gebhart/patrepeval huggingface dataset:
Structure and function of signaling proteins (2004)

We have investigated ligand protein interactions for two major signaling proteins, glutamate receptors and soluble guanylyl cyclase, using various spectroscopic methods with the aim of understanding the ligand control of protein functions that play important roles in various physiological processes. Glutamate receptors are the main excitatory neurotransmitter receptors in the mammalian central nervous system. They are essential in memory and learning, and play roles in a number of diseases and injury states. This work was aimed at gaining insight into the allosteric mode of function regulation in the glutamate receptors. We first used UV-Vis spectroscopy to clearly establish that the electronic environment of antagonists were similar in the isolated ligand binding domain of the receptor (S1S2) as in the native full receptors expressed in cells. Then the specific ligand protein interactions were characterized by using Fourier transform infrared (FTIR) spectroscopy. This allowed us to perform a time resolved study at the identified vibrations arising from the protein and ligand (glutamate) due to ligand binding. We focused on a mutant in which the kinetic steps were slower relative to the wild type receptor. These studies indicate that in the first step of ligand binding, the ligand glutamate docks at the α-carboxylate inducing large conformational changes in the protein (secondary structure), and the second step is established with small rearrangements resulting in the ligated state. Guanylate cyclase (sGC) converts GTP into second messenger cGMP upon activation by nitric oxide (NO). NO converts sGC into a high enzyme activity state, while carbon monoxide (CO) binding to sGC has little effect on the activity. The CO bound form exhibits high activity in the presence of allosteric effector, BAY-41-2272. Preliminary data indicated that the six coordinate heme in the CO-sGC, is converted to two new species, a five coordinate and a different six coordinate form. We have performed a systematic study of varying the concentration of BAY and temperature to determine the extent of the two forms by FTIR spectroscopy. These studies will be correlated to enzyme activity with the aim of obtaining insight into the role of these two species.
The wood from the trees: The use of timber in construction (2016)

Trees, and their derivative products, have been used by societies around the world for thousands of years. Contemporary construction of tall buildings from timber, in whole or in part, suggests a growing interest in the potential for building with wood at a scale not previously attainable. As wood is the only significant building material that is grown, we have a natural inclination that building in wood is good for the environment. But under what conditions is this really the case? The environmental benefits of using timber are not straightforward; although it is a natural product, a large amount of energy is used to dry and process it. Much of this can come from the biomass of the tree itself, but that requires investment in plant, which is not always possible in an industry that is widely distributed among many small producers. And what should we build with wood? Are skyscrapers in timber a good use of this natural resource, or are there other aspects of civil and structural engineering, or large-scale infrastructure, that would be a better use of wood? Here, we consider a holistic picture ranging in scale from the science of the cell wall to the engineering and global policies that could maximise forestry and timber construction as a boon to both people and the planet.
Murine dendritic cells transduced with an adenoviral vector expressing a defined tumor antigen can overcome anti-adenovirus neutralizing immunity and induce effective tumor regression. (1999)

In this study transduced dendritic cells (DCs) were used to enhance immunogenecity of a specific tumor antigen. Using a polyoma middle T (PyMT) transgenic mammary carcinoma model we found that injections of DCs transduced with an adenoviral (Ad) vector expressing PyMT (DCAd-PymT) led to potent specific anti-tumor immunity. Efficacy was not affected by neutralizing Abs (high or low titers) and naive animals did not produce detectable anti-Ad Abs following two injections of transduced DCs. Repeated injections of transduced DCs significantly improved therapeutic efficacy in mice with established lung metastases. These data emphasize the ability of Ad-infected DCs to: i) minimize anti-Ad Ab production, ii) overcome pre-existing anti-Ad humoral immunity, and iii) improve vaccination efficacy when injected more than once.
Suppression of Tumor Growth and Metastasis by Simultaneously Blocking Vascular Endothelial Growth Factor (VEGF)–A and VEGF-C with a Receptor-Immunoglobulin Fusion Protein (2010)

