gebhart/patrepeval huggingface dataset:
Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation (2015)

While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.
Photo-Cross-Linking of Type I Collagen Gels in the Presence of Smooth Muscle Cells:  Mechanical Properties, Cell Viability, and Function (2003)

The effectiveness of photomediated cross-linking of type I collagen gels in the presence of rat aortic smooth muscle cells (RASMC) as a method to enhance gel mechanical properties while retaining native collagen triple helical structure and maintaining high cell viability was investigated. Collagen was chemically modified to incorporate an acrylate moiety. Collagen methacrylamide was cast into gels in the presence of a photoinitiator along with RASMC. The gels were cross-linked using visible light irradiation. Neither acrylate modification nor the cross-linking reaction altered collagen triple helical content. The cross-linking reaction, however, moved the denaturation temperature beyond the physiologic range. A twelve-fold increase in shear modulus was observed after cross-linking. Cell viability in the range of 70% (n = 4, p > 0.05) was observed in the photo-cross-linked gels. Moreover the cells were able to contract the cross-linked gel in a manner commensurate with that observed for natural type I collagen. Methacrylate-mediated photo-cross-linking is a facile route to improve mechanical properties of collagen gels in the presence of cells while maintaining high cell viability. This enhances the potential for type I collagen gels to be used as scaffolds for tissue engineering.
Processes following changes of phase angle between current and voltage in electric circuits (1999)

Investigations of the changes of current frequency in R, L electric circuits supplied with 50 Hz sinusoidal voltage during changes of the phase angle between current and voltage are presented. Changes of reactance of the electric circuit are demonstrated as consequences of change of current frequency during the transient process, which is a possible new explanation of the occurrence of the aperiodical component of the current. For fast transient processes of phase angle change, current frequency is different from the voltage frequency.
ChemInform Abstract: Naturally Occurring Linear Fused Thiazoline‐Thiazole Containing Metabolites: Total Synthesis of (‐)‐Didehydromirabazole A, a Cytotoxic Alkaloid from Blue‐Green Algae. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Antigenic relationships among homologous structural polypeptides of porcine, feline, and canine coronaviruses (1982)

Transmissible gastroenteritis virus of swine (TGEV), feline infectious peritonitis virus (FIPV), and canine coronavirus were studied with respect to their serological cross-reactivity in homologous and heterologous virus neutralization, immune precipitation of radiolabeled TGEV, electroblotting, and enzyme-linked immunosorbent assay using individual virion polypeptides prepared by polyacrylamide gel electrophoresis. TGEV was neutralized by feline anti-FIPV serum, and the reaction was potentiated by complement; heterologous neutralization involved antibody reacting with the peplomer protein (P), the envelope protein (E), and cellular (glycolipid) components incorporated into the TGEV membrane. Electrophoretic analysis of immune precipitates containing [35S]methionine-labeled disrupted TGEV and feline anti-FIPV antibody confirmed the reaction with the P and E polypeptides and showed the nucleocapsid protein (N) in addition. Electroblotting, followed by incubation with antibody, 125I-labeled protein A, and fluorography, disclosed cross-reactions between the three viruses at the N and E levels and revealed differences in the apparent molecular weights of the latter. Enzyme immunoassays performed with standard amounts of immobilized P, N, and E polypeptides of the three viruses showed recognition of the antigens by homologous and heterologous antibody to comparable degrees. These results indicate a close antigenic relationship between TGEV, FIPV, and canine coronavirus due to common determinants on the three major virion proteins. The taxonomic implications of these findings are discussed.
Brousentsov's Ternary Principle, Bergman's Number System and Ternary Mirror-symmetrical Arithmetic (2002)

Journal Article Brousentsov's Ternary Principle, Bergman's Number System and Ternary Mirror-symmetrical Arithmetic Get access Alexey Stakhov Alexey Stakhov Search for other works by this author on: Oxford Academic Google Scholar The Computer Journal, Volume 45, Issue 2, 2002, Pages 221–236, https://doi.org/10.1093/comjnl/45.2.221 Published: 01 January 2002
Be on Target: Strategies of Targeting Alternative and Lectin Pathway Components in Complement-Mediated Diseases (2018)

