gebhart/patrepeval huggingface dataset:
Impact of hydration status on body composition as measured by dual energy X-ray absorptiometry in normal volunteers and patients on haemodialysis (1992)

To evaluate the influence of hydration status on the estimation of body composition using dual-energy X-ray absorptiometry (DXA), six normal volunteers and seven patients on maintenance haemodialysis were investigated using two different DXA machines (Lunar DPX, Hologic QDR 1000/W). Normal volunteers were studied (Hologic QDR 1000/W) before and 1 h after ingestion of breakfast, lunch and dinner (drinking various amounts of liquids at each meal, 0.5-2.4 kg). Whereas bone mineral content and body fat mass did not change, lean body mass of the trunk increased as a consequence of the meals. Conversely in patients on haemodialysis (Lunar DPX), lean body mass decreased in all segments of the body as a consequence of removal of 0.9-4.4 kg of salt-containing fluid by haemodialysis (trunk 61%, legs 30%, arms 5.5% and rest of the body 3.5%), whereas bone mineral content and body fat mass remained unchanged. However, this finding(s) did not hold true in one particular patient with bilateral hip prostheses. Measurement of body composition in eight normal volunteers on the same day with both machines showed similar results for lean and fat mass, whereas bone mineral content was found to be 17% higher using the Lunar DPX. In summary, in centres where both machines are available, follow-up of one individual patient should always be performed using the same equipment. In addition, hydration status and food intake must be taken into account when repetitive measurements of lean body mass are performed in the same patient.
Adeno-associated virus vectors for gene therapy. (1995)

Adeno-associated virus type 2 (AAV) is a non-pathogenic DNA virus which has been utilized as a eukaryotic gene transfer vector in vitro and in vivo. AAV possesses a unique set of characteristics which may make it useful for human gene therapy. AAV infection does not require host cell proliferation, although expression from AAV vectors may exhibit a relative preference for actively dividing cells. Both wild-type AAV and AAV vectors tend to persist in infected cells for prolonged periods of time, without any significant adverse consequences for the host. Wild-type AAV integrates frequently in one specific region of chromosome 19, whereas rep-deleted AAV vectors integrate in a less specific fashion in the host cell genome and may also persist in an episomal state. AAV vectors have been used to transduce a wide range of cell types in vitro including respiratory epithelial cells as well as bone marrow and lymphocyte-derived cells. As a prelude to AAV-based gene therapy for cystic fibrosis (CF), in vivo transduction and expression in the lungs has been observed in rodents and non-human primates after direct delivery to the airway surface, without any detectable toxicity. Based on these findings, the National Institutes of Health Recombinant DNA Advisory Committee (RAC) has recently approved a phase I human trial of CF gene therapy using an AAV vector.
Developmentally regulated expression of the bean β-phaseolin gene in tobacco seed (1985)

Recombinant phage lambda177.4 contains a gene for beta phaseolin, a major storage glycoprotein of French bean seed. A 3.8-kilobase Bgl II-BamHI fragment containing the entire 1700-base-pair coding region, together with 863 base pairs of 5' and 1226 base pairs of 3' flanking sequence, was inserted into the A66 Ti plasmid of Agrobacterium tumefaciens and used to transform tobacco. The level of phaseolin in the seeds of plants regenerated from cloned tissue was 1000-fold higher than in other tissues. The molecular weight of the phaseolin RNA transcript in tobacco seeds was identical to that found in bean seeds. The phaseolin protein in tobacco seed was glycosylated and appeared to undergo removal of the signal peptide. However, a large proportion of the phaseolin was cleaved into discrete peptides. These same peptides were formed as phaseolin was degraded during tobacco seed germination. The phaseolin gene appeared to be inserted as a single copy, and the proportion of phaseolin per genome copy in tobacco seeds (up to 3% of the total embryo proteins) resembled that in the bean seeds (40% of total seed protein, expressed from about 14 copies per diploid genome). Furthermore, the transplanted gene was turned on during tobacco seed development, and its protein product, phaseolin, was localized in the embryonic tissues. Finally, the phaseolin gene was inherited as a Mendelian dominant trait in tobacco.
Degradable Polyelectrolyte Multilayers that Promote the Release of siRNA (2011)

