gebhart/patrepeval huggingface dataset:
Proteolytic processing of avian sarcoma and leukosis viruses pol-endo recombinant proteins reveals another pol gene domain (1987)

Three pol gene products have been identified in avian retroviral particles: the full-length 95-kilodalton (kDa) beta chain of reverse transcriptase and two proteolytic cleavage products of beta, a 63-kDa reverse transcriptase alpha chain derived from the amino terminus of beta and a 32-kDa (pp32) endonuclease from its carboxy terminus. By using molecularly cloned retroviral DNA and synthetic oligonucleotides to introduce initiator ATGs and codons corresponding to the authentic N termini, we constructed two bacterial-expression clones; one clone contains the entire pol gene, and the other contains the region encoding the pp32 domain. A 99-kDa protein was synthesized in Escherichia coli by the full-length clone, and a 36-kDa protein was synthesized by the endonuclease domain clone. The recombinant proteins exceeded the size of both the mature viral beta chain and the pp32, respectively, by approximately 4 kDa. These larger sizes, however, are consistent with predictions from the DNA sequence of the pol gene. Processing of the recombinant pol proteins was examined by using p15 protease purified from virus particles and antisera directed against synthetic peptides corresponding to three domains in pol. Proteolytic digestion of the 99-kDa product with p15 produced a 63-kDa protein that comigrated on polyacrylamide gels with the alpha chain of reverse transciptase and a 36-kDa fragment that comigrated with the endonuclease domain product. Further digestion of the 36-kDa protein yielded a 32-kDa protein that comigrated with viral pp32 endonuclease. Thus, we concluded that two p15-sensitive sites exist in pol. Cleavage at the previously identified site produces alpha, and cleavage at the newly discovered site removes approximately 4 kDa from the C terminus of the primary protein product. Since the 36-kDa protein was also detected in protein isolated from virus particles, it seems probable that processing at the C-terminal site is a normal step in the production of mature beta and pp32 endonuclease products.
MCP-1 and IL-8 as Pain Biomarkers in Fibromyalgia: A Pilot Study (2011)

Although preliminary, our findings raise the hypothesis that IL-8 and MCP-1 may be involved in the pathogenesis of FM. If replicated in a larger study, IL-8 and MCP-1 may assist in determining prognosis and in monitoring of treatment response.
Mycobacterium bovis BCG recA Deletion Mutant Shows Increased Susceptibility to DNA-Damaging Agents but Wild-Type Survival in a Mouse Infection Model (2001)

Pathogenic microorganisms possess antioxidant defense mechanisms for protection from reactive oxygen metabolites which are generated during the respiratory burst of phagocytic cells. These defense mechanisms include enzymes such as catalase, which detoxifies reactive oxygen species, and DNA repair systems, which repair damage resulting from oxidative stress. To (i) determine the relative importance of the DNA repair system when oxidative stress is encountered by the Mycobacterium tuberculosis complex during infection of the host and to (ii) provide improved mycobacterial hosts as live carriers to express foreign antigens, the recA locus was inactivated by allelic exchange in Mycobacterium bovis BCG. The recA mutants are sensitive to DNA-damaging agents and show increased susceptibility to metronidazole, the first lead compound active against the dormant M. tuberculosis complex. Surprisingly, the recA genotype does not affect the in vitro dormancy response, nor does the defect in the DNA repair system lead to attenuation as determined in a mouse infection model. The recA mutants will be a valuable tool for further development of BCG as an antigen delivery system to express foreign antigens and as a source of a genetically stable vaccine against tuberculosis.
Selective Vector Perturbation Precoding and Peak to Average Power Ratio Reduction for OFDM Systems (2008)