The complement system has moved into the focus of drug development efforts in the last decade, since its inappropriate or uncontrolled activation has been recognized in many diseases. Some of them are primarily complement-mediated rare diseases, such as paroxysmal nocturnal hemoglobinuria, C3 glomerulonephritis, and atypical hemolytic uremic syndrome. Complement also plays a role in various multifactorial diseases that affect millions of people worldwide, such as ischemia reperfusion injury (myocardial infarction, stroke), age-related macular degeneration, and several neurodegenerative disorders. In this review, we summarize the potential advantages of targeting various complement proteins with special emphasis on the components of the lectin (LP) and the alternative pathways (AP). The serine proteases (MASP-1/2/3, factor D, factor B), which are responsible for the activation of the cascade, are straightforward targets of inhibition, but the pattern recognition molecules (mannose-binding lectin, other collectins, and ficolins), the regulatory components (factor H, factor I, properdin), and C3 are also subjects of drug development. Recent discoveries about cross-talks between the LP and AP offer new approaches for clinical intervention. Mannan-binding lectin-associated serine proteases (MASPs) are not just responsible for LP activation, but they are also indispensable for efficient AP activation. Activated MASP-3 has recently been shown to be the enzyme that continuously supplies factor D (FD) for the AP by cleaving pro-factor D (pro-FD). In this aspect, MASP-3 emerges as a novel feasible target for the regulation of AP activity. MASP-1 was shown to be required for AP activity on various surfaces, first of all on LPS of Gram-negative bacteria.
Axonal pathology in multiple sclerosis: relationship to neurologic disability (1999)

In this review, data is summarized supporting the hypothesis that axonal loss is a major pathologic process responsible for irreversible neurologic disability in patients with multiple sclerosis. Pathologic studies implicate inflammatory demyelination as a principal cause of axonal transection and subsequent axonal degeneration. Axonal degeneration caused by chronic demyelination in the absence of active inflammation may also contribute to progressive disability in the later stages of the disease. Studies using magnetic resonance spectroscopy suggest that axonal loss begins at the onset of the disease, and studies using magnetic resonance imaging have documented brain atrophy in the earliest stages of multiple sclerosis. Brain atrophy increases during the relapsing-remitting disease stage without concurrent disability progression. This suggests that compensatory mechanisms maintain neurologic function, despite progressive brain tissue loss during the early stages of the disease. Beyond a threshold, however, further axonal loss leads to continuously progressive neurologic disability. We hypothesize that the rate and extent of axonal loss during relapsing-remitting multiple sclerosis determines when a patient enters the secondary progressive stage of the disease. This view of disease pathogenesis has several important implications. First, surrogate markers of axonal loss are needed to monitor the disease process for patient care and for clinical trials. We propose brain parenchymal fraction, a precise measure of whole-brain atrophy, as an attractive candidate for this purpose. Second, disease-modifying therapy should be used early in multiple sclerosis patients, before extensive axonal loss has occurred. Third, neuroprotective drugs should be tested in combination with anti-inflammatory drugs in multiple sclerosis patients. Finally, studies of the time course of axonal loss, and its mechanisms are critical for effective therapeutic intervention.
Elevated levels of transforming growth factor alpha and epidermal growth factor receptor messenger RNA are early markers of carcinogenesis in head and neck cancer. (1993)

