gebhart/patrepeval huggingface dataset:
Secreted production of a custom-designed, highly hydrophilic gelatin in Pichia pastoris (2001)

A custom-designed, highly hydrophilic gelatin was produced in Pichia pastoris. Secreted production levels in single-copy transformants were in the range 3-6 g/l of clarified broth and purification to near homogeneity could be accomplished by differential ammonium sulfate precipitation. Despite the fact that gelatins are highly susceptible to proteolysis because of their unfolded structure, the recombinant protein was shown to be fully intact by SDS-PAGE, N-terminal sequencing, gel filtration chromatography and mass spectrometry. Owing to its highly hydrophilic nature, the migration of the synthetic gelatin in SDS-PAGE was severely delayed. Esterification of the carboxylic amino acid side chains resulted in normal migration. The high polarity of the synthetic gelatin also accounts for its negligible surface activity in water at concentrations up to 5% (w/v), as determined by tensiometry. Circular dichroism spectrometry showed that the non-hydroxylated gelatin did not form triple helices at 4 degrees C. The spectrum was even more representative of the random coil conformation than the spectrum of natural non-hydroxylated gelatins.
Arg-Gly-Asp-containing peptides expose novel collagen receptors on fibroblasts: implications for wound healing. (1991)

Integrins are a family of cell-surface receptors intimately involved in the interactions of cells with their extracellular matrix. These receptors comprise an alpha and beta subunit in noncovalent association and many have been shown to recognize and bind an arginine-glycine-aspartate (RGD) sequence contained within their specific extracellular matrix ligand. Fibroblasts express integrin receptors belonging to two major subfamilies. Some of the members within the subfamily defined by beta 1 (VLA) are receptors for collagen but, perhaps surprisingly, the other major subfamily of integrins on fibroblasts--that defined by the alpha chain of the vitronectin receptor, alpha v--all appear to bind primarily vitronectin and/or fibronectin. In the present study we show that RGD-containing peptides expose cryptic binding sites on the alpha v-associated integrins enabling them to function as collagen receptors. The addition of RGD-containing peptides to fibroblasts cultured on type I collagen induced dramatic cell elongation and, when the cells were contained within collagen matrices, the peptides induced marked contraction of the gels. These processes were inhibited by Fab fragments of a monoclonal antibody against an alpha v integrin. Also, alpha v-associated integrins from cell lysates bound to collagen I affinity columns in the presence, but not in the absence, of RGD-containing peptides. These data suggest a novel regulatory control for integrin function. In addition, because the cryptic collagen receptors were shown to be implicated in the contraction of collagen gels, the generation of such binding forces suggests that this may be the major biological role for these integrins in processes such as wound healing.
Characterization of a Soluble Nuclear Ribonucleoprotein Antigen Reactive with Sle Sera (1971)

Abstract A soluble nuclear ribonucleoprotein antigen reactive with SLE sera in precipitin and complement fixation reactions is described. The antigen was shown to be quite labile and was not recovered from human autopsy material (liver and spleen) but was easily demonstrated in extracts of surgically removed human thymoma and thymus, as well as in extracts of human chronic myeloid leukemia and normal bone marrow cells. It could also be extracted from calf thymus tissue and the thymus and spleen of the rabbit. It was characterized as ribonucleoprotein because the antigenic activity was destroyed by both ribonuclease and trypsin and the washed immune precipitate contained material which yielded an orcinol reaction product with an absorption spectrum indistinguishable from ribose. The antigen was found to be unstable at relatively moderate temperatures (40°C), at pH below 5.0 and above 9.0, and was destroyed by treatment with sodium metaperiodate. Antibodies to this antigen, designated Mo, were found in a high proportion of SLE sera and were absent from a variety of sera from patients with other connective tissue diseases as well as normal sera. The nuclear fluorescent pattern associated with this system was shown to be “speckled.”
Animal Groups in Three Dimensions (1997)

