gebhart/patrepeval huggingface dataset:
Solution Structure of Discrepin, a New K+-Channel Blocking Peptide from the α-KTx15 Subfamily, (2006)

Discrepin, isolated from the venom of the Venezuelan scorpion Tityus discrepans, blocks preferentially the I(A) currents of the voltage-dependent K+ channel of rat cerebellum granular cells in an irreversible way. It contains 38 amino acid residues with a pyroglutamic acid as the N-terminal residue [D'Suze, G., Batista, C. V., Frau, A., Murgia, A. R., Zamudio, F. Z., Sevcik, C., Possani, L. D., and Prestipino, G. (2004) Arch. Biochem. Biophys. 430, 256-63]. It is the most distinctive member of the alpha-KTx15 subfamily of scorpion toxins. Six members of the alpha-KTx15 subfamily have been reported so far to be specific for this subtype of the K+ channel; however, none of them have had their three-dimensional structure determined, and no information for the residues possibly involved in channel recognition and binding is available. Natural discrepin (n-discrepin) was prepared from scorpion venom, and its synthetic analogue (s-discrepin) was obtained by solid-phase synthesis. Analysis of two-dimensional 1H NMR spectra of n- and s-discrepin indicates that both peptides have the same structure. Here we report the solution structure of s-discrepin determined by NMR using 565 meaningful distance constraints derived from the volume integration of the two-dimensional NOESY spectrum, 22 dihedrals, and three hydrogen bonds. Discrepin displays the alpha/beta scaffold, characteristic of scorpion toxins. Some features of the proposed interacting surface between the toxin and channel as well as the opposite "alpha-helix surface" are discussed in comparison with those of other alpha-KTx15 members. Both n- and s-discrepin exhibit similar physiological actions as verified by patch-clamp and binding and displacement experiments.
AQUAPORINS: Production Optimization and Characterization (2011)

Aquaporins are water facilitating proteins embedded in the cellular membranes. Such channels have been identified in almost every living organism – including humans. They are vital molecules and their malfunction can lead to several severe disorders. An increased understanding of their structure, function and regulation is of utmost importance for developing current and future drugs.\n\nThe first problem to overcome is to acquire the proteins in sufficient amounts to enable characterization. To achieve this, proteins are often produced in a host organism. One of the most successful hosts for recombinant overproduction is the yeast Pichia pastoris. Using this yeast we could obtain exceptional yield of aquaporin 1, whereas some others were below the threshold needed for successful subsequent characterization. In this process, we have established methods allowing fast and accurate determination of the initial production yield. Furthermore, we optimized the yield for low producing targets, enabling studies of proteins previously out of reach, exemplified with human aquaporin 4.\n\nCharacterization has been performed on aquaporins obtained in sufficient quantities, and the functionality of aquaporin 1, 5 and 10 has been assessed. Furthermore, a glycosylation was found to stabilize the aquaporin 10 tetramer although only a minority of the monomers where modified. Moreover, we used protein crystallography to determine the three dimensional structure of a hAQP5 mutant, providing insight into regulation of the protein by trafficking.\n\nTaken together, these results provide insight into factors directing high production of eukaryotic membrane proteins. The subsequent characterization, including functional and structural determination, reveals new knowledge about aquaporin activity and regulation.
First-Principles Studies on Cation Dopants and Electrolyte|Cathode Interphases for Lithium Garnets (2015)