The squamous mucosa of patients who develop head and neck cancer is "condemned" or predisposed to disregulated growth as reflected by the high incidence of synchronous and metachronous primary tumors. We hypothesized that transformed and nontransformed mucosa from head and neck cancer patients would produce increased levels of transforming growth factor alpha (TGF-alpha) and its cell surface receptor, the epidermal growth factor receptor (EGFR), thereby contributing to this predisposition. Using molecular biological techniques, we examined the incidence and mechanism of TGF-alpha and EGFR overproduction in tumors and histologically normal mucosa excised from patients with squamous cell carcinoma of the head and neck (SCCHN) to test this hypothetical mechanism of field cancerization. Northern blot hybridization was used to evaluate the frequency of increased TGF-alpha and EGFR mRNA production in tissue excised from 24 patients with SCCHN and 10 cell lines compared with 7 control patients without cancer or a history of alcohol and tobacco use. Southern blot hybridization was used to examine for gene amplification. In patients with SCCHN, TGF-alpha mRNA was elevated by a mean of 5-fold in 95% of histologically "normal" mucosa samples (P = 0.001) and by a mean of 5-fold in 87.5% of tumors (P = 0.0001) while EGFR mRNA was elevated by a mean of 29-fold in 91% of histologically normal mucosa specimens (P = 0.0005) and by a mean of 69-fold in 92% of tumors (P = 0.0005), compared with mRNA levels in control normal mucosa. In 10 SCCHN cell lines, TGF-alpha mRNA was increased by a mean of 16-fold and EGFR mRNA levels were increased by a mean of 77-fold. Increased production of TGF-alpha and EGFR mRNA in the histologically normal mucosa of patients at risk for a primary or secondary head and neck cancer may serve both as a marker for malignant transformation and as a target for preventive therapies.
<title>Impact of beam smoothing method on direct-drive target performance for the NIF</title> (1997)

The impact of smoothing method on the performance of a direct drive target is modeled and examined in terms of its l-mode spectrum. In particular, two classes of smoothing methods are compared, smoothing by spectral dispersion (SSD) and the induced spatial incoherence (ISI) method. It is found that SSD using sinusoidal phase modulation results in poor smoothing at low l-modes and therefore inferior target performance at both peak velocity and ignition. This disparity is most notable if the effective imprinting integration time of the target is small. However, using SSD with more generalized phase modulation can result in smoothing at low l-modes which is identical to that obtained with ISI. For either smoothing method, the calculations indicate that at peak velocity the surface perturbations are about 100 times larger than that which leads to nonlinear hydrodynamics. Modeling of the hydrodynamic nonlinearity shows that saturation can reduce the amplified nonuniformities to the level required to achieve ignition for either smoothing method. The low l-mode behavior at ignition is found to be strongly dependent on the induced divergence of the smoothing method. For the NIF parameters the target performance asymptotes for smoothing divergence larger than approximately 100 (mu) rad.
Anode modification in organic light-emitting diodes by low-frequency plasma polymerization of CHF3 (2001)

Plasma polymerization of CHF3 at low frequencies was utilized for anode modification in organic light-emitting diodes. The polymerized fluorocarbon films have a high ionization potential and a relatively low resistivity. The devices with a polymer-coated anode of indium–tin–oxide exhibited enhanced hole injection and superior operational stability.
The T cell receptor/CD3 complex and CD2 stimulate the tyrosine phosphorylation of indistinguishable patterns of polypeptides in the human T leukemic cell line Jurkat (1991)

Stimulation of the T cell receptor (TcR)/CD3 complex of Jurkat T cells with a monoclonal antibody to the CD3 epsilon chain induced the tyrosine phosphorylation of multiple polypeptides, ranging in size from 21 to 155 kDa. The protein tyrosine phosphorylation was characterized by its rapidity and its transient nature, returning to baseline levels by 60 min. Protein tyrosine kinase activity was also induced when the Jurkat T cells were stimulated with a mitogenic pair of antibodies directed against CD2. Comparison of the polypeptides which were phosphorylated on tyrosine in response to stimulation of the two receptors, by either one- or two-dimensional analysis, failed to reveal any differences. These data suggest that the TcR/CD3 complex and CD2 activated the same tyrosine kinase or kinases. A model is proposed in which CD2 functions as a signal amplifier in physiological responses to antigen/major histocompatibility complex without changing the qualitative nature of the signal generated via the TcR/CD3 complex.
Targeting Nuclear Import Shuttles, Importins/Karyopherins alpha by a Peptide Mimicking the NFκB1/p50 Nuclear Localization Sequence (2013)