This book is about the ways in which many animals form groups; for instance, schools of fish, flocks of birds, and swarms of insects. Covering both invertebrate and vertebrate species, the authors investigate three-dimensional animal aggregations from a variety of disciplines, from physics to mathematics to biology. The first section is devoted to the various methods, mainly optical and acoustic, used to collect three-dimensional data over time. The second section focuses on analytical methods used to quantify pattern, group kinetics, and interindividual interactions within the group. The section on behavioural ecology and evolution deals with the functions of aggregative behaviour from the point of view of an inherently selfish individual member. The final section uses models to elucidate how group dynamics at the individual level creates emergent pattern at the level of the group.
Epidemiology of Kaposi's sarcoma. (1991)

The AIDS epidemic drew attention to KS, a previously rare and little studied condition. The epidemiological evidence summarized here strongly suggests that the disease is caused by a transmissible agent, in addition to HIV. Sexual contact is the most important mode of transmission of the agent, although transmission by blood and perinatally may also occur (Beral et al, 1990).
Highly Active Soluble Processed Forms of the Transglutaminase 1 Enzyme in Epidermal Keratinocytes (1995)

The transglutaminase 1 (TGase 1) enzyme is required for the formation of a cornified cell envelope in epidermal keratinocytes. We show here that in addition to its membrane-anchored form, soluble forms of it are also important in keratinocytes. Proliferating cells contain soluble full-length enzyme of 106 kDa, but terminally differentiating cells contain a soluble 67-kDa form often complexed with a 33-kDa protein as well. The amino terminus of the 67 kDa form is residue 93 of the TGase 1 protein, corresponding to the site of proteolytic activation of the factor XIIIa TGase. The amino terminus of the 33-kDa protein is residue 573, corresponding to the site of a second proteolytic cleavage site of factor XIIIa, and of the site for proteolytic activation of the TGase 3 enzyme. The specific activity of the 67/33-kDa soluble complex is twice that of the soluble 67-kDa form and 10 times that of full-length TGase 1. The half-lives of the 67/33- and 106-kDa forms are about 7 or 20 h, respectively. Thus the TGase 1 enzyme is complex, since it exists in keratinocytes as multiple soluble forms, either intact or proteolytically processed at conserved sites, and which have varying specific activities and likely functions.
Targeted DNA degradation using a CRISPR device stably carried in the host genome (2015)

Once an engineered organism completes its task, it is useful to degrade the associated DNA to reduce environmental release and protect intellectual property. Here we present a genetically encoded device (DNAi) that responds to a transcriptional input and degrades user-defined DNA. This enables engineered regions to be obscured when the cell enters a new environment. DNAi is based on type-IE CRISPR biochemistry and a synthetic CRISPR array defines the DNA target(s). When the input is on, plasmid DNA is degraded 10(8)-fold. When the genome is targeted, this causes cell death, reducing viable cells by a factor of 10(8). Further, the CRISPR nuclease can direct degradation to specific genomic regions (for example, engineered or inserted DNA), which could be used to complicate recovery and sequencing efforts. DNAi can be stably carried in an engineered organism, with no impact on cell growth, plasmid stability or DNAi inducibility even after passaging for >2 months.
Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regions (2007)

We report the development of a real-time Invader assay combined with multiplex PCR (mPCR-RETINA), an SNP-based approach that can measure the allelic ratio in copy number variation (CNV) regions of a genome. RETINA monitors the real-time fluorescence intensity of each allele during the Invader assay and detects allelic asymmetries caused by genomic duplication/multiplication in heterozygous individuals. By combining mPCR-RETINA and real-time quantitative PCR that detects total copy number, we can estimate the copy number of each allele in CNV regions, which should be useful for investigating the functional significance of allele copy number with disease susceptibilities and drug responses. Also, mPCR-RETINA can efficiently refine the detailed structures of CNV regions. Due to the combination of RETINA with multiplex PCR, mPCR-RETINA requires a very small amount of genomic DNA for analysis (0.1-0.38 ng/locus). Additionally, mPCR-RETINA has clear advantages in its simple protocol and target-specific reaction, even in nonunique regions. We believe mPCR-RETINA will provide a significant contribution to identifying functional alleles in CNV regions.
Oral tolerance with Copolymer 1 for the treatment of multiple sclerosis (1999)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Genetic and Functional Analyses of Membrane Cofactor Protein (CD46) Mutations in Atypical Hemolytic Uremic Syndrome (2006)

