gebhart/patrepeval huggingface dataset:
Efficient Incorporation of Human CD4 Protein into Avian Leukosis Virus Particles (1990)

Virus envelope (Env) proteins are thought to contain specific signals for selective uptake by virus particles. In the course of attempting to define these signals by testing virus incorporation of CD4-Env chimeric proteins, normal human CD4 was found to be efficiently and selectively assembled into avian leukosis virus particles in quail cells. Viruses bearing CD4 at their surface may be useful reagents in the design of retrovirus-mediated gene therapy for the acquired immune deficiency syndrome.
Treatment strategies for multiple sclerosis: When to start, when to change, when to stop? (2015)

Multiple sclerosis (MS) is a chronic inflammatory condition of the central nervous system determined by a presumed autoimmune process mainly directed against myelin components but also involving axons and neurons. Acute demyelination shows as clinical relapses that may fully or partially resolve, while chronic demyelination and neuroaxonal injury lead to persistent and irreversible neurological symptoms, often progressing over time. Currently approved disease-modifying therapies are immunomodulatory or immunosuppressive drugs that significantly although variably reduce the frequency of attacks of the relapsing forms of the disease. However, they have limited efficacy in preventing the transition to the progressive phase of MS and are of no benefit after it has started. It is therefore likely that the potential advantage of a given treatment is condensed in a relatively limited window of opportunity for each patient, depending on individual characteristics and disease stage, most frequently but not necessarily in the early phase of the disease. In addition, a sizable proportion of patients with MS may have a very mild clinical course not requiring a disease-modifying therapy. Finally, individual response to existing therapies for MS varies significantly across subjects and the risk of serious adverse events remains an issue, particularly for the newest agents. The present review is aimed at critically describing current treatment strategies for MS with a particular focus on the decision of starting, switching and stopping commercially available immunomodulatory and immunosuppressive therapies.
The glycophosphatidylinositol-anchored Thy-1 molecule interacts with the p60fyn protein tyrosine kinase in T cells. (1992)

Stimulation of murine T cells by engagement of the multi-component T cell antigen receptor or by cross-linking the Thy-1 molecule leads to a similar response characterized by lymphocyte activation and lymphokine production. The early biochemical events induced by engaging these molecules also are similar and begin with activation of a tyrosine kinase pathway and tyrosine phosphorylation of a comparable set of substrates. Previous work demonstrates that the protein tyrosine kinase p60fyn is associated with the antigen receptor and therefore it may participate in the tyrosine phosphorylations that are observed with antigen receptor signaling. In this study we demonstrate that the Thy-1 molecule is also associated with p60fyn in a murine T cell hybridoma and in murine thymocytes. The interaction is independent of antigen receptor expression. Thy-1 is a member of the class of molecules anchored to the plasma membrane by a glycophosphatidylinositol (GPI) group. The association of Thy-1 with p60fyn is dependent on the GPI linkage, since cleavage of the GPI anchor disrupts the interaction. The association of Thy-1 and p60fyn suggests a means by which Thy-1 cross-linking leads to tyrosine phosphorylation and T cell activation.
South Africa - Greater Addo Elephant National Park Project : resettlement action plan (2003)

Implementation of the Greater Addo Elephant National Park Project will establish a mega-biodiversity conservation area in, and around the existing Addo Elephant National Park, an area of global biodiversity value, which contains five, out of seven plant biomes found within South Africa, in addition to the proposed adjoining marine environment, which is also of considerable biodiversity value. The project will therefore support the expansion of the Park, and marine protected areas, significantly boosting eco-tourism. To this end, land acquisition is already taking place, therefore, this resettlement action plan sets the policy framework in compliance with the Bank operational policy, and the country's legal framework guiding the principles for compensation, income restoration, and implementation and monitoring arrangements. A Resettlement Working Group has been set up to include maximum participation by the affected people in the resettlement process, to identify displaced populations from appropriated farms. Alternative accommodation, and facilities will be provided for loss of access to farms, also allowing, the possibility to work for the Poverty Relief program, while SANParks negotiates with the Department of Housing, the necessary funds per household to build new housing in the town of the affected people's choice. Appropriate jobs have been identified for displaced persons, and, training will be provided to ensure satisfactory performances in their new jobs, as part of the identified capacity building program. An investigation of the viability of alternative income generating strategies is ongoing, particularly through negotiations with the Department of Land Affairs in terms of the Land Reform Grants, which would afford a specified grant for each household, through which profitable agricultural activities may result.
Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres. (1995)

