gebhart/patrepeval huggingface dataset:
HTTP Authentication: Basic and Digest Access Authentication (1999)

HTTP/1.0, includes the specification for a Basic Access Authentication scheme. This scheme is not considered to be a secure method of user authentication (unless used in conjunction with some external secure system such as SSL [5]), as the user name and password are passed over the network as cleartext.
[Receptors and molecular heterogeneity of lipoprotein particles containing apolipoprotein A-I]. (1988)

High density lipoproteins (HDL) are heterogeneous, with respect to their hydrated density (HDL2, HDL3), and to their apolipoprotein composition (Lp A-I : A-II contains both apolipoprotein A-I and A-II, Lp A-I contains apolipoprotein A-I but not apolipoprotein A-II). Lp A-I and Lp A-I and Lp A-I : A-II particles have different metabolic functions. Only Lp A-I particles seem to be involved in the antiatherogenic role of HDL. Alcohol consumption raises Lp A-I : A-II level but not Lp A-I. Different tissue possess specific binding sites for HDL: steroidogenic tissue, hepatocytes peripheral cells. Apolipoprotein A-I and/or A-II are possible ligands. HLD, after binding to the receptor, can provide the cells with cholesterol, or promote an efflux of cholesterol from the cells and the "reverse cholesterol transport" from the peripheral cells to the liver. The HDL subfractions possess different metabolic roles: binding of Lp A-I to mouse adipose cell receptors promotes cholesterol efflux. Apo A-II are antagonists for this effect.
Dissecting enzyme function with microfluidic-based deep mutational scanning (2015)

Natural enzymes are incredibly proficient catalysts, but engineering them to have new or improved functions is challenging due to the complexity of how an enzyme's sequence relates to its biochemical properties. Here, we present an ultrahigh-throughput method for mapping enzyme sequence-function relationships that combines droplet microfluidic screening with next-generation DNA sequencing. We apply our method to map the activity of millions of glycosidase sequence variants. Microfluidic-based deep mutational scanning provides a comprehensive and unbiased view of the enzyme function landscape. The mapping displays expected patterns of mutational tolerance and a strong correspondence to sequence variation within the enzyme family, but also reveals previously unreported sites that are crucial for glycosidase function. We modified the screening protocol to include a high-temperature incubation step, and the resulting thermotolerance landscape allowed the discovery of mutations that enhance enzyme thermostability. Droplet microfluidics provides a general platform for enzyme screening that, when combined with DNA-sequencing technologies, enables high-throughput mapping of enzyme sequence space.
Muscleblind‐like 2 (Mbnl2) ‐deficient mice as a model for myotonic dystrophy (2008)

Abstract Myotonic dystrophy (DM), the most common adult‐onset muscular dystrophy, is caused by CTG or CCTG microsatellite repeat expansions. Expanded DM mRNA microsatellite repeats are thought to accumulate in the nucleus, sequester Muscleblind proteins, and interfere with alternative mRNA splicing. Muscleblind2 ( Mbnl2 ) is a member of the family of Muscleblind RNA binding proteins (that also include Mbnl1 and Mbnl3 ) that are known to bind CTG/CCTG RNA repeats. Recently, it was demonstrated that Mbnl1 ‐deficient mice have characteristic features of human DM, including myotonia and defective chloride channel expression. Here, we demonstrate that Mbnl2 ‐deficient mice also develop myotonia and have skeletal muscle pathology consistent with human DM. We also find defective expression and mRNA splicing of the chloride channel (Clcn1) in skeletal muscle that likely contributes to the myotonia phenotype. Our results support the hypothesis that Muscleblind proteins and specifically MBNL2 contribute to the pathogenesis of human DM. Developmental Dynamics 237:403–410, 2008. © 2008 Wiley‐Liss, Inc.
A system for the analysis of foot and ankle kinematics during gait (1996)

A five-camera Vicon (Oxford Metrics, Oxford, England) motion analysis system was used to acquire foot and ankle motion data. Static resolution and accuracy were computed as 0.86 +/- 0.13 mm and 98.9%, while dynamic resolution and accuracy were 0.1 +/- 0.89 and 99.4% (sagittal plane). Spectral analysis revealed high frequency noise and the need for a filter (6 Hz Butterworth low-pass) as used in similar clinical situations. A four-segment rigid body model of the foot and ankle was developed. The four rigid body foot model segments were 1) tibia and fibula, 2) calcaneus, talus, and navicular, 3) cuneiforms, cuboid, and metatarsals, and 4) hallux. The Euler method for describing relative foot and ankle segment orientation was utilized in order to maintain accuracy and ease of clinical application. Kinematic data from a single test subject are presented.
Vacuum therapy in dermatology: a review (2006)

