gebhart/patrepeval huggingface dataset:
The Challenge of Preparing and Testing Combinatorial Compound Libraries in the Fast Lane, at the Front End of Drug Development (1994)

Combinatorial Compound Libraries (CCL) are at the front end of the development of new chemical entities. They are the result of a pragmatic, goal-oriented attitude, which emphasizes the discovery side of research activities. The odds to bump into a discovery, however, are pushed to the extreme with rigorously planned rationales. The CCL field has its origin in peptide chemistry but is migrating into general organic chemistry. The incentive is the coveted goal to be able to prepare large libraries of 'small molecules'. Efforts are directed towards an expansion of the repertoire of high yield reactions on solid phase, in order to readily access semi-rigid globular ligands. The CCL approach comes with its own strategies to provide a massive increase of compound evaluations by taking full advantage of the integrated preparation process with the option to control the physical format of compound ensembles or to classify them into defined subpopulations. A noticeable impact on the drug discovery process is expected. The libraries' preparation and evaluation principles are briefly discussed in this essay.
Mechanisms of ligand binding by monoclonal anti-fluorescyl antibodies. (1982)

Binding of fluorescyl ligand by five IgG anti-fluorescyl hybridoma proteins (4-4-20, 6-10-6, 20-4-4, 20-19-=1, 20-20-3) was examined. Relative reduction in fluorescence of bound fluorescein, deuterium oxide (D2O)-induced enhancement of fluorescence, and the effects of pH on binding kinetics were measured for each clone. Individual hybridoma proteins (all of which bind fluorescein with relatively high affinity) exhibited significant differences in the relative contribution of various forces (hydrophobicity, hydrogen bonding, ionic interactions) to binding and hence, affinity. The extent of such variations in binding mechanisms among monoclonal antibodies binding the same hapten is indicative of the extreme functional diversity of active sites. In addition, ligand binding by clone 20-20-3 was examined in greater detail. ABsorption spectra of ligand bound by purified intact antibody, Fab fragments, and reassociated heavy and light chains indicated that protonation of the fluorescyl ligand by a residue within the active site contributed significantly to the binding free energy. Comparative dissociation rates of fluorescein and a structural analog, rhodamine 110, were used to quantitatively substantiate the contribution of this interaction. Association and dissociation rate studies with fluorescein and antibody indicated that: 1) the active site appeared to undergo a conformational change upon ligand binding, and 2) neither intact disulfides nor intersite cooperativity affected the dissociation rate of bound ligand. Observed mechanisms of ligand binding are discussed in terms of proposed mechanisms of antibody affinity maturation and diversity.
Molecular cloning and chromosomal localization of human membrane cofactor protein (MCP). Evidence for inclusion in the multigene family of complement-regulatory proteins. (1988)

Membrane cofactor protein (MCP), a regulatory molecular of the complement system with cofactor activity for the factor I-mediated inactivation of C3b and C4b, is widely distributed, being present on leukocytes, platelets, endothelial cells, epithelial cells, and fibroblasts. MCP was purified from a human T cell line (HSB2) and the NH2-terminal 24-amino acid sequence obtained by Edman degradation. An oligonucleotide probe based on this sequence was used to identify a clone from a human monocytic (U937) cDNA library. Nucleotide sequencing showed a 43-bp 5'-untranslated region, an open reading frame of 1,152 bp, and a 335-bp 3'-untranslated region followed by a 16-bp poly(A) track. The deduced full-length MCP protein consists of a 34-amino acid signal peptide and a 350-amino acid mature protein. The protein has, beginning at the NH2 terminus, four approximately 60-amino acid repeat units that match the consensus sequence found in a multigene family of complement regulatory proteins (C3b-receptor or CR1, C3d-receptor or CR2, decay-accelerating factor, C4-binding protein, and factor H), as well as several other complement and non-complement proteins. The remainder of the MCP protein consists of 25 amino acids that are rich in serine and threonine (probable site of heavy O-linked glycosylation of MCP), 17 amino acids of unknown significance, and a 23-amino acid transmembrane hydrophobic region followed by a 33-amino acid cytoplasmic tail. The MCP gene was localized to human chromosome 1, bands 1q31-41, by analysis of human x rodent somatic cell hybrid clones and by in situ hybridization. This same genetic region contains the multigene family of complement-regulatory proteins, which is thereby enlarged to include the functionally and structurally related MCP.
Embedding Graphs into the Extended Grid (2007)