We report an approach to the design of degradable polyelectrolyte-based films for the controlled release of siRNA from surfaces. Our approach is based on stepwise, layer-by-layer assembly of multilayered polyelectrolyte films (or "polyelectrolyte multilayers", PEMs) using siRNA and a hydrolytically degradable poly(β-amino ester) (polymer 1). Fabrication of films using siRNA sequences for green fluorescent protein (GFP) or firefly luciferase resulted in linear growth of ultrathin films (∼50 nm thick) that promoted the surface-mediated release of siRNA upon incubation in physiologically relevant media. Physicochemical characterization of these siRNA-containing films revealed large differences in film growth profiles, physical erosion profiles, and siRNA release profiles as compared to PEMs fabricated using polymer 1 and larger plasmid DNA constructs. For example, whereas films fabricated using plasmid DNA erode gradually and release DNA over a period of ∼48 h, films fabricated using siRNA released ∼65% of incorporated siRNA within the first hour of incubation, prior to the onset of any observed film erosion. This initial burst of release was followed by a second, slower phase of release (accompanied by gradual film erosion) over the next 23 h. These differences in release profiles and other behaviors likely result, at least in part, from large differences in the sizes of siRNA and plasmid DNA. Finally, we demonstrate that the siRNA in these films is released in a form that remains intact, functional, and able to silence targeted protein expression upon administration to mammalian cells in vitro. The results of this investigation provide a platform for the design of thin films and coatings that could be used to localize the release of siRNA from surfaces in a variety of fundamental and applied contexts (e.g., for development of new research tools or approaches to delivery from film-coated implants and other devices).
Integrated Computational and Experimental Approach for Lead Optimization and Design of Compstatin Variants with Improved Activity (2003)

A novel structure-activity-based combinatorial computational optimization methodology for the design of peptides that are candidates to become therapeutics is presented. This methodology has been successfully applied in the design of a 7-fold more active analogue, among other active analogues, in the case of the complement inhibitor compstatin. The main steps of the approach involve the availability of NMR-derived structural templates, combinatorial selection of sequences based on optimization of parametrized pairwise residue interaction potentials, prediction of fold stabilities using deterministic global optimization, and experimental validation with immunological activity measurements. This work is direct evidence that an integrated experimental and theoretical approach can make the engineering of compounds with enhanced immunological properties possible.
Evidence for α-Helical Conformation of an Essential N-terminal Region in the Human Bcl2 Protein (1996)

A region occupying approximately 24 amino acids near the N terminus of human Bcl2 is essential for this cytoplasmic membrane protein's ability to inhibit apoptosis. Systematic mutagenesis of this N-terminal region indicates that only five hydrophobic and aromatic residues within it are specifically required for function. Computerized secondary structure prediction, together with circular dichroism spectroscopy of synthetic peptides, indicates that the region encompassing these five residues has the propensity to take on an alpha-helical conformation in the presence of SDS micelles, which presumably mimic the hydrophobic surfaces of cellular membranes or polypeptides. The five critical residues are predicted to be clustered on one face of this putative helix, where they might serve to mediate protein-protein contacts involved in the multimerization of Bcl2 or in the interaction of Bcl2 with other, as yet unidentified components of the apoptotic pathway. Apparent structural homologues of this helical motif are also present in at least some other anti-apoptotic proteins from the Bcl2 family but not in those family members that tend to potentiate, rather than inhibit, apoptosis.
Antibody-Dependent Cell-Mediated Cytotoxicity Against Influenza Virus-Infected Cells (1983)