The major cause of cancer mortality is the metastatic spread of tumor cells that can occur via multiple routes, including the vascular system and the lymphatic system. In this study, we developed an IgG-like fusion protein molecule [vascular endothelial growth factor (VEGF) receptor 31-immunoglobulin (VEGFR31-Ig)] which could simultaneously bind the angiogenic growth factor VEGF-A and the lymphangiogenic growth factor VEGF-C. Importantly, VEGFR31-Ig exhibited VEGF-A-binding affinity similar to that of VEGFTrap, the most potent VEGF-A binder, and VEGF-C-binding affinity comparable with that of the soluble fusion protein VEGFR3-Ig (sVEGFR3). Pharmacokinetic analysis in mice showed that VEGFR31-Ig had improved pharmacokinetic properties compared with either VEGFTrap or sVEGFR3. In a highly metastatic human hepatocellular carcinoma (HCCLM3) model in severe combined immunodeficient mice, VEGFR31-Ig potently blocked both tumor angiogenesis and lymphangiogenesis, effectively inhibiting primary tumor growth and metastasis to lungs and lymph nodes. In contrast, VEGFTrap only suppressed primary tumor growth and metastasis to lungs by inhibiting tumor angiogenesis, whereas VEGFR3 was only effective in suppressing tumor metastasis to lymph nodes by blocking tumor lymphangiogenesis. Although a combination of VEGFTrap (25 mg/kg twice weekly) and sVEGFR3 (25 mg/kg twice weekly) can achieve the same therapeutic effect as VEGFR31-Ig (25 mg/kg twice weekly) in the HCCLM3 xenograft mouse model, developing two separate receptor-Ig fusion proteins for clinical use as combination therapy is impractical, mainly owing to regulatory hurdles and cost. Taken together, the VEGFR31-Ig fusion protein presented here has been suggested to have great potential for the treatment of metastatic cancer.
Simultaneous analysis of diphenhydramine and a stable isotope analog (2H10)diphenhydramine using capillary gas chromatography with mass selective detection in biological fluids from chronically instrumented pregnant ewest (1993)

This report describes both the synthesis of a stable isotope analog of the H1 receptor antagonist diphenhydramine (DPHM), and the simultaneous quantitation of DPHM and a deuterated stable isotope analog of DPHM, viz. (2H10)DPHM in biological fluids from the chronically instrumented pregnant ewe. (2H10)DPHM was synthesized and purified, and both its structure and purity were verified. Biological samples were prepared for analysis using liquid-liquid extraction prior to capillary gas chromatography/mass spectrometry. The method employed electron impact ionization with selective ion monitoring of ions with m/z 165 for DPHM and m/z 173 for (2H10)DPHM. The minimal quantifiable concentration of DPHM and (2H10)DPHM from a 1.0 ml sample was 2.0 ng ml-1 in fetal and maternal plasma, fetal tracheal fluid and amniotic fluid. The method was validated from 2.0 ng ml-1 to 200.0 ng ml-1 for both DPHM and (2H10)DPHM in plasma, fetal tracheal fluid and amniotic fluid. Differences in the disposition between DPHM and (2H10)DPHM were not apparent during a control experiment in which both labeled and unlabeled DPHM were administered to a chronically instrumented fetal lamb. This method provides the required sensitivity and selectivity for the simultaneous quantitation of unlabeled and labeled DPHM during pharmacokinetic experiments conducted in near-term pregnant sheep.
Adsorption of Carbon Dioxide and Methane and Their Mixtures on an Activated Carbon:  Simulation and Experiment (1999)

The aim of this work is to predict the adsorption of pure-component and binary mixtures of methane and carbon dioxide in a specific activated carbon, A35/4, using grand canonical Monte Carlo (GCMC) simulation. Methane is modeled as a one-center Lennard-Jones (LJ) fluid and carbon dioxide as a two-center LJ plus point quadrupole fluid. Experimental adsorption data for the system have been obtained with a new flow desorption apparatus. The pore size distribution (PSD) for the carbon was determined from both of the experimental CH4 and CO2 isotherms at 293 K. To extract numerically the PSD, GCMC-simulated isotherms for both pure components in slit-shaped pores ranging from 5.7 to 72.2 Å were used. Using only pure experimental CO2 isotherm data, it was not possible to determine a PSD that allowed a reasonable prediction of the pure methane adsorption. However, with both experimental data sets for the pure components, it was possible to derive a PSD that allowed both experimental pure-component isotherms to be fitted. With this PSD and the simulated adsorption densities in single pores, it was possible to predict in good agreement with experiment (i) the adsorption of binary mixtures of CO2 and CH4 and (ii) the adsorption of both pure components at higher temperatures. However, the model was unable to reproduce precisely the experimental pressure dependence of the CO2 selectivity.
A genome-wide survey of short coding sequences in streptococci (2007)

