gebhart/patrepeval huggingface dataset:
Mutation of NH2-terminal glycine of p60src prevents both myristoylation and morphological transformation. (1985)

p60src, the transforming protein kinase of Rous sarcoma virus, contains the 14-carbon saturated fatty acid, myristic acid, linked through an amide bond to the alpha-amino group of its NH2-terminal glycine residue. Myristic acid is known to be attached to four other eukaryotic proteins. In each case the fatty acid is also linked through an amide bond to an NH2-terminal glycine. We have used oligonucleotide-directed mutagenesis to examine the amino acid specificity of the enzyme that myristoylates the NH2 terminus of these proteins. Replacement of the NH2-terminal glycine in p60src with either alanine or glutamic acid prevented myristoylation completely. This indicates that the myristoylating enzyme may have an absolute specificity for glycine. Strikingly, neither nonmyristoylated mutant src protein induced morphological transformation of infected cells, even though wild-type levels of phosphorylation of cellular proteins on tyrosine were observed in these cells. Since conversion of the NH2-terminal residue from glycine to alanine should have little effect on the conformation of p60src, the inability of this mutant p60src protein to induce morphological transformation suggests that the myristoyl moiety is essential for the transforming activity of the protein.
The structure and maturation of intermediates in bacteriophage T7 DNA replication (1978)

Concatemeric DNA from T7-infected cells consists of phage genomes in a linear head-to-tail arrangement. Adjacent genomes within a concatemer overlap for the length of the terminal repetition. Fast-sedimenting T7 DNA contains single-stranded regions at roughly unit-lentth intervals but these interruptions are heterogeneously distributed and do not occur at the genetic termini. Mutations in either bacteriophage genes 9, 18, or 19 (required for DNA maturation and packaging) lead to the synthesis and persistence of DNA with fewer interruptions than normal.
Biocompatibility of the Bioelastic Materials, Poly(GVGVP) and Its γ-Irradiation Cross-Linked Matrix: Summary of Generic Biological Test Results (1991)

The complete series of the recommended generic biological tests for materials and devices in contact with tissues and tissue fluids and blood have been carried out by an independent testing laboratory on the elastic protein-based (bioelastic) polymer, Poly(L-Val 1 -L-Pro 2 -Gly 3 -L-Val 4 -Gly 5 ) with a degree of polymerization greater than 120, and its 20 Mrad γ-irradiation cross linked elastic matrix, X 20 -poly(VPGVG). The specific tests and the summarized results given in parentheses are: (1) the Ames mutagenicity test (non- mutagenic), (2) cytotoxicity-agarose overlay (non-toxic), (3) acute systemic tox icity (non-toxic), (4) intracutaneous toxicity (non-toxic), (5) muscle implantation (favorable), (6) acute intraperitoneal toxicity (non-toxic), (7) systemic antigenic ity (non-antigenic), (8) dermal sensitization—the Magnusson and Kligman maximization method (non-sensitizing), (9) pyrogenicity (non-pyrogenic), (10) Lee White clotting study (normal clotting time), and (11) in vitro hemolysis test (non-hemolytic). Thus, this new elastomeric polypeptide biomaterial which is based on the most striking repeating sequence in the mammalian elastic fiber exhibits an extraordinary biocompatibility. This parent bioelastic material and a wide range of component peptide variations are under development for an equally wide range of potential medical applications such as prevention of adhesions, drug delivery, and synthetic arteries.
Red team vs. blue team hardware trojan analysis (2013)

We infiltrate the ASIC development chain by inserting a small denial-of-service (DoS) hardware Trojan at the fabrication design phase into an existing VLSI circuit, thereby simulating an adversary at a semiconductor foundry. Both the genuine and the altered ASICs have been fabricated using a 180 nm CMOS process. The Trojan circuit adds an overhead of only 0.5% to the original design. In order to detect the hardware Trojan, we perform side-channel analyses and apply IC-fingerprinting techniques using templates, principal component analysis (PCA), and support vector machines (SVMs). As a result, we were able to successfully identify and classify all infected ASICs from non-infected ones. To the best of our knowledge, this is the first hardware Trojan manufactured as an ASIC and has successfully been analyzed using side channels.
Electrochemical Principles for Active Control of Liquids on Submillimeter Scales (1999)