Hemolytic uremic syndrome (HUS) is characterized by the triad of thrombocytopenia, microangiopathic hemolytic anemia, and acute renal failure. The non-Shiga toxin-associated HUS (atypical HUS [aHUS]) has been shown to be a disease of complement dysregulation. Mutations in the plasma complement regulators factor H and factor I and the widely expressed membrane cofactor protein (MCP; CD46) have been described recently. This study looked for MCP mutations in a panel of 120 patients with aHUS. In this cohort, approximately 10% of patients with aHUS (11 patients; nine pedigrees) have mutations in MCP. The onset typically was in early childhood. Unlike patients with factor I or factor H mutations, most of the patients do not develop end-stage renal failure after aHUS. The majority of patients have a mutation that causes reduced MCP surface expression. A small proportion expressed normal levels of a dysfunctional protein. As in other studies, incomplete penetrance is shown, suggesting that MCP is a predisposing factor rather than a direct causal factor. The low level of recurrence of aHUS in transplantation in patients with MCP mutations is confirmed, and the first MCP null individuals are described. This study confirms the association between MCP deficiency and aHUS and further establishes that a deficiency in complement regulation, specifically cofactor activity, predisposes to severe thrombotic microangiopathy in the renal vasculature.
High χ–Low N Block Polymers: How Far Can We Go? (2015)

Block polymers incorporating highly incompatible segments are termed "high χ" polymers, where χ is the Flory-Huggins interaction parameter. These materials have attracted a great deal of interest because low molar mass versions allow for the formation of microphase-separated domains with very small (<10 nm) feature sizes useful for nanopatterning at these extreme dimensions. Given that well-established photolithographic techniques now face difficult challenges of implementation at scales of 10 nm and below, the drive to further develop high χ block polymers is motivated by trends in the microelectronics industry. This Viewpoint highlights our perspective on this niche of block polymer self-assembly. We first briefly review the relevant recent literature, exploring the various block polymer compositions that have been specifically designed for small feature size patterning. We then overview the now standard method for the benchmarking χ values between different pairs of polymers and the consequences of low <i>N</i> and high χ on the thermodynamic aspects of microphase separation. Finally, we comment on restrictions going forward and offer our perspective on the future of this exciting area of block polymer self-assembly.
Cell surface display of hepatitis B virus surface antigen by using Pseudomonas syringae ice nucleation protein (1999)

A new system designed for cell surface display of recombinant proteins on Escherichia coli was evaluated for expression of eukaryotic viral antigens. The major surface antigen of hepatitis B virus (HBsAg) was fused to the ice nucleation protein (INP), an outer membrane protein of Pseudomonas syringae. Western blotting, immunofluorescence microscopy, whole-cell ELISA, and ice nucleation activity assay confirmed expression of recombinant proteins on the surface of Escherichia coli. This study indicated that INP-based cell surface display can be used for epitope mapping and recombinant bacteria expressing hepatitis viral antigens may be used for developing live vaccines.
Clock routing for high-performance ICs (1990)

Routing techniques for optimizing clock signals in small-cell (e.g., standard-cell, sea-of-gate, etc.) application-specific ICs (ASICs) are addressed. In previously reported works, the routing of a clock net has been performed using ordinary global routing techniques based on a minimum spanning or minimal Steiner tree that have little understanding of clock-routing problems. The authors present a novel approach to the clock-routing that all but eliminates clock skew and yields excellent phase delay results for a wide range of chip sizes, net sizes (pin count), minimum feature sizes, and pin distributions on both randomly created and standard industrial benchmarks. For certain classes of pin distributions a decrease in skew with an increase in net size was proven theoretically and observed experimentally. A two to three order magnitude reduction in skew when compared to a minimum rectilinear spanning tree was observed. >
bcr rearrangement: potential false positive secondary to an Eco RI restriction fragment length polymorphism. (1989)