High peak to average power ratio (PAPR) is a serious drawback for orthogonal frequency division multiplexing (OFDM) system as it reduces the efficiency of high-power amplifiers commonly used in the transmitter and causes spectral spillage. OFDM transmissions are also sensitive to frequency selective fading channels which can severely attenuate certain parts of the signal making it much more vulnerable to additive noise. This paper proposes an effective precoding technique with the dual ability to both reduce PAPR and condition the OFDM signal against frequency selective fading channels. It will be demonstrated that by advisedly creating diversity among the subcarriers of one OFDM symbol, and exploiting it with a dirty- paper-coding (DPC) approach, excellent bit-error-rate (BER) performance is achieved without reducing transmission rate. Low PAPR factor can also be obtained through a proper selection of diversity matrix that distributes the power of each modulated symbol over the OFDM block. Simulation results show that the proposed technique has not only better BER performance than the ordinary channel inversion but also similar PAPR reduction ability to the selective mapping (SLM) technique.
Foundations of Cryptography: Basic Tools (2000)

Cryptography is concerned with the conceptualization, definition and construction of computing systems that address security concerns. The design of cryptographic systems must be based on firm foundations. This book presents a rigorous and systematic treatment of the foundational issues: defining cryptographic tasks and solving new cryptographic problems using existing tools. It focuses on the basic mathematical tools: computational difficulty (one-way functions), pseudorandomness and zero-knowledge proofs. The emphasis is on the clarification of fundamental concepts and on demonstrating the feasibility of solving cryptographic problems, rather than on describing ad-hoc approaches. The book is suitable for use in a graduate course on cryptography and as a reference book for experts. The author assumes basic familiarity with the design and analysis of algorithms; some knowledge of complexity theory and probability is also useful
High-Performance Membrane Chromatography of Small Molecules (1999)

High-performance membrane chromatography (HPMC) proved to be a very efficient method for fast protein separations. Recently, it was shown to be applicable also for the isocratic chromatography of plasmid DNA conformations. However, no study about the separation of small molecules has been performed until now. In this work, we investigated the possibility of gradient and isocratic HPMC of small molecules with Convective Interaction Media disks of different chemistries and tried to explain the mechanism that enables their separation. We demonstrated that it is possible to achieve efficient separations of oligonucleotides and peptides in the ion-exchange mode as well as the separation of small hydrophobic molecules in the reversed-phase mode. It was shown that similar peak resolution can be provided in both gradient and isocratic modes.
Characterization of a Liver Organoid Tissue Composed of Hepatocytes and Fibroblasts in Dense Collagen Fibrils (2013)

The adult liver is wrapped in a connective tissue sheet called the liver capsule, which consists of collagen fibrils and fibroblasts. In this study, we set out to construct a liver organoid tissue that would be comparable to the endogenous liver, using a bioreactor. In vitro liver organoid tissue was generated by combining collagen fibrils, fibroblasts, and primary murine hepatocytes or Hep G2 on a mesh of poly-lactic acid fabric using a bioreactor. Then, the suitability of this liver organoid tissue for transplantation was tested by implanting the constructs into partially hepatectomized BALB/cA-nu/nu mice. As determined by using scanning and transmission electron microscopes, the liver organoid tissues were composed of densely packed collagen fibrils with fibroblasts and aggregates of oval or spherical hepatocytes. Angiogenesis was induced after the transplantation, and blood vessels connected the liver organoid tissue with the surrounding tissue. Thus, a novel approach was applied to generate transplantable liver organoid tissue within a condensed collagen fibril matrix. These results suggested that a dense collagen network populated with fibroblasts can hold a layer of concentrated hepatocytes, providing a three-dimensional microenvrionment suitable for the reestablishment of cell-cell and cell-extracellular matrix (ECM) interactions, and resulting in the maintenance of their liver-specific functions. This liver organoid tissue may be useful for the study of intrahepatic functions of various cells, cytokines, and ECMs, and may fulfill the fundamental requirements of a donor tissue.
Shaping Crystals with Biomolecules (2004)

The complex shapes of biominerals cannot be explained with simple mechanistic models of crystal growth. In their Perspective,
 De Yoreo and Dove,
 argue that the popular stereochemical recognition model, which postulates that some shapes are stabilized through the binding of peptides and proteins to otherwise unstable faces, is not the full answer, either. According to recent studies, specific interactions between growth modifiers such as proteins and the edges of individual steps on existing crystal faces change the elementary step change to generate a similarly modified bulk crystal shape. The emergence of new faces is a macroscopic manifestation of the kinetics caused by molecular-scale interactions at the step edges.
Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies (2019)