Electrochemical methods were combined with redox-active surfactants to actively control the motions and positions of aqueous and organic liquids on millimeter and smaller scales. Surfactant species generated at one electrode and consumed at another were used to manipulate the magnitude and direction of spatial gradients in surface tension and guide droplets of organic liquids through simple fluidic networks. Solid microparticles could be transported across unconfined surfaces. Electrochemical control of the position of surface-active species within aqueous films of liquid supported on homogeneous surfaces was used to direct these films into periodic arrays of droplets with deterministic shapes and sizes.
Activation of IFN-β expression by a viral mRNA through RNase L and MDA5 (2011)

IFNs play a critical role in innate immunity against viral infections. Melanoma differentiation-associated protein 5 (MDA5), an RNA helicase, is a key component in activating the expression of type I IFNs in response to certain types of viral infection. MDA5 senses noncellular RNA and triggers the signaling cascade that leads to IFN production. Synthetic double-stranded RNAs are known activators of MDA5. Natural single-stranded RNAs have not been reported to activate MDA5, however. We have serendipitously identified a viral mRNA from parainfluenza virus 5 (PIV5) that activates IFN expression through MDA5. We provide evidence that the signaling pathway includes the antiviral enzyme RNase L. The L mRNA of PIV5 activated expression of IFN-β. We have mapped the RNA to a region of 430 nucleotides within the L mRNA of PIV5. Our results indicate that a viral mRNA, with 5'-cap and 3'-poly (A), can activate IFN expression through an RNase L-MDA5 pathway.
Miniantibodies: use of amphipathic helixes to produce functional, flexibly linked dimeric FV fragments with high avidity in Escherichia coli (1992)

We have designed dimeric antibody fragments that assemble in Escherichia coli. They are based on single-chain FV fragments, with a flexible hinge region from mouse IgG3 and an amphiphilic helix fused to the C-terminus of the antibody fragment. The sequence of the helix was taken either from that of a previously reported four-helix bundle design or from a leucine zipper, optionally extended with a short cysteine-containing peptide. The bivalent fragments associate in vivo, either with covalent linkage or with a monomer-dimer equilibrium, and results from ultracentrifugation sedimentation studies and SDS-PAGE are consistent with dimers. All constructs are able to bind to surface-bound antigen under conditions in which only bivalent but not monovalent antibody fragments bind. The covalent bundle helix construct shows binding characteristics nearly identical to those of the much larger whole mouse antibody, resulting in substantially more stable immunoglobulin-antigen complexes than in the case of monovalent fragments. This modular design of natural and engineered protein domains directly leads to a boost of avidity, and it allows the construction of bispecific antibody fragments in functional form in E. coli.
Effects of end group polarity and molecular weight on the lower critical solution temperature of poly(N‐isopropylacrylamide) (2006)

Abstract The lower critical solution temperatures (LCSTs) for mass fractionated samples of poly( N ‐isopropylacrylamide) (PNIPAM) were studied to determine the effect of polymer molecular weight on the LCST using a high throughput temperature gradient apparatus. PNIPAM fractions prepared by a conventional radical polymerization using azoisobutyronitrile (AIBN) as the initiator had LCSTs that were largely invariant with molecular weight or dispersity. Only slight deviations were noted with lower molecular weight samples. An 18‐kDa sample had a 0.6 °C higher LCST. A 56‐kDa sample had a 0.2 °C higher LCST. PNIPAM derivatives prepared with a triphenylmethyl (trityl) functionalized azo initiator were also prepared and mass fractionated. These samples' LCSTs were identical to those of PNIPAM samples prepared using AIBN initiation when higher molecular weight samples were compared. The trityl‐containing PNIPAM fractions' LCSTs varied when the molecular weight decreased below 100 kDa. Acidolysis of the trityl end groups provided a third set of PNIPAM derivatives whose LCST differed only with samples with M w values &lt; 60 kDa. These results show there is no effect of molecular weight on LCST until the degree of polymerization is such that end group structure becomes significant. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1492–1501, 2006
Repetitive DNA sequences as probes for Mycobacterium tuberculosis (1988)