Molecular studies have demonstrated that the Philadelphia chromosome (Ph) translocation characteristic of chronic granulocytic leukemia (CGL) and 50% of the cases of Ph positive acute lymphocytic leukemia (ALL) involves a limited 5.8 Kb region on chromosome 22 termed the breakpoint cluster region (bcr). Detection of bcr rearrangement by Southern blot analysis has proven to be a sensitive diagnostic method and can identify this translocation in some cases which appear cytogenetically negative. Restriction fragment length polymorphisms (RFLP) which involve bcr have the potential to be misinterpreted as gene rearrangements since they result in alteration of the DNA fragment size detected by Southern blot hybridization. We have identified a RFLP involving bcr that is detectable with Eco RI digestion but not with Bam HI, BgI II, or Xba I. The polymorphic fragments generated indicate that this RFLP is the result of an Eco RI restriction site sequence polymorphism.
Synthesis of some substituted α-carbolines (1970)

α-Carboline-1-oxide (I) with acetic anhydride gives 2-acetoxy-9-acetyl-α-carboline; with dimethyl sulphate it gives the salt (II; R = H). The latter salt is converted by alkali into the anhydronium base (III; R = OMe). The salt (II; R = H) and the base (III; R = OMe) are converted by sufficiently basic nucleophilic reagents into 2-substituted α-carbolines; the salt (II; R = Me) reacts even more readily with basic nucleophilic compounds.Diethyl malonate and ethyl acetoacetate with (III; R = OMe) give the ester (V; R = CH2CO2Et). The acid (V; R = CH2CO2H) is readily decarboxylated to 2-methyl-α-carboline.The benzotriazole (IV; R1= NO2, R2= H) in hot phosphoric acid does not give 3-nitro-α-carboline, but gives instead 2-nitropyrido[1,2-a]benzimidazole (VIII); the latter compound is also obtained by treating the amine (VII) with hydrochloric acid. However the benzotriazole (IV; R1= NH2, R2= H) is converted by phosphoric acid into 3-amino-α-carboline; the benzotriazole (IV; R1= H, R2= CO2H) is similarly converted into α-carboline-4-carboxylic acid. The preparation and proof of orientation of some 6-substituted α-carbolines are described.The 1H n.m.r. spectra of 2-, 3-, and 4-substituted α-carbolines are discussed.
Specific Chaperone-like Activity of Inhibitor of Caspase-activated DNase for Caspase-activated DNase (2000)

Caspase-activated DNase (CAD) is the enzyme that causes DNA fragmentation during apoptosis. CAD forms aggregates when it is synthesized in the absence of an inhibitor of CAD (ICAD). Here, using renaturation systems of chemically denatured CAD, we report that ICAD-L, a long form of ICAD, has a chaperone-like activity specific for CAD. Murine CAD carries 14 cysteines, most of which were found to be in reduced form. Reducing agents enhanced the production of the functional CAD in an in vitro translation system. The denatured CAD could be efficiently renatured under highly reducing conditions only in the presence of ICAD-L. This process was ATP-independent. In contrast, reticulocyte lysates stimulated ICAD-L- and ATP-dependent renaturation of denatured CAD without requiring a high concentration of reducing agents. These results indicate that ICAD-L works not only as a specific inhibitor but also as a specific chaperone for CAD.
Two-metal ion mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV RNase H inhibitors (2003)

Human immunodeficiency virus (HIV) RNase H activity is essential for the synthesis of viral DNA by HIV reverse transcriptase (HIV-RT). RNA cleavage by RNase H requires the presence of divalent metal ions, but the role of metal ions in the mechanism of RNA cleavage has not been resolved. We measured HIV RNase H activity associated with HIV-RT protein in the presence of different concentrations of either Mg2+, Mn2+, Co2+ or a combination of these divalent metal ions. Polymerase-independent HIV RNase H was similar to or more active with Mn2+ and Co2+ compared with Mg2+. Activation of RNase H by these metal ions followed sigmoidal dose-response curves suggesting cooperative metal ion binding. Titration of Mg2+-bound HIV RNase H with Mn2+ or Co2+ ions generated bell-shaped activity dose-response curves. Higher activity could be achieved through simultaneous binding of more than one divalent metal ion at intermediate Mn2+ and Co2+ concentrations, and complete replacement of Mg2+ occurred at higher Mn2+ or Co2+ concentrations. These results are consistent with a two-metal ion mechanism of RNA cleavage as previously suggested for a number of polymerase-associated nucleases. In contrast, the structurally highly homologous RNase HI from Escherichia coli is most strongly activated by Mg2+, is significantly inhibited by submillimolar concentrations of Mn2+ and most probably cleaves RNA via a one-metal ion mechanism. Based on this difference in active site structure, a series of small molecule N-hydroxyimides was identified with significant enzyme inhibitory potency and selectivity for HIV RNase H.
Spin–orbit torque-assisted switching in magnetic insulator thin films with perpendicular magnetic anisotropy (2016)