Let $G=(V,E)$ be an arbitrary undirected source graph to be embedded in a target graph $EM$, the extended grid with vertices on integer grid points and edges to nearest and next-nearest neighbours. We present an algorithm showing how to embed $G$ into $EM$ in both time and space $O(|V|^2)$ using the new notions of islands and bridges. An island is a connected subgraph in the target graph which is mapped from exactly one vertex in the source graph while a bridge is an edge between two islands which is mapped from exactly one edge in the source graph. This work is motivated by real industrial applications in the field of quantum computing and a need to efficiently embed source graphs in the extended grid.
Controlled Growth of Nanoparticles from Solution with In Situ Liquid Transmission Electron Microscopy (2011)

Direct visualization of lead sulfide nanoparticle growth is demonstrated by selectively decomposing a chemical precursor from a multicomponent solution using in situ liquid transmission electron microscopy. We demonstrate reproducible control over growth mechanisms that dictate the final morphology of nanostructures while observing growth in real-time with subnanometer spatial resolution. Furthermore, while an intense electron beam can initiate nanoparticle growth, it is also shown that a laser can trigger the reaction independently of the imaging electrons.
Heparin and Activin-Binding Determinants in Follistatin and FSTL3 (2004)

Local regulation of pituitary FSH secretion and many other cellular processes by follistatin (FS) can be ascribed to its potent ability to bind and bioneutralize activin, in conjunction with binding to cell surface heparan-sulfate proteoglycans through a basic heparin-binding sequence (HBS; residues 75-86) in the first of the three FS domains. The FS homolog, FSTL3, also binds activin, but lacks any HBS and cannot associate with cell surfaces. We have used mutational analyses to define the determinants for heparin binding and activin interaction in FS and to determine the effects of conferring heparin binding to FSTL3. Mutants expressed from 283F cells were tested for cell surface and heparin affinity binding, for competitive activin binding and for bioactivity by suppression of pituitary cell FSH secretion. Replacement of the HBS or the full-length FS-domain 1 abolished cell surface binding but enhanced activin binding 4- to 8-fold. Surface binding was partially reduced after mutation of either lysine pair 75/76 or 81/82 and eliminated after mutation of both pairs. The 75/76 mutation reduced activin binding and, therefore, pituitary cell bioactivity by 5-fold. However, insertion of the HBS into FSTL3 did not restore heparin binding or pituitary-cell bioactivity. These results show that 1) the residues within the HBS are necessary but not sufficient for heparin binding, and 2) the HBS also harbors determinants for activin binding. Introduction of the full domain from FS conferred heparin binding to FSTL3, but activin binding was abolished. This implies an evolutionary safeguard against surface binding by FSTL3, supporting other evidence for physiological differences between FS and FSTL3.
Surviving cyber warfare with a hybrid multiagent-base intrusion prevention system (2010)

We have entered a new age of cyber warfare that threatens the survival and reliability of e-organizations. This threat necessitates developing a new generation of security solutions that are able to provide instantaneous in-line layered preemptive protection. Developing such a security solution is a challenge, since threats against e-organizations have increased in number and sophistication, to the point where many security experts believe that the situation is out of control.
Immunotherapeutic strategies to prevent and treat human herpesvirus 6 reactivation after allogeneic stem cell transplantation (2012)