Three cloned segments of Mycobacterium tuberculosis DNA which are promising as clinical probes were identified. An MboI digest of DNA from a clinical isolate of M. tuberculosis was cloned into bacteriophage M13. To identify recombinants specific for the M. tuberculosis complex, plaque lifts were hybridized with M. bovis and M. kansasii DNA. Recombinants which selectively hybridized with M. bovis DNA were characterized by probing slot blots and restriction digests of DNA from various mycobacteria. Three recombinants that did not hybridize to a significant extent with DNA from nontuberculous mycobacteria were identified. These three probes are of special interest because they are each repeated multiple (10 to 16) times in the M. tuberculosis chromosome. These probes were also shown to be useful for fingerprinting strains for epidemiological studies.
ELISPOT Refinement Using Spot Morphology for Assessing Host Responses to Tuberculosis (2012)

Tuberculosis is a global health problem. The Mycobacterium bovis Bacille Calmette Guerin (BCG) vaccine has variable efficacy (0-80%) so there is a drive to develop novel vaccines. The cytokine, interferon gamma (IFNγ), is an essential component of the protective response to M. tuberculosis (M. tb) infection and is also produced in response to BCG vaccination. Induction of an IFNγ response is used as a biomarker of successful vaccination in the assessment of new tuberculosis (TB) vaccines. The IFNγ ELISPOT assay provides an important tool for TB research. It is used for both the diagnosis of infection (T.Spot assay), and for the evaluation of the immunogenicity of new TB vaccine candidates in human clinical trials, in the non-human primate (NHP) model of TB infection studies. The ELISPOT assay captures IFNγ produced by peripheral blood mononuclear cells (PBMCs) following specific stimulation, onto a membrane so individual cells can be enumerated and the frequency of responding cells determined. Hence spot forming units (SFU) per 106 cells provide the traditional measure for ELISPOT assays. The discriminatory power of SFU is limited. In some situations, the number of SFU in BCG vaccinated, and unvaccinated, subjects was found to be similar, although the spots were observed to be larger in vaccinated subjects. Spot size potentially provides a measure of the quantity of cytokine produced by individual cells. The AID ELISPOT plate reader software used to determine frequency of spots also has the capability to determine the size of each spot. Consideration of spot size in combination with spot forming units was investigated in our studies of BCG immunogenicity. This additional readout was found to enhance the discriminatory power of the ELISPOT assay, and provide more information on the immune response to BCG vaccination and infection with M.tb.
Molecular Recognition and Binding of a GC Site-Avoiding Thiazole-Lexitropsin to the Decadeoxyribonucleotide d-[CGCAATTGCG]2:1H-NMR Evidence for Thiazole Intercalation (1990)

The structural and dynamic aspects of the interaction of the thiazole containing lexitropsin (1) with an oligodeoxyribonucleotide were studied by high field 1H-NMR spectroscopy. Complete assignment of the 1H-NMR resonances of lexitropsin 1 was accomplished by 2D-NMR techniques. The complexation-induced chemical shifts and NOE cross peaks in the NOESY map of the 1:1 complex of lexitropsin (1) and d-[CGCAATTGCG]2 reveal that the thiazole ring of the lexitropsin (1) intercalates between dA4.A5 bases and the rest of the ligand resides in the minor groove of the AT rich core of decamer, thus occupying the 5'-AATT sequence on the DNA. Intercalation of the thiazole moiety of the drug has been detected by the presence of intermolecular NOEs both in the major and the minor groove of the decamer helix. The absence of intranucleotide NOEs between base protons and H1'/H2' protons suggested local unwinding of the binding site on the DNA. From COSY and NOESY methods of 2D-NMR, it was established that the N-formyl (amino) terminus of the thiazole lexitropsin (1) is projecting into the major groove towards A5H8 while the amidinium terminus lies in the minor groove towards the T7G8 base pairs of the opposite strand. The expected intranucleotide NOEs confirmed that the decadeoxyribonucleotide in the 1:1 complex exists in a right handed B-conformation. The presence of exchange signals along the binding site 5'-AATT indicated an exchange of the bound drug process wherein the rate of exchange between the two equivalent sites was estimated to be congruent to 130 s-1 at 30 degrees C and with delta G degrees of 62.4 kJ mol-1. Force field and Pi calculations permitted a rationalization of the experimentally observed binding mode in terms of preferred conformation of the ligand and repeat length in lexitropsins compared with the DNA receptor.
Synthetic peptides representing discontinuous CD4 binding epitopes of HIV‐1 gp120 that induce T cell apoptosis and block cell death induced by gp120 (1998)