As an in-plane charge current flows in a heavy metal film with spin-orbit coupling, it produces a torque on and thereby switches the magnetization in a neighbouring ferromagnetic metal film. Such spin-orbit torque (SOT)-induced switching has been studied extensively in recent years and has shown higher efficiency than switching using conventional spin-transfer torque. Here we report the SOT-assisted switching in heavy metal/magnetic insulator systems. The experiments used a Pt/BaFe12O19 bilayer where the BaFe12O19 layer exhibits perpendicular magnetic anisotropy. As a charge current is passed through the Pt film, it produces a SOT that can control the up and down states of the remnant magnetization in the BaFe12O19 film when the film is magnetized by an in-plane magnetic field. It can reduce or increase the switching field of the BaFe12O19 film by as much as about 500 Oe when the film is switched with an out-of-plane field.
Insect immunity: isolation from immune blood of the dipteran Phormia terranovae of two insect antibacterial peptides with sequence homology to rabbit lung macrophage bactericidal peptides. (1989)

We have isolated from the hemolymph of immunized larvae of the dipteran insect Phormia terranovae two peptides that are selectively active against Gram-positive bacteria. They are positively charged peptides of 40 residues containing three intramolecular disulfide bridges and differ from one another by only a single amino acid. These peptides are neither functionally nor structurally related to any known insect immune response peptides but show significant homology to microbicidal cationic peptides from mammalian granulocytes (defensins). We propose the name "insect defensins" for these insect antibiotic peptides.
A level set method for inverse problems (2001)

This paper is devoted to the solution of shape reconstruction problems by a level set method. The basic motivation for the setup of this level set algorithm is the well-studied method of asymptotic regularization, which has been developed for ill-posed problems in Hilbert spaces. Using analogies to this method, the convergence analysis of the proposed level set method is established and it is shown that the evolving level set converges to a solution in the symmetric difference metric as the artificial time evolves to infinity. Furthermore, the regularizing properties of the level set method are shown, if the discrepancy principle is used as a stopping rule.
The solution, solid state stability and kinetic investigation in degradation studies of lercanidipine: study of excipients compatibility of lercanidipine (2011)

The objectives of this research were to evaluate the stability of lercanidipine in solution state and solid state and explore the compatibility of drug with oils, surfactants and cosurfactants as excipients. The effect of pH on the degradation in solution state was studied through pH-rate profile of lercanidipine in constant ionic strength buffer solutions in pH range 1-8 which gives the pH of maximum stability. Powdered lercanidipine was stored under 40°C/0%~75% relative humidities (RH) or 0% RH/5~50°C to study the influence of RH and temperature on the stability of lercanidipine in solid state. Binary mixtures of lercanidipine and different excipients were stored at 40°C/75% RH, 40°C and at room temperature for excipient compatibility evaluation. The degradation of lercanidipine at different pH appears to fit a typical first-order reaction, but in solid state, it does not fit any obvious reaction model. Moisture content and temperature both play important roles affecting the degradation rate. Lercanidipine exhibits good compatibility with surfactants, cosurfactants and oils as excipients under stressed conditions of different storage temperature in a 3-week screening study. Moreover, the proposed high-performance liquid chromatography method was utilized to investigate the kinetics of the acidic and alkaline degradation processes of lercanidipine at different temperatures.