Large terminal fragments of human chromosomes 2p, 6p, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease (RARE) cleavage analysis of genomic DNA samples from II unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-YACs studied. The cloned fragments provide telomeric closure of maps for the respective chromosome arms and will supply the reagents needed for analyzing and sequencing these distal subtelomeric regions.
Changes in an HER-2 Peptide Upregulating HLA-A2 Expression Affect Both Conformational Epitopes and CTL Recognition (1995)

The HER-2/neu protooncogene (HER-2) is overexpressed in a significant number of breast and ovarian tumors. Peptides of HER-2 sequence were recently found to reconstitute recognition of cytotoxic T lymphocytes (CTLs) from tumor-associated (TALs) and tumor-infiltrating (TILs) lymphocytes, indicating that they reconstitute natural epitopes recognized by CTLs on HLA-A2+ tumors. Because HER-2 is an important antigen (Ag) for tumor-specific CTL induction and the immunogenicity of peptides for CTL induction is dependent on their presentation as stable complexes with HLA-A2, we identified peptides of high and low stabilizing activity from the sequence of HER-2 and the folate-binding protein (FBP). Distinct sequence patterns in the region positions (P)3-P5 and P1 were found for peptides with high (HSA) and low (LSA) stabilizing ability. A low-HLA-A2-affinity HER-2 peptide, P1 of the CTL epitope, was found to be permissive to substitutions that enhanced HLA-A2-stabilizing ability and conserved CTL recognition. In contrast, the region P3-P5 was not permissive to sequence changes. We conclude that the selective permissivity of P1 and P9 in the tumor epitope sequence may have important implications for optimization of tumor Ag presentation, and "neoantigenicity" of self-antigens, aiming toward induction of tumor-reactive CTLs of defined affinity and specificity for target Ags.
Data-Dependent Fingerprints for Wireless Device Authentication (2014)

Abstract : While authenticating wireless radios based on the unique imperfections in their transmitted waveform has become a topic of some interest, such fingerprinting techniques are vulnerable to an attacker who can listen to a radio's transmission and later mimic the transmission using a sophisticated arbitrary waveform generator. However, this type of vulnerability can be reduced if the authentication is accomplished using a random selection from a long list of possible challenge-response pairs and if the node requesting network access has a fingerprint that changes with each valid response. This work provides a first study of such a concept using a tunable filter, used during the authentication exchange, whose tuning voltages are determined from the response data. The work uses simulations and measurements to demonstrate the effectiveness of estimating the distortion function introduced by the tunable filter and using it to identify the device. Results show that the technique can achieve near perfect discrimination between devices and can reject an attacker with very high probability.
Storage of human platelet concentrates in an artificial medium without dextrose (1988)

It was shown previously that human blood platelets stored in an artificial medium (PCD) for up to 5 days remain functional in vitro and have normal survival and recovery in vivo. This report demonstrates that the medium can be simplified further by the removal of dextrose, leaving for study a medium consisting simply of balanced salts and citrate anticoagulant (PC). Some dextrose, 3.2 mM, was present in the fresh PC platelet concentrates due to plasma carryover in the production of platelet concentrates, but this dextrose concentration was considerably less than the 22.6 to 25.5 mM present in platelet concentrates in PCD or plasma. Platelet count, pH, PCO2, and PO2, as well as platelet aggregation and release responses to stimulation, in vitro, were as well preserved in the PCD or PC media as in the plasma controls. In the PC medium, platelets consumed 2.5 mM dextrose over 5 days and left 0.7 mM dextrose. The same consumption of dextrose was noted in PCD platelet concentrates, while platelets in plasma metabolized twice as much dextrose and formed twice as much lactate. Thus, the rate of glycolysis in platelet concentrates was independent of the dextrose concentration in the medium, and the platelet functions were well preserved.
Structure of Human Pro-Matrix Metalloproteinase-2: Activation Mechanism Revealed (1999)