Identification of short genes that encode peptides of fewer than 60 aa is challenging, both experimentally and in silico. As a consequence, the universe of these short coding sequences (CDSs) remains largely unknown, although some are acknowledged to play important roles in cell-cell communication, particularly in Gram-positive bacteria. This paper reports a thorough search for short CDSs across streptococcal genomes. Our bioinformatic approach relied on a combination of advanced intrinsic and extrinsic methods. In the first step, intrinsic sequence information (nucleotide composition and presence of RBSs) served to identify new short putative CDSs (spCDSs) and to eliminate the differences between annotation policies. In the second step, pseudogene fragments and false predictions were filtered out. The last step consisted of screening the remaining spCDSs for lines of extrinsic evidence involving sequence and gene-context comparisons. A total of 789 spCDSs across 20 complete genomes (19 Streptococcus and one Enterococcus) received the support of at least one line of extrinsic evidence, which corresponds to an average of 20 short CDSs per million base pairs. Most of these had no known function, and a significant fraction (31%) are not even annotated as hypothetical genes in GenBank records. As an illustration of the value of this list, we describe a new family of CDSs, encoding very short hydrophobic peptides (20-23 aa) situated just upstream of some of the positive transcriptional regulators of the Rgg family. The expression of seven other short CDSs from Streptococcus thermophilus CNRZ1066 that encode peptides ranging in length from 41 to 56 aa was confirmed by real-time quantitative RT-PCR and revealed a variety of expression patterns. Finally, one peptide from this list, encoded by a gene that is not annotated in GenBank, was identified in a cell-envelope-enriched fraction of S. thermophilus CNRZ1066.
Physical and genetic characterization of a 75-kilobase deletion associated with al, a recessive lethal allele at the mouse agouti locus. (1989)

The agouti locus (A) of the mouse determines the timing and type of pigment deposition in the growing hair bulb, and several alleles at this locus are lethal when homozygous. Apparent instances of intragenic recombination and complementation between different recessive lethal alleles have suggested that the locus has a complex structure. We have begun to investigate the molecular basis of agouti gene action and recessive lethality by using a series of genetically linked DNA probes and pulsed field gel electrophoresis to detect structural alterations in radiation-induced agouti mutations. Hybridization probes from the Src and Emv-15 loci do not reveal molecular alterations in DNA corresponding to the ae, ax, and al alleles, but a probe from the parotid secretory protein gene (Psp) detects a 75-kilobase (kb) deletion in DNA containing the non-agouti lethal allele (al). The deletion is defined by a 75-kb reduction in the size of BssHII, NotI, NruI and SacII high molecular weight restriction fragments detected with the Psp probe and is located between 25 kb and 575 kb from Psp coding sequences. Because the genetic distance between A and Emv-15 is much less than A and Psp, there may be a preferred site of recombination close to Psp, or suppression of recombination between A and Emv-15. The al deletion has allowed us to determine the genotype of mice heterozygous for different recessive lethal alleles. We find that three different recessive lethal complementation groups are present at the agouti locus, two of which are contained within the al deletion.
Carboxyl terminus of the glycine transporter GLYT1 is necessary for correct processing of the protein. (1994)

The high affinity glycine transporter in neurons and glial cells is the primary means of inactivating synaptic glycine. To understand the structure-function relationships, especially the role of the intracellular carboxyl- and amino-terminal domains, we have modified the glycine transporter GLYT1 by using a polymerase chain reaction-based mutagenesis approach. Deletion of the first 30 amino acids of the amino terminus does not alter transport of glycine. Truncation of the last 34 amino acids of the carboxyl terminus did not impair glycine transport, but progressively more extensive deletions produced a progressive decrease in transport activity. All the fully active or partially active forms of the transporter retain the characteristic sodium and chloride dependence of the wild type. When the nonfunctional mutants of the carboxyl terminus were examined by an immunofluorescence technique, the carrier was no longer found in the membrane. This suggests that the carboxyl terminus of GLYT1 may be involved in the membrane insertion process. Moreover, the transporter that is not fully processed is not functional, because transport activity cannot be rescued in a solubilization-reconstitution experiment.
Biosynthetic profiles of neutrophil serine proteases in a human bone marrow-derived cellular myeloid differentiation model. (2005)