These results provide direct evidence that N50 peptide selectively targets Imp α5, encouraging further refinement of NLS-derived peptides as new tools to modulate inflammatory disorders.
Overview of posttransplant B-cell lymphoproliferative disorders. (1999)

Epstein-Barr virus-associated B-cell lymphoproliferations are a serious complication of organ or bone marrow transplantation whose incidence is strongly influenced by a number of risk factors. The disease represents a model of Epstein-Barr virus-driven lymphoid neoplasia in the setting of immunodeficiency. The incidence and pathogenesis of posttransplant lymphoproliferations are examined in relation to the nature of the transplanted organ, the Epstein-Barr virus infection, and the use of specific immunosuppressive regimens. Pathologic classifications and molecular mechanisms for neoplasia are reviewed. Clinical manifestations, pathologic features, and diagnostic considerations are summarized, with emphasis on those aspects that differ significantly from classic non-Hodgkin's lymphoma. Existing data regarding treatment are reviewed, including reduction in immunosuppression, surgery, radiation, chemotherapy, interferon-alpha, monoclonal anti-B-cell antibodies, and T-cell therapy. A basis for the selection of therapeutic options is suggested.
Combination strategies for enhancing the efficacy of immunotherapy in cancer patients (2010)

A major challenge in cancer immunotherapy is the identification of effective strategies for enhancing its clinical efficacy. One approach is based on adjuvants capable of breaking tolerance against tumor-associated antigens. Interferon-alpha(IFN-alpha), an antiviral cytokine with a long record of clinical use, has recently been shown to act as an effective adjuvant in cancer patients. Notably, a special interest is currently focused on the use of dendritic cells (DC) generated in the presence of IFN-alpha (IFN-DC) for the preparation of anticancer vaccines. An additional approach for enhancing the response to immunotherapy relies on its combination with chemotherapy. In fact, an ensemble of results from both studies in animal models and pilot clinical trials suggest that certain chemotherapeutic agents can act, under defined conditions, as strong adjuvants for enhancing the efficacy of immunotherapy. These results open new opportunities for designing mechanism-based combination therapies involving both chemotherapy and new-generation cancer vaccines, including IFN-DC-based vaccines.
Mirk/dyrk1B Is a Rho-induced Kinase Active in Skeletal Muscle Differentiation (2003)

The Rho family of small GTPases regulates numerous signaling pathways that control the organization of the cytoskeleton, transcription factor activity, and many aspects of the differentiation of skeletal myoblasts. We now demonstrate that the kinase Mirk (minibrain-related kinase)/dyrk1B is induced by members of the Rho-family in myoblasts and that Mirk is active in skeletal muscle differentiation. Mirk is an arginine-directed serine/threonine kinase which is expressed at elevated levels in skeletal muscle compared with other normal tissues. A Mirk promoter construct was activated when C2C12 myoblasts were switched from growth to differentiation medium and was also activated by the Rho family members RhoA, Cdc42, and to a lesser degree Rac1, but not by MyoD or Myf5. Mirk protein levels increased following transient expression of constitutively active Cdc42-QL, RhoA-QL, or Rac1-QL in C2C12 cells. High concentrations of serum mitogens down-regulated Mirk through activation of the Ras-MEK-Erk pathway. As a result, Mirk transcription was induced by the MEK1 inhibitor PD98059 and by the switch from growth to differentiation medium. Mirk was induced with similar kinetics to another Rho-induced differentiation gene, myogenin. Mirk protein levels increased 10-fold within 24-48 h after primary cultured muscle cells; C2C12 mouse myoblasts or L6 rat myoblasts were induced to differentiate. Thus Mirk was induced following the commitment stage of myogenesis. Stable overexpression of Mirk enabled myoblasts to fuse more rapidly when placed in differentiation medium. The function of Mirk in muscle differentiation was established by depletion of endogenous Mirk by small interfering RNA, which prevented myoblast fusion into myotubes and inhibited induction of markers of differentiation, including myogenin, fast twitch troponin T, and muscle myosin heavy chain. Other members of the dyrk/minibrain/HIPK family of kinases in lower organisms have been shown to regulate the transition from growth to differentiation, and Mirk is now shown to participate in skeletal muscle development.
Migration and proliferation of guinea pig and human airway epithelial cells in response to tachykinins (1995)