Human herpesvirus (HHV) 6 causes substantial morbidity and mortality in the immunocompromised host and has no approved therapy. Adoptive transfer of virus specific T cells has proven safe and apparently effective as prophylaxis and treatment of other virus infections in immunocompromised patients; however, extension to subjects with HHV6 has been hindered by the paucity of information on targets of cellular immunity. We now characterize the cellular immune response from 20 donors against 5 major HHV6B antigens predicted to be immunogenic and define a hierarchy of immunodominance of antigens based on the frequency of responding donors and the magnitude of the T-cell response. We identified specific epitopes within these antigens and expanded the HHV6 reactive T cells using a GMP-compliant protocol. The expanded population comprised both CD4(+) and CD8(+) T cells that were able to produce multiple effector cytokines and kill both peptide-loaded and HHV6B wild-type virus-infected target cells. Thus, we conclude that adoptive T-cell immunotherapy for HHV6 is a practical objective and that the peptide and epitope tools we describe will allow such cells to be prepared, administered, and monitored in human subjects.
Ultraporous 3D polymer meshes by low‐temperature electrospinning: Use of ice crystals as a removable void template (2007)

Abstract While electrospinning provides an excellent preparation method for the manufacturing of polymer fibers with defined diameter, controlling the overall porosity of the resulting fiber assemblies has remained elusive, particularly at higher porosities. In this study, the use of a low‐temperature fiber collection device in air with controlled humidity allowed the simultaneous deposition of polymer fibers and ice particles from condensing humidity. The ice particles were intimately embedded within the polymer fibers and served as a pore template thus defining the mesh porosity after drying of the collected fiber assemblies. The amount of water condensation therefore contributes to the control of the mean interfiber distance and the resulting porosity. This simple and well accessible use of ice crystals as void templates gives access to the preparation of biodegradable tissue engineering scaffolds with an up to four times higher porosity if compared to conventional fiber electrospinning. The successful application of low‐temperature electrospinning using polyesters or polyurethanes suggests a broad, material independent applicability of the process for the preparation of highly porous polymer structures. POLYM. ENG. SCI., 47:2020–2026, 2007. © 2007 Society of Plastics Engineers
Selective glutaraldehyde-mediated coupling of proteins to the 3'-adenine terminus of polymerase chain reaction products. (2008)

Attachment of proteins to the 3' end of DNA increases stability of the DNA in serum and retards clearance of DNA by major organs, thereby enhancing in vivo half-life and therapeutic potential of DNA. Unfortunately, the length of DNA molecules that can be produced with 3 ' modifications by solid-phase synthesis for protein attachment is limited to 45-60 nucleotides due to uncertainties about sequence fidelity for longer oligonucleotides. Here we describe selective covalent coupling of proteins or other molecules to the 3'-adenine overhang of unlabeled and fluorophore-labeled double-stranded polymerase chain reaction products putatively at the N6 position of adenine using 2.5% glutaraldehyde at pH 6.0 and 4 degrees C for at least 16 h. Gel mobility shift analyses and fluorescence analyses of the shifted bands supported conjugate formation between double-stranded polymerase chain reaction products and beta2-microglobulin. In addition, blunt-ended DNA ladder fragments treated with glutaraldehyde at 4 degrees C showed no evidence of DNA-DNA or DNA-protein conjugate formation. With the present cold glutaraldehyde technique, longer DNA-3'-protein conjugates might be easily mass-produced. The protein portion of a DNA-3'-protein conjugate could possess functionality as well, such as receptor binding for cell entry, cytotoxicity, or opsonization.
A Phase I Study of Nonmyeloablative Chemotherapy and Adoptive Transfer of Autologous Tumor Antigen-Specific T Lymphocytes in Patients With Metastatic Melanoma (2002)

This report describes a phase I clinical trial using nonmyeloablative, lympho-depleting chemotherapy in combination with adoptive immunotherapy in patients with metastatic melanoma. The chemotherapy-conditioning schedule that induced transient lymphopenia consisted of cyclophosphamide (30 or 60 mg/kg per day for 2 days) followed by fludarabine (25 mg/m(2) per day for 5 days). Immunotherapy for all patients consisted of in vitro expanded, tumor-reactive, autologous T-cell clones selected for high avidity recognition of melanoma antigens. Cohorts of three to six patients each received either no interleukin (IL)-2, low-dose IL-2 (72,000 IU/kg intravenously three times a day to a maximum of 15 doses), or high-dose IL-2 (720,000 IU/kg intravenously three times a day for a maximum of 12 doses). The toxicities associated with this treatment were transient and included neutropenia and thrombocytopenia that resolved in all patients. High dose intravenous IL-2 was better tolerated by patients after chemotherapy than during previous immunotherapy cycles without chemotherapy. No patient exhibited an objective clinical response to treatment, although five patients demonstrated mixed responses or transient shrinkage of metastatic deposits. This study established a nonmyeloablative-conditioning regimen that could be safely administered in conjunction with adoptive T-cell transfer and IL-2 in patients with metastatic melanoma.
Prostate cancer bone metastasis: Reactive oxygen species, growth factors and heparan sulfate proteoglycans provide a signaling triad that supports progression (2008)