Modern wound therapy is developing continuously. Vacuum therapy is an established procedure to treat wounds. Available on the market is, among others, the V.A.C. (Vacuum Assisted Closure) therapy system. Here, we report the various effects of the vacuum therapy on wounds such as reducing the bacterial contamination, improving granulation and microcirculation and focus on the practical use of the V.A.C., possible complications, contraindications and the economic aspects of the therapy. Since V.A.C. therapy allows rapid mobilization of patients especially with postoperative or posttraumatic wounds, infrequent dressing changes and relative analgesia, this treatment modality is well-accepted by patients with acute or chronic wounds. One explanation for the high acceptance on part of the therapists and the widespread use of the method are the excellent clinical results.
An adenovirus type 5 E1A protein with a single amino acid substitution blocks wild-type E1A transactivation. (1987)

The E1A gene of adenovirus type 5 encodes a 289-amino-acid (289R) protein that transactivates early adenovirus promoters. We showed that the 289R protein of the E1A missense mutant gene hr5 is novel in that it inhibits the wild-type (wt) E1A protein from stimulating transcription from each of the early viral promoters E2, E3, and E4. Since both the hr5 and wt genes produced similar levels of E1A proteins, the ability of hr5 E1A to block transactivation was attributed to the replacement of serine by asparagine as position 185. We confirmed that this single amino acid substitution was responsible for blocking transactivation by showing equal inhibition with an hr5-wt hybrid E1A gene containing this missense mutation as the only alteration. The smaller 243R E1A protein of hr5 was not necessary for inhibition. Transcriptional activity from each early promoter was inhibited by at least 50% when the hr5 and wt E1A genes were present in equimolar amounts; complete inhibition occurred with a fivefold molar excess of the hr5 gene. Two other E1A missense mutant genes (hr3 and hr4) with amino acid substitutions in close proximity to that of hr5 failed to block wt E1A-induced transcription when similarly tested. Also, the hr5 E1A gene failed to impede the pseudorabies immediate early gene from transactivating the adenovirus E3 promoter, demonstrating that hr5 E1A inhibits wt E1A activation at the transcriptional, rather than the posttranscriptional, level. Although several possibilities were considered to account for this inhibition, the most likely is that the nonfunctional hr5 E1A protein competes with the wt 289R protein for a cellular transcription factor required for transactivation.
Cloaking and Redirection: A Preliminary Study (2005)

Cloaking and redirection are two possible search engine spamming techniques. In order to understand cloaking and redirection on the Web, we downloaded two sets of Web pages while mimicking a popular Web crawler and as a common Web browser. We estimate that 3% of the first data set and 9% of the second data set utilize cloaking of some kind. By checking manually a sample of the cloaking pages from the second data set, nearly one third of them appear to aim to manipulate search engine ranking.
Dual-band Sierpinski fractal monopole antenna (2002)

A new top-loaded reduced-sized dual-band (1.9 GHz and 3.5 GHz) monopole antenna for wireless communications is presented. The antenna provides better than -15 dB input return loss and keeps the same radiation pattern over both bands. In addition, a low-profile performance is achieved.
Using Affinity Capillary Electrophoresis To Determine Binding Stoichiometries of Protein-Ligand Interactions (1994)

We have developed a new method utilizing affinity capillary electrophoresis (ACE) for the determination of binding stoichiometries in biochemical systems. Using the same concentration of a ligand in the sample and the electrophoresis buffer, the appearance of an inverted peak corresponding to the free ligand in the resulting electropherogram provides a criterion of binding of a ligand to its receptor protein. For both low (fast off rates) and high (slow off rates) affinity systems, analysis of the integration of free ligand peak in electropherograms as a function of the total concentration of a ligand in samples at constant concentration of receptor protein yields the binding stoichiometry of the ligand to the protein. Applications of this technique to studies of (i) the inhibition of carbonic anhydrases (CA, EC 4.2.1.1, from human and bovine erythrocytes) by 4-alkylbenzenesulfonamide 1, (ii) the interaction of a monoclonal antibody to human serum albumin (anti-HSA) with its antigen HSA, and (iii) the binding of streptavidin (from Streptomyces avidinii) to biotin derivatives (monobiotinylated oligodeoxyribonucleotide 2, fluorescein biotin, or Lucifer Yellow biotin) yield stoichiometries of 1:1, 1:2, and 1:4, respectively. For multivalent, tight-binding systems, this ACE method can readily separate stable intermediate species. This method is generally applicable to both tight- and weak-binding systems, requires only nanograms of proteins and ligands, involves no radioactive materials, and does not require changes in electrophoretic mobilities of receptor proteins upon binding with ligands. It thereby provides a rapid, sensitive, and convenient method for measuring binding stoichiometries of ligands to proteins.
Substrate specificity of the periplasmic dipeptide-binding protein from Escherichia coli: experimental basis for the design of peptide prodrugs (1999)