Lithium garnet with the formula Li7La3Zr2O12 (LLZO) has many properties of an ideal electrolyte in all-solid state lithium batteries. However, internal resistance in batteries utilizing these electrolytes remains high. For widespread adoption, the LLZO’s internal resistance must be lowered by increasing its bulk conductivity, reducing grain boundary resistance, and/or pairing it with an appropriate cathode to minimize interfacial resistance. Cation doping has been shown to be crucial in LLZO to stabilize the higher conductivity cubic structure, yet there is still little understanding about which cations have high solubility in LLZO. In this work, we apply density functional theory (DFT) to calculate the defect energies and site preference of all possible dopants in these materials. Our findings suggest several novel dopants such as Zn2+ and Mg2+ predicted to be stable on the Li- and Zr-sites, respectively. To understand the source of interfacial resistance between the electrolyte and the cathode, we investigate the thermodynamic stability of the electrolyte|cathode interphase, calculating the reaction energy for LLMO (M = Zr, Ta) against LiCoO2, LiMnO2, and LiFePO4 (LCO, LMO, and LFP, respectively) cathodes over the voltage range seen in lithium-ion battery operation. Our results suggest that, for LLZO, the LLZO|LCO is the most stable, showing only a low driving force for decomposition in the charged state into La2O3, La2Zr2O7, and Li2CoO3, while the LLZO|LFP appears to be the most reactive, forming Li3PO4, La2Zr2O7, LaFeO3, and Fe2O3. These results provide a reference for use by researchers interested in bonding these electrolytes to cathodes.
Experimental models of sepsis and septic shock: an overview (2004)

Sepsis remains a major cause of morbidity and mortality in surgical patients and trauma victims, mainly due to sepsis-induced multiple organ dysfunction. In contrast to preclinical studies, most clinical trials of promising new treatment strategies for sepsis have fails to demonstrate efficacy. Although many reasons could account for this discrepancy, the misinterpretation of preclinical data obtained from experimental studies, and especially the use of animal models that do not adequately mimic human sepsis may have been contributing factors. In this review, the benefits and limitations of various animal models of sepsis are discussed to clarify the extend to which findings are relevant to human sepsis, particularly with respect to the subsequent design and execution of clinical trials. Such models include intravascular infusion of endotoxin or live bacteria, bacterial peritonitis, cecal ligation and perforation, soft tissue infection, pneumonia or meningitis models, using different animal species including rats, mice, rabbits, dogs, pigs, sheep and nonhuman primates. Despite several limitations, animal models remain essential in the development of all new therapies for sepsis and septic shock, because they provide fundamental information about the pharmacokinetics, toxicity, and mechanism of drug action that cannot be duplicated by other methods. New therapeutic agents should be studies in infection models, even after the initiation of the septic process. Furthermore, debility conditions need to be reproduced to avoid the exclusive use of healthy animals, which often do not represent the human septic patient.
TCR-Engineered, Customized, Antitumor T Cells for Cancer Immunotherapy: Advantages and Limitations (2011)

The clinical outcome of the traditional adoptive cancer immunotherapy approaches involving the administration of donor-derived immune effectors, expanded ex vivo, has not met expectations. This could be attributed, in part, to the lack of sufficient high-avidity antitumor T-cell precursors in most cancer patients, poor immunogenicity of cancer cells, and the technological limitations to generate a sufficiently large number of tumor antigen-specific T cells. In addition, the host immune regulatory mechanisms and immune homeostasis mechanisms, such as activation-induced cell death (AICD), could further limit the clinical efficacy of the adoptively administered antitumor T cells. Since generation of a sufficiently large number of potent antitumor immune effectors for adoptive administration is critical for the clinical success of this approach, recent advances towards generating customized donor-specific antitumor-effector T cells by engrafting human peripheral blood-derived T cells with a tumor-associated antigen-specific transgenic T-cell receptor (TCR) are quite interesting. This manuscript provides a brief overview of the TCR engineering-based cancer immunotherapy approach, its advantages, and the current limitations.
Expansion of CD4+ CD25+ Foxp3+ T cells by bone marrow‐derived dendritic cells (2008)