The three major immunocompetent cells in human peripheral blood (lymphocytes, neutrophils, and monocytes) were shown to be effector cells for antibody-dependent cell-mediated cytotoxicity (ADCC) against influenza virus-infected baby hamster kidney cells in vitro. Lymphocyte cytotoxicity was mediated by FcIgG receptor-bearing null cells and T gamma cells. These effector populations were best defined by HNK-1, a monoclonal antibody to human natural killer and ADCC-mediator cells. Antibody responsible for ADCC against influenza virus-infected cells was detectable in sera of young children after natural infection and after vaccination with inactivated and live attenuated viruses. ADCC antibody appeared before hemagglutination-inhibiting antibody and persisted for at least one year after vaccination with live attenuated vaccine. ADCC antibody was subtype-specific but quite broadly reactive within a subtype. Both hemagglutinin and neuraminidase were antigenic determinants for ADCC antibody. An anamnestic response to the original strain was observed after challenge with influenza virus of a heterologous subtype.
Final maturation of dendritic cells is associated with impaired responsiveness to IFN-gamma and to bacterial IL-12 inducers: decreased ability of mature dendritic cells to produce IL-12 during the interaction with Th cells. (1999)

Activation of immature CD83- dendritic cells (DC) in peripheral tissues induces their maturation and migration to lymph nodes. Activated DC become potent stimulators of Th cells and efficient inducers of Th1- and Th2-type cytokine production. This study analyzes the ability of human monocyte-derived CD1a+ DC at different stages of IL-1 beta and TNF-alpha-induced maturation to produce the major Th1-driving factor IL-12. DC at the early stages of maturation (2 and 4 h) produced elevated amounts of IL-12 p70 during interaction with CD40 ligand-bearing Th cells or, after stimulation with the T cell-replacing factors, soluble CD40 ligand and IFN-gamma. The ability to produce IL-12 was strongly down-regulated at later time points, 12 h after the induction of DC maturation, and in fully mature CD83+ cells, at 48 h. In contrast, the ability of mature DC to produce IL-6 was preserved or even enhanced, indicating their intact responsiveness to CD40 triggering. A reduced IL-12-producing capacity of mature DC resulted mainly from their impaired responsiveness to IFN-gamma, a cofactor in CD40-induced IL-12 p70 production. This correlated with reduced expression of IFN-gamma R (CD119) by mature DC. In addition, while immature DC produced IL-12 and IL-6 after stimulation with LPS or Staphylococcus aureus Cowan I strain, mature DC became unresponsive to these bacterial stimuli. Together with the previously described ability of IL-10 and PGE2 to stably down-regulate the ability to produce IL-12 in maturing, but not in fully mature, DC, the current data indicate a general resistance of mature DC to IL-12-modulating factors.
Non-Woven Electrostatic Media for Chromatographic Separation of Biological Particles (2009)

Nano alumina fibers, 2 nm in diameter and approximately 0.25 µm long are electroadhesively grafted to a microglass fiber. A non-woven media is formed by conventional wet-laid paper making technology. The media has a high affinity for virus, DNA/RNA, proteins, endotoxins, and antigens. A model was developed using data from adsorption of 30 nm latex spheres and was verified with MS2 coliphage.
On the Relation Between Pinna Reflection Patterns and Head-Related Transfer Function Features (2012)

This paper studies the relationship between head-related transfer functions (HRTFs) and pinna reflection patterns in the frontal hemispace. A pre-processed database of HRTFs allows extraction of up to three spectral notches from each response taken in the median sagittal plane. Ray-tracing analysis performed on the obtained notches' central frequencies is compared with a set of possible reflection surfaces directly recognizeable from the corresponding pinna picture. Results of such analysis are discussed in terms of the reflection coefficient sign, which is found to be most likely negative. Based on this finding, a model for real-time HRTF synthesis that allows to control separately the evolution of different acoustic phenomena such as head diffraction, ear resonances, and reflections is proposed through the design of distinct filter blocks. Parameters to be fed to the model are derived either from analysis or from specific anthropometric features of the subject. Finally, objective evaluations of reconstructed HRTFs in the chosen spatial range are performed through spectral distortion measurements.
Engineering the Salmonella type III secretion system to export spider silk monomers (2009)

