the composite films was comparable to standard metallization alloys.
Alprolix (recombinant Factor IX Fc fusion protein): extended half-life product for the prophylaxis and treatment of hemophilia B (2014)

Hemophilia B is a genetic disease caused by mutation of the gene for coagulation protein Factor IX. When severe, the disease leads to spontaneous life-threatening bleeding episodes. Current therapy requires frequent intravenous infusions of therapeutic recombinant or plasma-derived protein concentrates containing Factor IX. Alprolix™ (recombinant Factor IX Fc fusion protein), is a therapeutic Factor IX preparation that has been engineered for a prolonged half-life in circulation, has completed pivotal clinical trials and has been approved recently in the USA, Canada, Australia and Japan for use in the clinic for patients with hemophilia B. This promising therapy should allow patients to use fewer infusions to maintain appropriate Factor IX activity levels in all clinical settings, and its use may be indicated in both on demand and prophylactic treatments.
Effects of manganese on growth of Mycoplasma salivarium and Mycoplasma orale (1994)

The growth of Mycoplasma salivarium ATCC 23064 and Mycoplasma orale ATCC 15539 was inhibited by MnCl2. The growth-inhibitory effect was much more remarkable on M. orale than M. salivarium and was much more remarkable in medium supplemented with 10% (vol/vol) horse serum (HS) than 20% (vol/vol) HS. It was suggested that isolates of Mycoplasma from the oral cavity could be roughly identified as either M. salivarium and M. orale by examination of the growth (color changes) in PPLO broth supplemented with 10% (vol/vol) HS and 0.2 mM MnCl2.
Determination of the Putative Binding site for Fibronectin on Platelet Glycoprotein IIb-IIIa Complex through a Hydropathic Complementarity Approach (1989)

We have applied the principle of complementary hydropathy to the prediction of the binding site for fibronectin (FN) and for the alpha-chain of fibrinogen in the platelet receptor complex glycoprotein (GP) IIb-IIIa. Since both ligands bind to it through their respective RGDS (Arg-Gly-Asp-Ser) domains and since both have been cloned, we were able to deduce the amino acid sequence of the binding site from the nucleotide sequence coding for RGDS in both proteins. The deduced peptides were very similar. Antibodies raised against a synthetic peptide WTVPTA (Trp-Thr-Val-Pro-Thr-Ala) deduced from the cloned rat FN RGDS domain block ADP-mediated platelet aggregation; this block can be overcome by additional fibrinogen. In Western blots of whole cell platelet extracts run under reducing conditions, this antibody binds to a 108-kDa band. It also binds to affinity-purified GP IIIa. Furthermore, it reacts strongly with GP IIIa immunoprecipitated by a commercially available anti-GP IIb-IIIa monoclonal antibody. Binding of affinity-purified GP IIb-IIIa complex to fibronectin is inhibited by the 110-kDa FN fragment. Similar inhibitions can be effected by WTVPTA (Trp-Thr-Val-Pro-Thr-Ala) and GAVSTA (Gly-Ala-Val-Ser-Thr-Ala) predicted from the rat and human fibronectin nucleotide sequences, respectively. GAGSTA (Gly-Ala-Gly-Ser-Thr-Ala) and GARSTA (Gly-Ala-Arg-Ser-Thr-Ala) related to the human peptide but with discrepant hydropathies are noninhibitory.
Amino-terminal sequences of the bacillus anthracis exosporium proteins BCLA and BCLB important for localization and attachment to the spore surface (2008)

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.
Moore or Less the Night Before Christmas (1996)

In turning a poem on its opposite pole, the parodist must be wary of exact opposites to the author's words. They don't always reverse the sense, and they can land you back in the original meaning. Just as two negatives make a positive, "what should appear" = "it can't stay hidden." Keep a copy of Clement Moore's "A Visit From St. Nicholas" next to you to keep track and compare.
Palladium-catalyzed condensation of aryl halides with phenylsulfonylacetonitrile and diethyl cyanomethylphosphonate. (1990)

The palladium(0)-catalyzed condensation of aryl halides with the sodium salts of phenylsulfonylacetonitrile and diethyl cyanomethylphonate in dimethoxyethane gave the corresponding α-phenylsulfonylareneacetonitriles and diethyl arylcyanomethylphosphonates in good yields.The α-phenylsulfonylareneacetonitriles were easily desulfonylated with zinc to give the areneacetonitriles, and the arylcyanomethylphonates were converted to the alkylideneareneacetonitriles by means of the Horner-Emmons reaction.
Investigation of the Conversion Reaction Mechanisms for Binary Copper(II) Compounds by Solid-State NMR Spectroscopy and X-ray Diffraction (2009)

The conversion reaction mechanisms of CuS, CuF2, and CuO during the electrochemical reaction with Li are studied by solid-state 63Cu, 19F, and 7Li nuclear magnetic resonance (NMR) and X-ray diffraction (XRD). For CuS, a two-step reaction is observed that is associated with an insertion reaction involving first limited incorporation of Li into CuS and then a two-phase reaction to form a material with the approximate composition LiCuS. This is followed by a conversion reaction to form Li2S and Cu, Cu1.96S being formed as a side product of the decomposition of LiCuS. Evidence for the insertion phases is found from both NMR and XRD. A direct conversion reaction to form LiF and Cu is seen for CuF2, whereas the 7Li NMR results indicate that CuO can tolerate a small amount of Li substitution before reacting to form Li2O and Cu. Both the diffraction and NMR results indicate that the size of the Cu particles formed on discharge are much larger in the CuS system, which is thought to result from the higher Cu1+ mobilities in the intermediate intercalation compounds LixCuS. The factors that control the possible mechanisms for these conversion reactions are discussed.
Rapid generation of nested chromosomal deletions on mouse chromosome 2 (2000)

Nested chromosomal deletions are powerful genetic tools. They are particularly suited for identifying essential genes in development either directly or by screening induced mutations against a deletion. To apply this approach to the functional analysis of mouse chromosome 2, a strategy for the rapid generation of nested deletions with Cre recombinase was developed and tested. A loxP site was targeted to the Notch1 gene on chromosome 2. A targeted line was cotransfected with a second loxP site and a plasmid for transient expression of Cre. Independent random integrations of the second loxP site onto the targeted chromosome in direct repeat orientation created multiple nested deletions. By virtue of targeting in an F(1) hybrid embryonic stem cell line, F(1)(129S1xCast/Ei), the deletions could be verified and rapidly mapped. Ten deletions fell into seven size classes, with the largest extending six or seven centiMorgans. The cytology of the deletion chromosomes were determined by fluorescent in situ hybridization. Eight deletions were cytologically normal, but the two largest deletions had additional rearrangements. Three deletions, including the largest unrearranged deletion, have been transmitted through the germ line. Several endpoints also have been cloned by plasmid rescue. These experiments illustrate the means to rapidly create and map deletions anywhere in the mouse genome. They also demonstrate an improved method for generating nested deletions in embryonic stem cells.
Optical path length trimming technique using thinfilm heaters for silica-based waveguides on Si (1996)

The authors propose a practical optical path length trimming technique and demonstrate this using thin film heaters for silica based planar lightwave circuits (PLCs). Irreversible refractive index changes up to 1.5 × 10-4 can be obtained to trim the PLC response by simply controlling the heating power and time. This technique is applied successfully to thermo-optic switches to maximise their extinction ratios.
Embedded computation meets the World Wide Web (2000)

An infinitely accessible Web-linked physical environment united by a multitude of tiny servers could mean a life of information ease.