Summary Dendritic cells (DCs) are the most important antigen‐presenting cells of the immune system and have a crucial role in T‐lymphocyte activation and adaptive immunity initiation. However, DCs have also been implicated in maintaining immunological tolerance. In this study, we evaluated changes in the CD4 + CD25 + Foxp3 + T‐cell population after co‐culture of lymph node cells from BALB/c mice with syngeneic bone marrow‐derived DCs. Our results showed an increase in CD4 + CD25 + Foxp3 + T cells after co‐culture which occurred regardless of the activation state of DCs and the presence of allogeneic apoptotic cells; however, it was greater when DCs were immature and were pulsed with the alloantigen. Interestingly, syngeneic apoptotic thymocytes were not as efficient as allogeneic apoptotic cells in expanding the CD4 + CD25 + Foxp3 + T‐cell population. In all experimental settings, DCs produced high amounts of transforming growth factor (TGF)‐β. The presence of allogeneic apoptotic cells induced interleukin (IL)‐2 production in immature and mature DC cultures. This cytokine was also detected in the supernatants under all experimental conditions and enhanced when immature DCs were pulsed with the alloantigen. CD4 + CD25 + Foxp3 + T‐cell expansion during co‐culture of lymph node cells with DCs strongly suggested that the presence of alloantigen enhanced the number of regulatory T cells (Tregs) in vitro . Our data also suggest a role for both TGF‐β and IL‐2 in the augmentation of the CD4 + CD25 + Foxp3 + population.
Onset and recurrence of proliferative vitreoretinopathy in various vitreoretinal disease. (1995)

PVR starts earliest at 2 weeks after an event and subsequently quietens down within a maximum of 45 months after treatment (median 2 months). PVR may recur more than once but the time course of the disease is likely to be the same for each recurrence.
Topology of mannosidase II in rat liver Golgi membranes and release of the catalytic domain by selective proteolysis. (1986)

The orientation of mannosidase II, an integral Golgi membrane protein involved in asparagine-linked oligosaccharide processing, has been examined in rat liver Golgi membranes. Previous studies on mannosidase II purified from Golgi membranes revealed an intact subunit of 124,000 daltons, as well as a catalytically active 110,000-dalton degradation product generated during purification (Moremen, K. W., and Touster, O. (1985) J. Biol. Chem. 260, 6654-6662). In Triton X-100 extracts of Golgi membranes, the intact enzyme was cleaved by a variety of proteases to generate degradation products similar to those observed previously. At appropriate concentrations, chymotrypsin, pronase, and proteinase K generated 110,000-dalton species, while trypsin and Staphylococcus aureus V8 protease generated 115,000-dalton forms. Cleavage by chymotrypsin under mild conditions (10 micrograms/ml, 10 min, 20 degrees C) resulted in a complete conversion to a catalytically active 110,000-dalton form of the enzyme which was extremely resistant to further degradation. Attempts to demonstrate these protease digestions in nonpermeabilized Golgi membranes were unsuccessful, a result suggesting that the protease-sensitive regions are not accessible on the external surface of the membrane. In Golgi membranes permeabilized by treatment with 0.5% saponin, mannosidase II could readily be cleaved to the 110,000-dalton form by digestion with chymotrypsin under conditions similar to those which result in a proteolytic inactivation of galactosyltransferase, a lumenal Golgi membrane marker. Although mannosidase II catalytic activity was not diminished by this chymotrypsin digestion, as much as 90% of the enzyme activity was converted to a nonsedimentable form. To examine the effect of the proteolytic cleavage on the partition behavior of the enzyme, control and chymotrypsin-treated Triton X-114 extracts of Golgi membranes were examined by phase separation at 35 degrees C. The undigested enzyme partitioned into the detergent phase consistent with its location as an integral Golgi membrane protein, while the 110,000-dalton chymotrypsin-digested enzyme partitioned almost exclusively into the aqueous phase in a manner characteristic of a soluble protein. These results suggest that mannosidase II catalytic activity resides in a proteolytically resistant, hydrophilic 110,000-dalton domain. Attachment of this catalytic domain to the lumenal face of Golgi membranes is achieved by a proteolytically sensitive linkage to a 14,000-dalton hydrophobic membrane anchoring domain.
A system for the automated office environment (1981)

The OFS application has evolved over a period of ten years of use and experimentation. The broad-based objectives of office systems have guided the ongoing development. VM/CMS has proved to be ideal as the control program base for such an activity. Actual user experience and feedback have been an invaluable means of validating both implementation and presentation techniques. We have found that with every new insight several new questions surface. The current OFS application is the product of this evolutionary process.
Projection subtypes of rat neostriatal matrix cells revealed by intracellular injection of biocytin (1990)