A vaccine against HIV-1 virus would block initial infection and must target conserved residues. Since initial infection depends on binding of the viral envelope protein gp120 to CD4 on the cell surface, the CD4 binding site of gp120 is a target for vaccine design. To identify the optimal biologically active site, we synthesized a series of 32-mer peptides, based on conserved residues in the C3 and C4 regions of gp120. These included three of five sequence discontinuous residues known to be involved in CD4 binding, one or two of which were substituted with alanine. We also synthesized a 44-mer peptide with an additional branch to incorporate an extra C4 region sequence including a fourth CD4 binding residue. All these peptides used an oxidized Cys-X-Cys bridge to link the discontinuous sequence elements in a manner suggested by the known conserved disulfide bridges in gp120. Polyclonal sera raised to these peptides indicate that they all contain both B and T lymphocyte epitopes. Binding of the peptides to CD4-transfected HeLa cells reveals a hierarchy dependent on the number of relevant CD4 binding residues present. Furthermore, antibody cross-linking of peptides bound to the surface of human T cells results in apoptosis that is similar to the known properties of gp120. The peptide incorporating three CD4 binding residues competitively inhibited gp 120-induced T lymphocyte apoptosis. Thus, we have synthesized novel, branched peptides incorporating conserved discontinuous sequences from two different conserved domains of HIV-1 gp120 that contain T and B lymphocyte epitopes and mimic biological functions of the native protein. These synthetic peptides are candidates for future vaccine development.
The role of DC-STAMP in maintenance of immune tolerance through regulation of dendritic cell function (2008)

Regulation of dendritic cell (DC) function is critical for maintaining self-tolerance and preventing autoimmunity. The dendritic cell-specific transmembrane protein (DC-STAMP) plays a key role in cell-cell fusion of osteoclasts and foreign body giant cells, but though originally identified in DCs, its specific roles there remain undefined. Here, we report that aged DC-STAMP-deficient mice display several systemic autoimmune symptoms such as spontaneous lymphoproliferation, splenomegaly associated with infiltration of T cells in several organs and increased serum anti-double-stranded DNA antibody production. Although a lack of DC-STAMP did not inhibit DC differentiation or proliferation, antigen presentation activity of DC-STAMP-deficient DCs was significantly up-regulated in both class I and II pathways through increased phagocytotic activity compared with wild-type DCs, an activity likely leading to autoimmunity. Our results indicate that DC-STAMP is required for proper regulation of DC activity and maintenance of immune self-tolerance.
Calculation of the Parameters of Ridge Waveguides (1957)

In this paper an algebraic expression which constitutes an approximation to Cohn's transcendental equation is given for the determination of the dominant-mode cutoff wavelength of ridge waveguides. A modified derivation of Mihran's equation for calculating the characteristic impedance of ridge waveguides is discussed. Based upon these formulas, nomography are constructed to permit the determination of these parameters with sufficient accuracy when the waveguide and the ridge dimensions vary. Experimental verification of the calculated cutoff wavelength is included.
The importance of the elastic and plastic components of strain in tensile and compressive fatigue of human cortical bone in relation to orthopaedic biomechanics. (2006)