Matrix metalloproteinases (MMPs) catalyze extracellular matrix degradation. Control of their activity is a promising target for therapy of diseases characterized by abnormal connective tissue turnover. MMPs are expressed as latent proenzymes that are activated by proteolytic cleavage that triggers a conformational change in the propeptide (cysteine switch). The structure of proMMP-2 reveals how the propeptide shields the catalytic cleft and that the cysteine switch may operate through cleavage of loops essential for propeptide stability.
Absorption Spectra, Photophysical Properties, and Redox Behavior of Ruthenium(II) Polypyridine Complexes Containing Accessory Dipyrromethene−BF2Chromophores (2006)

The six multichromophoric species 1-6, containing the potentially luminescent Ru(II) polypyridine subunits and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene fluorophores (dipyrromethene-BF(2) dyes, herein after called bodipy), have been prepared and their absorption spectra, luminescence properties (both at room temperature in fluid solution and at 77 K in rigid matrix), and redox properties have been investigated (for the structuralformulas of all the compounds, see Figure 1). For comparison purposes, also the same properties of the bodipy-based free ligands have been examined. Three of the multichromophoric species (1-3) are based on the Ru(bpy)(3)-type metal subunit, whereas 4-6 are based on the Ru(terpy)(2)-type metal subunit. Transient absorption spectroscopy at room temperature of all the compounds has also been performed. The absorption spectra of all the metal complexes show features that can be assigned to the Ru(II) polypyridine subunits and to the bodipy centers. In particular, the lowest energy spin-allowed pi-pi* transition of the bodipy groups dominates the visible region, peaking at about 530 nm. All the new complexes exhibit a rich redox behavior, with reversible processes attributed to specific sites, indicating a small perturbation of each redox center and therefore highlighting the supramolecular nature of the multichromophoric assemblies. Despite the good luminescence properties of the separated components, 1-6 do not exhibit any luminescence at room temperature; however, transient absorption spectroscopy evidences that for all of them a long-lived (microsecond time scale) excited state is formed, which is identified as the bodipy-based triplet state. Pump-probe transient absorption spectroscopy suggests that such a triplet state is formed from the promptly prepared bodipy-based (1)pi-pi* state in most cases by the intervention of a charge-separated level. At 77 K, all the complexes except complex 1 exhibit the bodipy-based fluorescence, although with a slightly shortened lifetime compared to the corresponding free ligand(s), and 4-6 also exhibit a phosphorescence assigned to the bodipy subunits. Phosphorescence of bodipy species had never been reported in the literature to the best of our knowledge: in the present cases we propose that it is an effective decay process thanks to the presence of the ruthenium heavy atom and of the closely lying (3)MLCT state of the Ru(terpy)(2)-type subunits.
[What to do if pills do not work for urge incontinence--still many questions and ambiguities]. (2012)

Bladder training and antimuscarinics are first-line treatments for the symptoms of an overactive bladder. Unfortunately, many patients stop using drugs due to undesirable effects or limited efficacy. The paper by Smits et al. contains a summarisation of various neuromodulation treatments that can be offered to patients after first-line treatments have failed, e.g. sacral neuromodulation, posterior tibial nerve stimulation, pudendal neuromodulation and intravesical botulinum toxin A. An unambiguous treatment algorithm based on RCTs is lacking at this time; however, postulation of a patient's profile is possible. Research in the field of dysfunctional voiding should focus on comparing the different treatment options in order to create an algorithm based on science.
Distribution and Abundance of MAAs in 33 Species of Microalgae across 13 Classes (2010)