4504 Introduction and Objective: Prostate cancer (PCa) bone metastasis often present in patients after a long latent period. Dormant cancer cells in contact with bone stromal cells can be reactivated under certain pathophysiologic conditions. We characterized novel molecular pathways leading to PCa bone metastasis in animal models.  Methods: Tissue microarrays of normal (4), PIN (13), benign (22), primary (19) PCa and PCa bone metastasis (58) were analyzed by IHC for the expression of β2-microglobulin (β2-M), a novel growth factor and signaling molecule, focal adhesion kinase (FAK), a key cell adhesion molecule, LIV-1, a zinc transporter involved in epithelial to mesenchymal transition, BDNF, a chemokine, and heparanase (HPSE), a heparan sulfate (HS) degrading enzyme. IHC was scored blindly by one pathologist. Data were analyzed by Kruskal-Wallis test for p-value and logistic regression analysis to differentiate Gleason scores.  Results: PCa cells with mitochondrial DNA mutations or activated by β2-M provoked consistently higher levels of reactive oxygen species (ROS) production. ROS stimulated HS proteoglycan, perlecan, expression and augmented PCa cell growth in bone microenvironment. Downstream targets of ROS, HS/perlecan and β2-M signaling were identified: FAK, LIV-1, and BDNF. Results showed that β2-M (p
Combinatorial Analysis of mRNA Expression Patterns in Mouse Embryos Using Hybridization Chain Reaction (2015)

Multiplexed fluorescent hybridization chain reaction (HCR) and advanced imaging techniques can be used to evaluate combinatorial gene expression patterns in whole mouse embryos with unprecedented spatial resolution. Using HCR, DNA probes complementary to mRNA targets trigger chain reactions in which metastable fluorophore-labeled DNA HCR hairpins self-assemble into tethered fluorescent amplification polymers. Each target mRNA is detected by a probe set containing one or more DNA probes, with each probe carrying two HCR initiators. For multiplexed experiments, probe sets for different target mRNAs carry orthogonal initiators that trigger orthogonal DNA HCR amplification cascades labeled by spectrally distinct fluorophores. As a result, in situ amplification is performed for all targets simultaneously, and the duration of the experiment is independent of the number of target mRNAs. We have used multiplexed fluorescent in situ HCR and advanced imaging technologies to address questions of cell heterogeneity and tissue complexity in craniofacial patterning and anterior neural development. In the sample protocol presented here, we detect three different mRNA targets: Tg(egfp), encoding the enhanced green fluorescent protein (GFP) transgene (typically used as a control); Twist1, encoding a transcription factor involved in cell lineage determination and differentiation; and Pax2, encoding a transcription factor expressed in the mid-hindbrain region of the mouse embryo.
The biology , function , and biomedical applications of exosomes (2020)

The study of extracellular vesicles (EVs) has the potential to identify unknown cellular and molecular mechanisms in intercellular communication and in organ homeostasis and disease. Exosomes, with an average diameter of ~100 nanometers, are a subset of EVs. The biogenesis of exosomes involves their origin in endosomes, and subsequent interactions with other intracellular vesicles and organelles generate the final content of the exosomes. Their diverse constituents include nucleic acids, proteins, lipids, amino acids, and metabolites, which can reflect their cell of origin. In various diseases, exosomes offer a window into altered cellular or tissue states, and their detection in biological fluids potentially offers a multicomponent diagnostic readout. The efficient exchange of cellular components through exosomes can inform their applied use in designing exosome-based therapeutics.
Heat shock proteins in pancreatic diseases (2008)