The type III secretion system (T3SS) exports proteins from the cytoplasm, through both the inner and outer membranes, to the external environment. Here, a system is constructed to harness the T3SS encoded within Salmonella Pathogeneity Island 1 to export proteins of biotechnological interest. The system is composed of an operon containing the target protein fused to an N-terminal secretion tag and its cognate chaperone. Transcription is controlled by a genetic circuit that only turns on when the cell is actively secreting protein. The system is refined using a small human protein (DH domain) and demonstrated by exporting three silk monomers (ADF-1, -2, and -3), representative of different types of spider silk. Synthetic genes encoding silk monomers were designed to enhance genetic stability and codon usage, constructed by automated DNA synthesis, and cloned into the secretion control system. Secretion rates up to 1.8 mg l(-1) h(-1) are demonstrated with up to 14% of expressed protein secreted. This work introduces new parts to control protein secretion in Gram-negative bacteria, which will be broadly applicable to problems in biotechnology.
High‐Contrast Electrochromism and Controllable Dissolution of Assembled Prussian Blue/Polymer Nanocomposites (2004)

Abstract To maintain the momentum and impact of the field, assembled materials systems must increasingly incorporate broad functionality to meet real‐world applications. Here we describe nanocomposite films of specially synthesized inorganic Prussian blue (PB) nanoparticles and linear poly(ethylene imine) (LPEI) that possess the unusual functional combination of high‐performance electrochromism for displays and controllable dissolution for drug delivery. Fabrication using layer‐by‐layer (LBL) assembly was followed by spectroelectrochemical characterization, allowing a full composition determination rarely achieved for LBL films. The electrochromic performance of thick LPEI/PB nanocomposites most relevant to applications surpassed that of inorganic PB films with competitive switching speed and superior contrast. Oxidation beyond the primary electrochromic transition removes nanoparticle ionization and can controllably dissolve the films. Because PB is non‐toxic we suggest this mechanism for controlled in‐vivo drug delivery. The performance and multifunctional quality of these nanocomposites promise a strong impact on flexible displays, electrochromic windows, and even biomedical devices.
Sequence Analysis, Biogenesis, and Mitochondrial Import of the α-Subunit of Rat Liver Propionyl-CoA Carboxylase (1989)

We have cloned and sequenced cDNAs encoding the alpha-subunit of rat liver propionyl-CoA carboxylase (PCC), a biotin-dependent, mitochondrial matrix protein. The full-length cDNA spans 3327 base pairs, has a long (895 base pairs) 5'-untranslated region, and encodes a protein of 721 amino acids. In vitro transcription and translation of the full-length rat alpha-PCC cDNA produces a product which is immunoprecipitable with antibodies specific to PCC and has the same apparent molecular weight as in vivo synthesized alpha-PCC. Rat liver alpha-PCC precursor is not quantitatively biotinylated when synthesized in a cell-free rabbit reticulocyte system. Nevertheless, when incubated with isolated rat liver mitochondria in vitro, the precursor is imported and proteolytically cleaved to its mature form. A sequence comparison of rat liver alpha-PCC and other biotinylated polypeptides reveals the absolute conservation of three glycines and one valine in the region surrounding the biotinylated lysine residue. This pattern of conserved residues is also present in lipoylated proteins, where lipoic acid is similarly, covalently attached to a lysine residue. A possible functional role for the conserved glycine residues and further sequence similarity surrounding the site of biotinylation and lipoylation is discussed.
Purification and properties of the Escherichia coli dnaK replication protein. (1984)

The Escherichia coli dnaK+ gene was cloned into the "runaway" plasmid vector pMOB45 resulting in a large overproduction of the dnaK protein. The dnaK protein was purified by following its ability to complement the replication of single-stranded M13 bacteriophage DNA in a reaction system dependent on the presence of the lambda O and P DNA replication proteins. The DNA replication activity of the dnaK protein is also essential for lambda dv DNA replication in vitro, since antibodies against it were shown to inhibit the reaction. Purified dnaK protein preparations possess a weak ATPase activity and an autophosphorylating activity which copurify with its DNA replication activity throughout all purification steps. The dnaK protein is an acidic largely monomeric protein of Mr = 72,000 and 78,400 under denaturing and native conditions, respectively. The amino acid composition and N-terminal amino acid sequence match those predicted from the DNA sequence of the dnaK gene (Bardwell, J.C.A., and Craig, E. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 848-852).
Meningococcal Serogroup C Conjugate Vaccine Is Immunogenic in Infancy and Primes for Memory (1999)