Restoration of the epithelial lining of a damaged airway is a necessary component of airway repair. Tachykinins, including substance P (SP) and neurokinin A (NKA), are localized to sensory nerves within the airway mucosa. These tachykinins regulate several airway functions, but their role in the repair of the epithelium has not been explored. To determine whether tachykinins stimulate migration and proliferation of airway epithelial cells, guinea pig tracheal epithelial (GPTE) and human bronchial epithelial (HBE) cells were grown in primary culture for 4-5 days. Epithelial cell migration was assessed in a blindwell chemotaxis chamber, and proliferation was determined by immunohistochemistry after incorporation of the thymidine analogue 5-bromo-2'-deoxyuridine (BrdU). Both GPTE and HBE cells migrated after stimulation with 10(-11) M NKA [23.0 +/- 3.6 vs. 5.4 +/- 1.2 cells per 10 high-power fields (hpf), P < 0.001, n = 8 for GPTE cells; 18.4 +/- 2.3 vs. 3.8 +/- 0.5 cells per 10 hpf for control, P < 0.001, n = 4 for HBE cells]. Migration was stimulated within 2 h, was maximal after 6 h, and was attenuated substantially by the neurokinin 2 (NKA)-receptor antagonist SR-48968. NKA-stimulated migration was both chemokinetic and chemotactic, and it could be blocked by inhibition of protein synthesis with cyclohexamide, inhibition of microtubular function with colchicine, or inhibition of actin microfilament elongation with cytochalasin D.(ABSTRACT TRUNCATED AT 250 WORDS)
Cellular and Molecular Mechanisms for the Initiation and Progression of β Cell Destruction Resulting from the Collaboration Between Macrophages and T Cells (1998)

Insulin-dependent diabetes mellitus (IDDM) is caused by the progressive autoimmune destruction of insulin-producing pancreatic beta cells. Although the pathogenesis of autoimmune IDDM has been extensively studied, the precise mechanisms involved in the initiation and progression of beta cell destruction remain unclear. Animal models used in the study of IDDM, such as the BioBreeding (BB) rat and the nonobese diabetic (NOD) mouse, have greatly enhanced our understanding of the pathogenic mechanisms involved in this disease. In these animals, macrophages and/or dendritic cells are the first cell types to infiltrate the pancreatic islets. Macrophages must be involved in the pathogenesis of IDDM early on, since inactivation of macrophages results in the near-complete prevention of insulitis and diabetes in both NOD mice and BB rats. The presentation of beta cell-specific autoantigens by macrophages and/or dendritic cells to CD4+ T helper cells, in association with MHC class II molecules, is considered the initial step in the development of autoimmune IDDM. The activated macrophages secrete IL-12, which stimulates Th1 type CD4+ T cells. The CD4+ T cells secrete IFN-gamma and IL-2. IFN-gamma activates other resting macrophages, which, in turn, release cytokines, such as IL-1beta, TNF-alpha, and free radicals, which are toxic to beta cells. During this process, IL-2 and other cytokines induce the migration of CD8+ peripheral T cells to the inflamed islets, perhaps by inducing the expression of a specific homing receptor. The precytotoxic CD8+ T cells that bear beta cell-specific autoantigen receptors differentiate into cytotoxic effector T cells upon recognition of the beta cell-specific peptide bound to MHC class I molecules in the presence of beta cell-specific CD4+ T helper cells. The cytotoxic CD8+ T cells then effect beta cell damage by releasing perforin and granzyme, and by Fas-mediated apoptosis. In this way, macrophages, CD4+ T cells, and CD8+ T cells synergistically destroy beta cells, resulting in the onset of autoimmune IDDM.