Heat shock proteins (HSPs) are chaperone proteins that protect living cells against injury-inducing stimuli. Dysregulated expression of HSPs has been observed in various disease conditions including cancer. Using knock-out and transgenic animal approach, as well as standard, methods of heat shock protein 70 (HSP70) induction (i.e. thermal stress and arsenite administration), it has been shown that HSP70 protects against cell injury and acinar necrosis in experimental model of pancreatitis in animals. Animals in which HSP70 is induced prior to cerulein administration in a cerulein model of pancreatitis have reduced severity of pancreatitis, as demonstrated by lower serum amylase, lesser acinar necrosis on histology and decreased neutrophilic infiltration, suggesting that HSP70 is protective against cell death. Similar to the protective role of HSP70 in a pancreatitis model, HSP70 overexpression has been observed in pancreatic cancer and is believed to protect cancer cells from cell death. HSP70 is overexpressed both at mRNA and protein levels in pancreatic cancer cell lines as compared to normal pancreatic ductal cells. On a more clinical note, HSP70 is present in great abundance in pancreatic cancer clinical specimens as compared to normal pancreatic margins. Inhibition of HSP70 expression in pancreatic cancer cells leads to caspase-dependent apoptotic cell death and is a novel therapeutic modality for pancreatic cancer. Triptolide is a pharmacological agent which highly effective inhibiting HSP70 expression in pancreatic cancer cells and thus induces cell death. Moreover, triptolide is highly efficacious in reducing growth as well as locoregional spread of pancreatic tumors in an orthotopic model of pancreatic cancer and has tremendous potential as a novel therapeutic agent.
Chondrocytes contain a growth factor that is localized in the nucleus and is associated with chromatin. (1980)

Bovine scapular and articular chondrocytes were isolated from fresh cartilage and disrupted by sonication. The disrupted cells had the ability to stimulate DNA synthesis and cell division in vitro in chondrocytes and in 3T3 cells. Subcellular fractions were prepared by two methods, enucleation with cytochalasin B and lysis of cells with Nonidet P-40. After enucleation of chondrocytes, karyoplasts and cytoplasts were collected, disrupted by sonication, and tested for their ability to stimulate DNA synthesis. Over 95% of the cellular growth factor activity was localized in the karyoplast. In addition, after lysis of chondrocytes in Nonidet P-40, over 95% of the growth factor activity was recovered in the nuclear fraction. Chondrocyte chromatin was prepared by low ionic strength detergent treatment of karyoplasts. All of the growth factor activity of the karyoplast was found to be associated with chromatin. The growth factor activity of chondrocytes, cytoplasts, karyoplasts, and chromatin was analyzed by gel filtration on Bio-Gel A-0.5 m equilibrated with 4 M guanidine . HCl and 5 mM dithiothreitol. Chondrocytes, chondrocyte karyoplasts, and chondrocyte chromatin had similar column elution profiles, with molecular weights in the range of 12,000-22,000.
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. (2002)

Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT) is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, thus flexible in participating in both de novo and salvage pathways of NAD synthesis. Human NMNAT also catalyzes the rate-limiting step of the metabolic conversion of the anticancer agent tiazofurin to its active form tiazofurin adenine dinucleotide (TAD). The tiazofurin resistance is mainly associated with the low NMNAT activity in the cell. We have solved the crystal structures of human NMNAT in complex with NAD, deamido-NAD, and a non-hydrolyzable TAD analogue beta-CH(2)-TAD. These complex structures delineate the broad substrate specificity of the enzyme toward both NMN and NaMN and reveal the structural mechanism for adenylation of tiazofurin nucleotide. The crystal structure of human NMNAT also shows that it forms a barrel-like hexamer with the predicted nuclear localization signal sequence located on the outside surface of the barrel, supporting its functional role of interacting with the nuclear transporting proteins. The results from the analytical ultracentrifugation studies are consistent with the formation of a hexamer in solution under certain conditions.