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel zoonotic coronavirus that was identified in 2012. MERS-CoV infection in humans can result in an acute, severe respiratory disease and in some cases multi-organ failure; the global mortality rate is approximately 35 %. The MERS-CoV spike (S) protein is a major target for neutralizing antibodies in infected patients. The MERS-CoV microneutralization test (MNt) is the gold standard method for demonstrating prior infection. However, this method requires the use of live MERS-CoV in biosafety level 3 (BSL-3) containment. The present work describes the generation and validation of S protein-bearing vesicular stomatitis virus (VSV) pseudotype particles (VSV-MERS-CoV-S) in which the VSV glycoprotein G gene has been replaced by the luciferase reporter gene, followed by the establishment of a pseudoparticle-based neutralization test to detect MERS-CoV neutralizing antibodies under BSL-2 conditions. Using a panel of human sera from confirmed MERS-CoV patients, the VSV-MERS-CoV particle neutralization assay produced results that were highly comparable to those of the microneutralization test using live MERS-CoV. The results suggest that the VSV-MERS-CoV-S pseudotype neutralization assay offers a highly specific, sensitive and safer alternative method to detect MERS-CoV neutralizing antibodies in human sera.
Dll4, a novel Notch ligand expressed in arterial endothelium (2000)

We report the cloning and characterization of a new member of the Delta family of Notch ligands, which we have named Dll4. Like other Delta genes, Dll4 is predicted to encode a membrane-bound ligand, characterized by an extracellular region containing several EGF-like domains and a DSL domain required for receptor binding. In situ analysis reveals a highly selective expression pattern of Dll4 within the vascular endothelium. The activity and expression of Dll4 and the known actions of other members of this family suggest a role for Dll4 in the control of endothelial cell biology.
On the utilization of carbon in fertilizers through rice roots under pot experimental condition (1962)

Abstract Kursanov et al. conducted a series of studies on the CO2 uptake by roots and translocation and uilization in plant, using carbon-l4 labelled CO2. Kursanov, Kuzin and Mamul1) first studied the uptake of CO2 by the roots of intact bean seedlings and found that after 18-hours exposure in the light, most of the radioactive carbon was translocated upwards. Later on, in a more detailed paper2) these Russian workers estimated that under their experimental conditions, the amount of CO2 absorbed by roots is as much as 25 per cent of that taken up from the atmosphere by leaves. They also reported that soluble carbonates supplied as a fertilizer increased the yield of bean, barley, potato and sugar beet by 15 to 18 per cene). In addition Grinfeld 4) stated that 30–50 kg of CO2 per hectare, dressed as ammonium carbonate, increased the yield of sugar beet by 7 to 16 per cent.
The ISHAGE Guidelines for CD34+ Cell Determination by Flow Cytometry (1996)

The increased use of Peripheral Blood Stem Cells (PBSC) to reconstitute hematopoiesis in autotransplant and, more recently, allotransplant settings has not been associated with a consensus means to quality control the PBSC product. Since the small population of cells that bear the CD34 antigen are thought to be responsible for multilineage engraftment, graft assessment by flow cytometric quantitation of CD34+ cells should provide a rapid, reliable, and reproducible assay. Unfortunately, although a number of flow cytometric assays for CD34 enumeration have been described, the lack of a standardized method has led to the generation of widely divergent data. Furthermore, none of these assays has been validated as to interlaboratory reproducibility and suitability for widespread clinical application. In early 1995, the International Society of Hematotherapy and Graft Engineering (ISHAGE) established a Stem Cell Enumeration Committee, the mandate of which was to validate a simple, rapid, and sensitive flow cytometric method to quantitate CD34+ cells in peripheral blood and apheresis products. We also sought to establish its utility on a variety of flow cytometers in clinical laboratories and its reproducibility between transplant centers. Here, we describe the four-parameter flow methodology adopted by ISHAGE for validation in a multicenter study in North America.
<title>Moisture and impurities detection and removal in packaged MEMS</title> (2001)