The longevity, success, or failure of an orthopaedic implant is dependent on its osseointegration especially within the initial six months of the initial surgery. The development of strains plays a crucial role in both bone modelling and remodelling. For remodelling, in particular, strains of substantial values are required to activate the osteoblastic and osteoclastic activity for the osseointegration of the implant. Bone, however, is subject to "damage" when strain levels exceed a certain threshold level. Damage is manifested in the form of microcracks; it is linked to increased elastic strain amplitudes and is accompanied by the development of "plastic" (irrecoverable, residual) strains. Such strains increase the likelihood for the implant to subside or loosen. The present study examines the rates (per cycle) by which these two components of strain (elastic and "plastic") develop during fatigue cycling in two loading modes, tension and compression. The results of this study show that these strain rates depend on the applied stress in both loading modes. It also shows that elastic and plastic strain rates can be linked to each other through simple power law relationships so that one can calculate or predict the latter from the former and vice versa. We anticipate that such basic bone biomechanics data would be of great benefit to both clinicians and bioengineers working in the field of FEA modelling applications and orthopaedic implant surgery.
Emergence of Influenza B Viruses With Reduced Sensitivity to Neuraminidase Inhibitors (2007)

In this population, influenza B viruses with reduced sensitivity to neuraminidase inhibitors do not arise as frequently as resistant influenza A viruses. However, they appear to be transmitted within communities and families, requiring continued close monitoring.
A Method of Controlling Corn Rootworm Feeding Using a Bacillus thuringiensis Protein Expressed in Transgenic Maize (2005)

The corn rootworm (CRW; Diabrotica spp.) is one of the most serious pests of corn in the USA. Chemical insecticides and crop rotation have been the only two options available to growers for managing CRW. Unfortunately, both of these tactics can be ineffective as a result of either resistance or behavioral modifications. In this paper, we describe transgenic maize ( Zea mays L.) hybrids that control CRW. These hybrids were created with a Cry3Bb1 Bacillus thuringiensis ( Bt ) variant that is approximately eight times more lethal to corn rootworm larvae than the wild‐type protein. A DNA vector containing the modified cry3Bb1 gene was placed under control of a root‐enhanced promoter (4‐AS1) and was introduced into embryonic maize cells by microprojectile bombardment. Described here is the molecular genetic characterization, protein expression levels, and field performance of the recently commercialized MON863 hybrids.
Eotaxin-3/CC Chemokine Ligand 26 Is a Functional Ligand for CX3CR1 (2010)

Eotaxin-3/CCL26 is a functional ligand for CCR3 and abundantly produced by IL-4-/IL-13-stimulated vascular endothelial cells. CCL26 also functions as a natural antagonist for CCR1, CCR2, and CCR5. In this study, we report that CCL26 is yet a functional ligand for CX3CR1, the receptor for fractalkine/CX3CL1, which is expressed by CD16(+) NK cells, cytotoxic effector CD8(+) T cells, and CD14(low)CD16(high) monocytes. Albeit at relatively high concentrations, CCL26 induced calcium flux and chemotaxis in mouse L1.2 cells expressing human CX3CR1 but not mouse CX3CR1 and competed with CX3CL1 for binding to CX3CR1. In chemotaxis assays using human PBMCs, CCL26 attracted not only eosinophils but also CD16(+) NK cells, CD45RA(+)CD27(-)CD8(+) T cells, and CD14(low)CD16(high) monocytes. Intraperitoneal injection of CCL26 into mice rapidly recruited mouse eosinophils and intravenously transferred human CD16(+) NK cells into the peritoneal cavity. IL-4-stimulated HUVECs produced CCL26 and efficiently induced adhesion of cells expressing CX3CR1. Real-time PCR showed that skin lesions of psoriasis consistently contained CX3CL1 mRNA but not CCL26 mRNA, whereas those of atopic dermatitis contained CCL26 mRNA in all samples but CX3CL1 mRNA in only about half of the samples. Nevertheless, the skin lesions from both diseases consistently contained CX3CR1 mRNA at high levels. Thus, CCL26 may be partly responsible for the recruitment of cells expressing CX3CR1 in atopic dermatitis particularly when the expression of CX3CL1 is low. Collectively, CCL26 is another agonist for CX3CR1 and may play a dual role in allergic diseases by attracting eosinophils via CCR3 and killer lymphocytes and resident monocytes via CX3CR1.