We provide a direct comparison of the distribution and abundance of mycosporine-like amino acids (MAAs) in a diverse range of microalgal cultures (33 species across 13 classes) grown without supplementary ultraviolet radiation (UV). We compare the MAAs in cultures with those present in characterised natural phytoplankton populations from the English Channel. We detected 25 UV absorbing compounds including at least two with multiple absorption maxima. We used LC-MS to provide chemical characterisation of the six most commonly occurring MAAs, namely, palythene, palythine, mycosporine-glycine, palythenic acid, porphyra-334 and shinorine. MAAs were abundant (up to 7 pg MAA cell(-1)) in 10 species, with more minor and often unknown MAAs in a further 11 cultures. Shinorine was the most frequently occurring and abundant MAA (up to 6.5 pg cell(-1)) and was present in all but two of the MAA-containing species. The study provides further insight into the diversity and abundance of MAAs important from an ecological perspective and as potential source of natural alternatives to synthetic sunscreens.
Preoperative interleukin‐6 production by mononuclear blood cells predicts survival after radical surgery for colorectal carcinoma (2007)

IL-6 production in vitro by PBMC can predict survival after radical surgery for colorectal cancer.
Design, Synthesis, and Binding Affinities of Potential Positron Emission Tomography (PET) Ligands for Visualization of Brain Dopamine D3Receptors (2005)

We here report the synthesis of compounds structurally related to the high-affinity dopamine D(3) receptor ligand N-[4-[4-(2,3-dichlorophenyl)piperazin-1-yl]butyl]-7-methoxy-2-benzofurancarboxamide (1). All compounds were specifically designed as potential PET radioligands for brain D(3) receptors visualization, having lipophilicity within a range for high brain uptake and weak nonspecific binding (2 < ClogP < 3.5) and bearing a methoxy substituent for easy access to labeling with the positron emitter isotope (11)C. N-[4-[4-(5-methoxy-2-benzisoxazolyl)piperazin-1-yl]butyl]-4-(4-morpholinyl)benzamide (22), N-[4-[4-(5-methoxy-2-benzisoxazolyl)piperazin-1-yl]butyl]-4-(1H-imidazol-1-yl)benzamide (23), and N-[4-[4-(5-methoxy-2-benzisoxazolyl)piperazin-1-yl]butyl]-5-(2-furanyl)-1H-pyrazole-3-carboxamide (24) displayed good D(3) receptor affinities (K(i) values 38.0, 22.6, and 21.3 nM, respectively) and were selective over D(2) receptor. Moreover, compounds 22-24 were able to permeate the Caco-2 cell monolayer, differently from compound 1. Although the goal to identify potential PET radioligands with subnanomolar affinities for D(3) receptor was not achieved, the proposed strategy could be a starting point for future developments.
Two Distinct Cytokines Released from a Human Aminoacyl-tRNA Synthetase (1999)

Aminoacyl-tRNA synthetases catalyze aminoacylation of transfer RNAs (tRNAs). It is shown that human tyrosyl-tRNA synthetase can be split into two fragments with distinct cytokine activities. The endothelial monocyte-activating polypeptide II-like carboxy-terminal domain has potent leukocyte and monocyte chemotaxis activity and stimulates production of myeloperoxidase, tumor necrosis factor-alpha, and tissue factor. The catalytic amino-terminal domain binds to the interleukin-8 type A receptor and functions as an interleukin-8-like cytokine. Under apoptotic conditions in cell culture, the full-length enzyme is secreted, and the two cytokine activities can be generated by leukocyte elastase, an extracellular protease. Secretion of this tRNA synthetase may contribute to apoptosis both by arresting translation and producing needed cytokines.
The geology of ordovician rocks at Balbriggan, County Dublin, Eire (1967)

Abstract A thick series of Caradocian volcanics is described. The volcanics are basic‐intermediate and it is own that they have a number of characteristics which are peculiar to emplacement in a subaqueous environment. A new interpretation of the stratigraphy results from a consideration of the folding of the succession.
Construction and properties of retrovirus packaging cells based on gibbon ape leukemia virus (1991)

We have constructed hybrid retrovirus packaging cell lines that express the gibbon ape leukemia virus env and the Moloney murine leukemia virus gag-pol proteins. These cells were used to produce a retrovirus vector at over 10(6) CFU/ml, with a host range that included rat, hamster, bovine, cat, dog, monkey, and human cells. The gag-pol and env expression plasmids were separately transfected to reduce the potential for helper virus production, which was not observed. The NIH 3T3 mouse cells from which the packaging lines were made are not infectable by gibbon ape leukemia virus; thus, the generation and spread of possible recombinant viruses in the packaging cells is greatly reduced. These simian virus-based packaging cells extend the host range of currently available murine and avian packaging cells and should be useful for efficient gene transfer into higher mammals.
Peripheral opioid analgesia in experimental human pain models (2003)