The development of sensitive MEMS now requires either high purity inert atmosphere or a vacuum environment. Therefore, encapsulation is mandatory to ensure performances over the projected lifetime of the devices. The knowledge of the behavior of the MEMS components and assembly with respect to vacuum compatibility is therefore of outmost importance, both to understand and reduce the impurities' release mechanisms and to design a suitable solution to the lifetime issue. This solution is based on the use of specific getter materials and configurations to be incorporated into the MEMS cavity. Outgassing and residual gas composition data are necessary to address the choice of the proper getter material and provide information on the design of the getter. Different solutions can be envisaged depending on the type of gas to be sorbed, the process constraints and the operating conditions of each specific device. If moisture is the main gas to be removed from the cavity, the choice is between physical and chemical dryers. In case other species have also to be sorbed, then the choice of a non-evaporable getter (NEG) has to be preferred. The various getter materials and solutions to the vacuum problems in MEMS will be discussed in detail.
The influence of predegenerated nerve grafts on axonal regeneration from prelesioned peripheral nerves. (1996)

Recent in vitro work has indicated that predegenerated segments of peripheral nerve are more capable of supporting neurite growth from adult neurons than fresh segments of nerve, whereas previous in vivo studies which investigated whether predegenerated nerve segments used as grafts are capable of enhancing axonal regeneration produced conflicting results. We have reinvestigated this question by using predegenerated nerve grafts in combination with conditioning lesions of the host nerve to determine the optimal conditions for obtaining the maximal degree of regeneration of myelinated axons. The sciatic nerve of adult Dark Agouti rats were sectioned at midthigh level, and the distal portion was allowed to predegenerate for 0, 6 or 12 d in situ. 10-15 mm lengths of these distal nerve segments were then syngenically grafted onto the central stumps of sciatic nerves which had themselves received a conditioning lesion 0, 6, and 12 d previously, making a total of 9 different donor-host combinations. The grafts were assessed histologically 3 or 8 wk after grafting. Axonal regeneration in the 9 different donor-host combinations was determined by counting the numbers of myelinated axons in transverse sections through the grafts. All grafts examined contained regenerating myelinated axons. The rats given a 3 wk postgrafting survival period had an average of between 1400 and 5300 such axons. The rats given an 8 wk postgrafting survival period had between about 13,000 and 25,000 regenerating myelinated axons. Analysis of variance revealed significant main effects for both the Donor and Host conditions as well as Weeks (i.e. survival period after grafting). These results indicate that both a conditioning lesion of the host neurons and the degree of predegeneration of peripheral nerve segments to be used as grafts are of importance in influencing the degree of axonal regeneration. Of these 2 factors the conditioning lesion of the host appears to have the greater effect on the final number of regenerating myelinated axons.
Tumor-associated leukemia inhibitory factor and IL-6 skew monocyte differentiation into tumor-associated macrophage-like cells (2007)

Tumor-associated macrophages (TAMs), the most abundant immunosuppressive cells in the tumor microenvironment, originate from blood monocytes and exhibit an IL-10(high)IL-12(low) M2 profile. The factors involved in TAM generation remain unidentified. We identify here leukemia inhibitory factor (LIF) and IL-6 as tumor microenvironmental factors that can promote TAM generation. Ovarian cancer ascites switched monocyte differentiation into TAM-like cells that exhibit most ovarian TAM functional and phenotypic characteristics. Ovarian cancer ascites contained high concentrations of LIF and IL-6. Recombinant LIF and IL-6 skew monocyte differentiation into TAM-like cells by enabling monocytes to consume monocyte-colony-stimulating factor (M-CSF). Depletion of LIF, IL-6, and M-CSF in ovarian cancer ascites suppressed TAM-like cell induction. We extended these observations to different tumor-cell line supernatants. In addition to revealing a new tumor-escape mechanism associated with TAM generation via LIF and IL-6, these findings offer novel therapeutic perspectives to subvert TAM-induced immunosuppression and hence improve T-cell-based antitumor immunotherapy efficacy.
Synthesis of cartilage matrix by mammalian chondrocytes in vitro. I. Isolation, culture characteristics, and morphology. (1982)