Individual neostriatal-matrix spiny neurons were stained intracellularly with biocytin after intracellular recording in vivo, and their axons were traced into the globus pallidus (GP), entopeduncular nucleus (EP), and/or substantia nigra (SN). The locations of the neurons within the matrix compartment of the neostriatum (NS) were established by immunocytochemical counterstaining of sections containing the cell bodies using antibodies for calbindin-D28K. This allowed nearly complete visualization of the axonal projections of single NS neurons. On the basis of their intrastriatal axonal arborizations, matrix spiny neurons could be divided into 2 types. One type, which was the more common, had local axonal arborizations restricted to the region of the dendritic field, often with axon collaterals arborizing within the dendritic field of the cells of origin. A second, less common, cell type in the matrix had local axon collaterals distributed widely in the NS. Among matrix neurons with restricted local collateral fields, 3 subtypes could be distinguished on the basis of their efferent axonal projections. Type I cells projected only to the GP. Type IIa cells projected to the GP, EP, and SN pars reticulata. Type IIb cells projected to the GP and SN but not to the EP. The shapes and densities of the GP arborizations varied in the 3 cell types, with the cells projecting only to the GP (type I) projecting more heavily and filling a larger volume there than type II cells. The dendrites and intrastriatal axon collaterals of 3 subtypes were similar in morphology. The class of matrix spiny neurons with intrastriatal axon collaterals distributed widely in the NS were observed to project to the GP. Projections beyond the GP were not identified for this cell type, but could not be ruled out. Somatodendritic morphologies of neurons did not differ according to the projection site. These results demonstrate that NS matrix spiny cells are more heterogeneous in their efferent projection patterns than previously suspected on the basis of retrograde axonal tracing and immunocytochemical studies. As predicted by those previous studies, there is a class of matrix neurons that projects only to the GP. Presumably, these cells contain enkephalin. Cells projecting to the SN and EP, and so presumably containing substance P, give off a small projection to the GP, as well, and differ in their collateralization patterns within the 3 major target nuclei.
Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization (2017)

There is growing interest in studying and engineering integral membrane proteins (MPs) that play key roles in sensing and regulating cellular response to diverse external signals. A MP must be expressed, correctly inserted and folded in a lipid bilayer, and trafficked to the proper cellular location in order to function. The sequence and structural determinants of these processes are complex and highly constrained. Here we describe a predictive, machine-learning approach that captures this complexity to facilitate successful MP engineering and design. Machine learning on carefully-chosen training sequences made by structure-guided SCHEMA recombination has enabled us to accurately predict the rare sequences in a diverse library of channelrhodopsins (ChRs) that express and localize to the plasma membrane of mammalian cells. These light-gated channel proteins of microbial origin are of interest for neuroscience applications, where expression and localization to the plasma membrane is a prerequisite for function. We trained Gaussian process (GP) classification and regression models with expression and localization data from 218 ChR chimeras chosen from a 118,098-variant library designed by SCHEMA recombination of three parent ChRs. We use these GP models to identify ChRs that express and localize well and show that our models can elucidate sequence and structure elements important for these processes. We also used the predictive models to convert a naturally occurring ChR incapable of mammalian localization into one that localizes well.
Elevated Serum Levels of Interleukin-17A in Uveitis Patients (2013)

Serum IL-17A levels are elevated in uveitis patients, particularly in active uveitis.
Pentapeptide Nuclear Localization Signal in Adenovirus E1a (1987)