We demonstrate that azurophil granule proteins, including proforms of human leukocyte elastase, proteinase 3 and cathepsin G, are constitutively secreted to various degrees during in vitro myeloid differentiation of human hematopoietic progenitor cells, in addition to being stored intracellularly in active forms. These findings suggest protein-specific sorting mechanisms and may have implications for the regulation of granulopoiesis.
A Double-blind Comparison of Adhesive Bandages With the Use of Uniform Suction Blister Wounds (1992)

Identical wounds created with a suction blistering device can be used reliably to detect differences between the performances of wound dressings in healing superficial wounds. Superficial cutaneous wounds covered with a copolymer of polyurethane dressing demonstrated a superior rate of reepithelialization, less depression, and a better overall cosmetic appearance than wounds covered with two commercially available adhesive bandages.
Potent human neutralizing antibodies elicited by SARS-CoV-2 infection (2020)

Abstract The pandemic caused by emerging coronavirus SARS-CoV-2 presents a serious global public health emergency in urgent need of prophylactic and therapeutic interventions. SARS-CoV-2 cellular entry depends on binding between the viral Spike protein receptor-binding domain (RBD) and the angiotensin converting enzyme 2 (ACE2) target cell receptor. Here, we report on the isolation and characterization of 206 RBD-specific monoclonal antibodies (mAbs) derived from single B cells of eight SARS-CoV-2 infected individuals. These mAbs come from diverse families of antibody heavy and light chains without apparent enrichment for particular families in the repertoire. In samples from one patient selected for further analyses, we found coexistence of germline and germline divergent clones. Both clone types demonstrated impressive binding and neutralizing activity against pseudovirus and live SARS-CoV-2. However, the antibody neutralizing potency is determined by competition with ACE2 receptor for RBD binding. Surprisingly, none of the SARS-CoV-2 antibodies nor the infected plasma cross-reacted with RBDs from either SARS-CoV or MERS-CoV although substantial plasma cross-reactivity to the trimeric Spike proteins from SARS-CoV and MERS-CoV was found. These results suggest that antibody response to RBDs is viral species-specific while that cross-recognition target regions outside the RBD. The specificity and neutralizing characteristics of this plasma cross-reactivity requires further investigation. Nevertheless, the diverse and potent neutralizing antibodies identified here are promising candidates for prophylactic and therapeutic SARS-CoV-2 interventions.
Oligomeric amyloid β associates with postsynaptic densities and correlates with excitatory synapse loss near senile plaques (2009)

Synapse loss correlates with a cognitive decline in Alzheimer's disease (AD), but whether this is caused by fibrillar deposits known as senile plaques or soluble oligomeric forms of amyloid beta (Abeta) is controversial. By using array tomography, a technique that combines ultrathin sectioning of tissue with immunofluorescence, allowing precise quantification of small structures, such as synapses, we have tested the hypothesis that oligomeric Abeta surrounding plaques contributes to synapse loss in a mouse model of AD. We find that senile plaques are surrounded by a halo of oligomeric Abeta. Analysis of >14,000 synapses (represented by PSD95-stained excitatory synapses) shows that there is a 60% loss of excitatory synapses in the halo of oligomeric Abeta surrounding plaques and that the density increases to reach almost control levels in volumes further than 50 microm from a plaque in an approximately linear fashion (linear regression, r(2) = 0.9; P < 0.0001). Further, in transgenic cortex, microdeposits of oligomeric Abeta associate with a subset of excitatory synapses, which are significantly smaller than those not in contact with oligomeric Abeta. The proportion of excitatory synapses associated with Abeta correlates with decreasing density (correlation, -0.588; P < 0.0001). These data show that senile plaques are a potential reservoir of oligomeric Abeta, which colocalizes with the postsynaptic density and is associated with spine collapse, reconciling the apparently competing schools of thought of "plaque" vs. "oligomeric Abeta" as the synaptotoxic species in the brain of AD patients.
Prevention of encephalomyocarditis virus-induced diabetes by live recombinant Mycobacterium bovis bacillus Calmette-Guérin in susceptible mice. (2000)