We describe the isolation and the ultrastructural characteristics of adult bovine articular chondrocytes in vitro. Slices of bovine articular cartilage undergo sequential digestions with pronase and collagenase in order to release cells. Chondrocytes are plated at high density (1 x 10(5) cells/cm2) in culture dishes or roller bottles with Ham's F-12 medium, supplemented with 10% fetal bovine serum. Before culture, chondrocytes are freed of surrounding territorial matrix. Within the first few days of culture they re-establish a territorial matrix. As time progresses, chondrocytes synthesize both territorial and extraterritorial matrices. The matrices are rich in collagen fibrils and ruthenium red-positive proteoglycans. These features are most apparent in mass roller cultures in which aggregates of cells and matrix appear as long streaks and nodules. This morphology reveals an organization of chondrocytes and their matrices that is similar to that of the parent articular cartilage in vivo.
Inhibition of mitogen-activated protein kinase kinase selectively inhibits cell proliferation in human breast cancer cells displaying enhanced insulin-like growth factor I-mediated mitogen-activated protein kinase activation. (2000)

Mitogen-activated protein (MAP) kinase mediates cell proliferation, cell differentiation, and cell survival by regulating signaling pathways activated by receptor protein tyrosine kinases (RPTKs), including the insulin-like growth factor 1 receptor (IGF-IR). We analyzed the upstream signaling components of the MAP kinase pathway, including RPTKs, in human breast cancer cell lines and found that some of those components were overexpressed. Importantly, signaling molecules such as IGF-IR, insulin receptor, and insulin receptor substrate 1, leading to the MAP kinase pathway, were found to be concomitantly overexpressed within certain tumor lines, i.e., MCF-7 and T-47D. When compared with the nonmalignant and other breast tumor lines examined, MCF-7 and T-47D cells displayed a more rapid, robust, and sustained MAP kinase activation in response to insulin-like growth factor I (IGF-I) stimulation. By contrast, IGF-I treatment led to a sustained down-regulation of MAP kinase in those lines overexpressing ErbB2-related RPTKs. Interestingly, blocking the MAP kinase pathway with PD098059 had the greatest antiproliferative effect on MCF-7 and T-47D among the normal and tumor lines tested. Furthermore, addition of an IGF-IR blocking antibody to growth medium attenuated the ability of PD098059 to suppress the growth of MCF-7 and T-47D cells. Thus, our study suggests that concomitant overexpression of multiple signaling components of the IGF-IR pathway leads to the amplification of IGF-I-mediated MAP kinase signaling and resultant sensitization to PD098059. The enhanced sensitivity to PD098059 implies an increased requirement for the MAP kinase pathway in those breast cancer cells, making this pathway a potential target in the treatment of selected breast malignancies.
Synthesis of C‐nucleoside isosteres of 9‐(2‐hydroxyethoxymethyl)guanine (acyclovir) (1984)

Abstract Syntheses of 2‐amino‐7‐(2‐hydroxyethoxymethyl)imidazo[5,1‐ f ]‐1,2,4‐triazin‐4(3 H )‐one ( 2 ) and 6‐amino‐3‐(2‐hydroxyethoxymethyl)‐1,2,4‐triazolo[3,4‐ f ]‐1,2,4‐triazin‐8(7 H )‐one ( 3 ), novel isosteres of the antiviral agent acyclovir, are reported.
Ablative photodecomposition of organic polymer films by far-UV excimer laser irradiation (1983)

Radiation of wavelengths shorter than 200 nm is intensely absorbed by nearly all organic polymers. More than 95% of the photons are absorbed in a depth of ~3000 Å. Far-UV radiation has an efficiency of &gt;50% at breaking bonds in organic material. As a result when a laser pulse of 193-nm wavelength impinges on an organic film, numerous small fragments are created in a small volume. When the intensity of the pulse exceeds a threshold value (~10 mJ/cm2), the small fragments ablate—they explosively burst out of the irradiated volume.