This placebo-controlled, double-blind crossover study assessed whether exclusive activation of peripheral opioid receptors results in significant pain reduction. To achieve opioid activity restricted to the periphery, we used a short-term (2 h) low dose infusion of morphine-6-beta-glucuronide (M6G) because M6G does not pass the blood-brain barrier during this time in amounts sufficient to induce CNS effects. The lack of central opioid effects of M6G was confirmed by a lack of change of the pupil size and absence of other opioid-related CNS effects. As a positive control, morphine was infused at a dosage that definitely produced CNS effects. This was evident by a rapid decrease of the pupil size and by other typical opioid-related side effects including nausea, vomiting, itchiness, hiccup and sedation. Three different pain models were employed to evaluate the analgesic effects: (i) cutaneous inflammatory hyperalgesia induced by briefly freezing a small skin area to -30 degrees C ('freeze lesion'); (ii) muscle hyperalgesia induced by a series of concentric and eccentric muscle contractions (DOMS model; delayed onset of muscle soreness); and (iii) pain induced by electrical current (5 Hz sinus stimuli of 0-10 mA). M6G significantly reduced cutaneous hyperalgesia in the 'freeze lesion' model as assessed with von Frey hairs. It also reduced muscle hyperalgesia in the DOMS model. Electrical pain, however, was not affected by M6G. Morphine was significantly more active in the 'freeze lesion' and DOMS model, and also significantly increased the electrical pain threshold and tolerance. Subcutaneous tissue concentrations of M6G and morphine as assessed with microdialysis were about half those of the respective plasma concentrations. The results of the study indicate that M6G has antihyperalgesic effects in inflammatory pain through activation of peripheral opioid receptors. Since this occurs at concentrations that do not cause central opioid effects, M6G might be useful as a peripheral opioid analgesic.
A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex (1995)

The crystal structure of a nucleic acid triplex reveals a helix, designated P-form, that differs from previously reported nucleic acid structures. The triplex consists of one polypurine DNA strand complexed to a polypyrimidine hairpin peptide nucleic acid (PNA) and was successfully designed to promote Watson-Crick and Hoogsteen base pairing. The P-form helix is underwound, with a base tilt similar to B-form DNA. The bases are displaced from the helix axis even more than in A-form DNA. Hydrogen bonds between the DNA backbone and the Hoogsteen PNA backbone explain the observation that polypyrimidine PNA sequences form highly stable 2:1 PNA-DNA complexes. This structure expands the number of known stable helical forms that nucleic acids can adopt.
Trehalose Glycopolymers for Stabilization of Protein Conjugates to Environmental Stressors (2012)

Herein, we report the synthesis of trehalose side chain polymers for stabilization of protein conjugates to environmental stressors. The glycomonomer 4,6-O-(4-vinylbenzylidene)-α,α-trehalose was synthesized in 40% yield over two steps without the use of protecting group chemistry. Polymers containing the trehalose pendent groups were prepared via reversible addition-fragmentation chain transfer (RAFT) polymerization using two different thiol-reactive chain transfer agents (CTAs) for subsequent conjugation to proteins through disulfide linkages. The resulting glycopolymers were well-defined, and a range of molecular weights from 4200 to 49 500 Da was obtained. The polymers were conjugated to thiolated hen egg white lysozyme and purified. The glycopolymers when added or covalently attached to protein significantly increased stability toward lyophilization and heat relative to wild-type protein. Up to 100% retention of activity was observed when lysozyme was stressed ten times with lyophilization and 81% activity when the protein was heated at 90 °C for 1 h; this is in contrast to 16% and 18% retention of activity, respectively, for the wild-type protein alone. The glycopolymers were compared to equivalent concentrations of trehalose and poly(ethylene glycol) (PEG) and found to be superior at stabilizing the protein to lyophilization and heat. In addition, the protein-glycopolymer conjugates exhibited significant increases in lyophilization stability when compared to adding the same concentration of unconjugated polymer to the protein.