The D variant of encephalomyocarditis (EMC-D) virus causes diabetes in susceptible mice by direct cytolysis of pancreatic beta-cells. cDNA covering the major outer capsid protein (VP1) of the EMC-D virus was cloned into Mycobacterium bovis bacillus Calmette-Guerin (BCG). None of the SJL/J mice immunized with live recombinant BCG-VP1 (rBCG-VP1) became diabetic when challenged with the highly diabetogenic EMC-D virus, but the control mice inoculated with normal BCG developed diabetes during the same challenge. VP1-specific antibodies (including neutralizing antibodies) were markedly increased over time and reached the maximum titer at week 10 after a single immunization. The plateau of the titer lasted longer than 4 weeks. Mice and guinea pigs immunized with live rBCG-VP1 showed strong delayed-type hypersensitivity to the VP1 of the EMC-D virus. The preventive immunity still worked effectively 10 months after the primary immunization. At that time, the VP1-specific antibody was almost undetectable in the bloodstream, but a large number of VP1-specific lymphocytes was found in the spleen of the immunized mice. Our results show that live rBCG-VP1 elicits effective humoral and long-lasting cellular immune responses against EMC-D virus infection that results in the prevention of virus-induced diabetes in susceptible mice.
Glycopeptides bind MHC molecules and elicit specific T cell responses. (1993)

Carbohydrates are T cell independent antigens because they do not bind to MHC molecules. However, glycopeptides might potentially bind to MHC molecules via their peptide component for presentation to T cells. We have conjugated the disaccharide galabiose [Gal alpha (1-4)Gal beta] to the amino terminus of a T cell peptide determinant from hen egg-white lysozyme [HEL(52-61)]. The resulting glycopeptide (Gal2-52-61) and a nonglycosylated analogue containing tyrosine and glutamic acid at the amino-terminus (YE-52-61) bound equally well to purified I-Ak. T cell hybridomas were produced after immunization with Gal2-52-61. Many of the T cell hybridomas were glycopeptide-specific and responded to Gal2-52-61 but not to nonglycosylated synthetic peptides or to HEL presented by APC, indicating that the carbohydrate moiety influenced T cell recognition. Recognition was lost with the amino terminal attachment of the disaccharide to a peptide six amino acids longer at the amino terminus than HEL(52-61). Recognition also was lost with peptides containing only a single galactosyl residue or with galabiose bound to a different I-Ak binding peptide. T cells directed to Gal2-52-61 recognized glycopeptides having significant variation in the disaccharide structure, such as HEL(52-61) glycopeptides carrying lactose, cellobiose, or hepta-o-acetylated galabiose. Peptide residues were important features of the T cell epitope; Ala substitutions of two critical T cell contact residues of HEL(52-61) (Tyr53 and Leu56) abrogated T cell reactivity to the glycopeptides without affecting binding to I-Ak. In conclusion, we propose that these T cells recognize a peptide conformation specific to glycopeptide-I-Ak complexes and that this recognition does not involve specific interaction between the carbohydrate moiety and the T cell receptor.
Maternal antibody and respiratory syncytial virus infection in infancy (1981)

One hundred newborn infants were studied prospectively for 1 year for evidence of infection with respiratory syncytial virus (RSV). The indirect membrane fluorescence technique was used to determine specific antibody in sera. Infection was shown in 29 cases. In 31 infants exposed to an RSV epidemic season, there was no evidence of infection. Maternal antenatal sera were also tested, and wide range of IgG antibody to RSV was found. Mean titre of maternal IgG antibody to RSV was significantly higher (P less than 0.001) in those mothers whose babies remained uninfected than in those whose babies had proved RSV infection before 6 months of age. Babies born to mothers with high levels of IgG antibody to respiratory syncytial virus were protected against infection with this virus during the first months of life when the risk of severe disease was greatest.