The adenovirus E1a gene products are nuclear proteins important in transcriptional control of viral functions during infection. By producing normal E1a proteins and derivatives of E1a in bacteria and microinjecting these proteins into cultured cells, we were able to examine their ability to localize to the nucleus. We showed that a short peptide sequence at the carboxyl terminus of E1a is necessary for the rapid (30-min) nuclear localization of that protein. Additionally, we showed that just the last five amino acids of E1a are sufficient to direct nuclear accumulation of a heterologous protein, Escherichia coli galactokinase, with the same kinetics as native E1a. The mechanism by which this pentamer mediates rapid nuclear localization was examined by testing the ability of a galactokinase derivative which has no signal pentamer to exit the nucleus, as well as to enter it. Because neither free entry nor exit was detected, the effect of the signal is unlikely to be through increased nuclear retention of freely diffusible proteins but rather by enhancement of entry into the nucleus.
Stroma-Initiated Hedgehog Signaling Takes Center Stage in B-Cell Lymphoma (2008)

Hedgehog-mediated signaling has been shown to promote growth and dissemination of solid cancers, most prominently basal cell carcinomas and medulloblastoma. Recent findings indicate that hedgehog signals are also important for tumor growth in hematologic malignancies. Hedgehog ligands secreted by stromal cells could elicit Patched/Smoothened-mediated antiapoptotic signaling in mouse B-cell lymphomas. Inhibition of hedgehog signaling induced apoptosis in lymphoma cells and prolonged survival of lymphoma-bearing mice. Depletion of tumor cells proceeded in the absence of p53 via the mitochondrial apoptotic pathway. These and other recently published data on hedgehog inhibition in cancer cells and their implications will be discussed.
Site‐Specific Cytosine to Uracil Transition by Using Reversible DNA Photo‐crosslinking (2010)

Targeting a single cytosine in the presence of others: The deamination coupled with 3-cyanovinylcarbazole-nucleoside-mediated photo-crosslinking allows heat-induced conversion of cytosine into uracil with high site-specificity and without side reactions. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
OX40 Expressed on Fresh Leukemic Cells From Adult T-Cell Leukemia Patients Mediates Cell Adhesion to Vascular Endothelial Cells: Implication for the Possible Involvement of OX40 in Leukemic Cell Infiltration (1997)

We demonstrated previously that OX40 and its ligand, gp34, directly mediate adhesion of activated normal CD4+ T cells, as well as human T-cell leukemia virus type I (HTLV-I)-transformed T cells to vascular endothelial cells. In the present study, we examined expression of OX40 on fresh leukemic cells from patients with adult T-cell leukemia (ATL) and its possible involvement in cell adhesion. Flow cytometric analysis showed that peripheral blood mononuclear cells (PBMC) or lymph node tumor cells from 15 of 17 cases expressed significant levels of OX40 without stimulation. On the other hand, gp34 was not expressed on these cells, although its expression is also known to be associated with HTLV-I-infection. In Western blot analysis, a 50-kD protein band was detected by anti-OX40 monoclonal antibody (MoAb) in two ATL cases examined, as well as phytohemagglutinin (PHA) blasts and Hut102, an HTLV-I-infected T-cell line, but not in resting PBMC or Jurkat. Expression of OX40 mRNA was shown by reverse transcriptase-polymerase chain reaction in all ATL cases tested, PHA-blasts, and Hut102, but not in resting PBMC or Jurkat. We could not detect expression of HTLV-I viral mRNA in any of the cases tested. Cell adhesion assay was performed and in at least three cases, fresh ATL cells exhibited adhesion to human umbilical vein endothelial cells that could be considerably inhibited by either anti-OX40 MoAb or anti-gp34 MoAb. Immunohistochemical staining of skin biopsy specimens indicated that infiltrating mononuclear cells express OX40 in vivo. Taken together, these data indicate that leukemic cells from most, but not all, ATL patients constitutively express OX40, which may play a role in leukemic cell infiltration in addition to cell adhesion in vivo.
In vitro nanobody discovery for integral membrane protein targets (2014)

Nanobodies (Nbs) or single-domain antibodies are among the smallest and most stable binder scaffolds known. In vitro display is a powerful antibody discovery technique used worldwide. We describe the first adaptation of in vitro mRNA/cDNA display for the rapid, automatable discovery of Nbs against desired targets, and use it to discover the first ever reported nanobody against the human full-length glucose transporter, GLUT-1. We envision our streamlined method as a bench-top platform technology, in combination with various molecular evolution techniques, for expedited Nb discovery.