The safety, immunogenicity, and immunologic priming of 2 dosages (2 microgram or 10 microgram) of a meningococcal C oligosaccharide-CRM197 conjugate vaccine was evaluated in 114 infants vaccinated at ages 2, 3, and 4 months. Antibody persistence and response to boosting with 10 microgram of meningococcal C polysaccharide were assessed. The meningococcal conjugate vaccine produced fewer local reactions than concurrent routine immunizations. Total serogroup C-specific immunoglobulin geometric mean concentration (GMC) increased from 0.3 microgram/mL before vaccination to 13.1 microgram/mL at age 5 months. Serum bactericidal antibody (SBA) geometric mean titers (GMTs) rose from <1:4 to 1:1057 at 5 months and fell by 14 months to 1:19. Following boosting, anti-C-specific immunoglobulin GMC rose to 15.9 microgram/mL and SBA GMT to 1:495. Antibody responses in the 10-microgram dose cohort were significantly higher at 5 months (P<.01) than in the 2-microgram dose cohort but were lower after polysaccharide boosting (P=.02). This meningococcal conjugate vaccine was well tolerated and immunogenic and induced immunologic memory in infants.
Involvement of neurogranin in the modulation of calcium/calmodulin-dependent protein kinase II, synaptic plasticity, and spatial learning: A study with knockout mice (2000)

Neurogranin/RC3 is a neural-specific Ca(2+)-sensitive calmodulin (CaM)-binding protein whose CaM-binding affinity is modulated by phosphorylation and oxidation. Here we show that deletion of the Ng gene in mice did not result in obvious developmental or neuroanatomical abnormalities but caused an impairment of spatial learning and changes in hippocampal short- and long-term plasticity (paired-pulse depression, synaptic fatigue, long-term potentiation induction). These deficits were accompanied by a decreased basal level of the activated Ca(2+)/CaM-dependent kinase II (CaMKII) ( approximately 60% of wild type). Furthermore, hippocampal slices of the mutant mice displayed a reduced ability to generate activated CaMKII after stimulation of protein phosphorylation and oxidation by treatments with okadaic acid and sodium nitroprusside, respectively. These results indicate a central role of Ng in the regulation of CaMKII activity with decisive influences on synaptic plasticity and spatial learning.
Superantigen responses and co-stimulation: CD28 and CTLA-4 have opposing effects on T cell expansion in vitro and in vivo (1996)

Co-stimulation via the CD28/CTLA-4 system appears critical for T cell proliferation to peptide antigens presented in association with MHC. In this study, we examine the roles of CD28 and CTLA-4 in the response of murine T cells to the superantigen staphylococcal enterotoxin B (SEB). In vitro, antibodies against B7-1/B7-2 or Fab fragments of anti-CD28 antibodies significantly inhibit the response of splenocytes to SEB. Conversely, Fab fragments of anti-CTLA-4 antibodies augment the proliferative response. Further, addition of blocking antibodies directed against B7-1/B7-2 augment proliferation co-stimulated by intact anti-CD28 antibodies. These data support the hypothesis that CD28 and CTLA-4 exert opposing effects upon early T cell activation. In vivo, intact anti-CD28 antibodies and non-stimulatory Fab fragments of anti-CD28 appear to have similar inhibitory effects upon the expansion of V beta 8+ T cells. In contrast, both intact and Fab fragments of anti-CTLA-4 appear to amplify this expansion. We conclude that the SEB response is significantly augmented by CD28-derived signaling and this in turn may be attenuated by signals through CTLA-4.