Pure dipeptide-binding protein (DppA) from Escherichia coli was studied in a filter binding assay to determine its binding specificity. A substrate:DppA stoichiometry of 1:1 was found with both [14C]AlaAla and Ala[14C]Phe. Surprisingly, substrate binding did not vary over the pH range pH 3-9.5. Different dipeptides yielded liganded protein with various pI values, implying that DppA can undergo subtly different conformational changes to accommodate different substrates. Using [125I]Tyr-peptides as substrates in competition assays, the relative binding affinities for a range of dipeptides were found to parallel their overall transport rates into E. coli through the dipeptide permease (Dpp), showing that DppA alone controls the specificity of Dpp. With a series of substituted glycyl peptides, binding affinity was progressively enhanced by alkylation (with methyl to butyl) of the N-terminal alpha-amino group. Thus, results from this approach provide an essential experimental basis, which complements the information from the crystal structure of DppA, for the design of peptidomimetic antibacterials targeted for transport through Dpp.
5.3: Digital Paper™: Reflective Displays Using Interferometric Modulation (2000)

Abstract Reflective displays have been fabricated using Interferometric Modulators (IMods), which are interference based MEMS devices. The displays have exhibited reflectivities in excess of 80%, contrast ratios greater than 12:1, viewing angles up to ± 60°, and drive voltages &lt; 5 volts. They are being developed for portable electronic applications, and their status will be discussed.
Bitter peptides increase engulf of phagocytes in vitro and inhibit oxidation of myofibrillar protein in peeled shrimp (Litopenaeus vannamei) during chilled storage (2019)

We have shown that bitter peptides derived from the hydrolysates of pepsin digested fish protein can increase lymphocytes and lysozyme activity and improve fish survival in aquaculture. In this study, we investigated how the immune function of bitter peptides increases the phagocytes’ engulf of latex beads, and analyzed the antioxidation of myofibrillar protein in peeled shrimp during chilled storage with /without bitter peptides by evaluating the activity of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals, and the effects of the total carbonyl and sulfhydryl. Also, the bitter peptides’ effect on the structural stability of muscles protein throughout oxidation was examined in vitro by both scanning electron microscope (SEM) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The engulf assay demonstrated phagocytosis increased from the control group to the highest bitter peptide concentration of 1.2 mg/ml; the bitter peptides had a significant DPPH radical-scavenging activity, reducing the power of ferric ions and metal chelating ability. Chemical analysis showed that myofibrillar protein in chilled storage was highly susceptible to oxidation, and the results indicate that treating peeled shrimp with bitter peptides before chilled storage significantly decreases the formation of carbonyl derivatives and reduces the loss of thiol groups when compared with the water treated sample. In addition, the results of both SEM and SDS-PAGE confirm that there was less distortion of tissue structure and less degradation of the protein in the samples treated with bitter peptides. Bitter peptides are both beneficial for fish disease control and preservation of marine food.
Targeting of Genes to Specific Sites in the Mammalian Genome (1986)

Gene targeting — the homologous recombination of DNA sequences residing in the chromosome with newly introduced DNA sequences — provides the means for systematically altering the mammalian genome (Lin et al. 1985; Smithies et al. 1985; Thomas et al. 1986). A desired alteration would first be introduced into a cloned DNA sequence, and gene targeting would then transfer the alteration into the genome. Gene targeting should be equally effective for correcting or mutating the desired chromosomal locus.
Mathematics and painting (2002)

AbstractAbstractMathematics and painting are interrelated in many ways. At a technical level mathematics can be used to enhance our appreciation of paintings. This was recently demonstrated beautifully by Taylor, Micolich, and Jones in their analysis of Jackson Pollock's drip paintings, which led them to the conclusion that Pollock's paintings are in a way figurative pictures. Relations also exist at a more basic level. Painting and mathematics can share subject matter, as is illustrated here by a discussion of the mathematical concepts 'open' and 'closed', which are related to paintings by Pollock, Kandinsky, Turner, and van Gogh. It is suggested in conclusion that mathematics and painting are so closely related and have so many similarities that it is reasonable to consider them simply as two different but complementary ways of visualising aspects of the concrete or abstract reality in which we are embedded.
Quantitative immunofluorescent analysis of surface phenotypes of murine B cell lymphomas and plasmacytomas with monoclonal antibodies. (1981)

In this study, a large series of murine B lymphomas and plasmacytomas were examined by quantitative flow cytometry analysis using a panel of monoclonal antibodies against murine differentiation antigens. These cell lines appear to represent subpopulations of lymphoid cells arrested at distinct stages of differentiation. In general, the pattern of reactions of these monoclonal antibodies with the B cell neoplasms was comparable to the reactions seen with normal cells in the same lineage. The Thy-1.2, Lyt-2, and T-30 differentiation antigens were not detected on any B lymphoma or plasmacytoma. However, certain surface Ig-positive B lymphomas do express the Lyt-1 antigen. With respect to other differentiation markers examined, including E2, F1, ThB, Lgp-100 (Ly 9.1), G2, and T-200 (Ly 5), the reaction of the B cell tumors reflected the expression of these markers on comparable normal cells. This investigation also emphasized the marked intratumor and intertumor heterogeneity that is observed when cloned cell lines are analyzed quantitatively for a large number of surface markers. Thus, this approach may be particularly useful in defining heterogeneity in maturation states within cloned tumor cell lines.
A 2 year, open ended trial of methotrexate in systemic lupus erythematosus. (1994)

MTX appears to be useful in selected patients with SLE, especially those with persistent synovitis.
Cloning, characterization, and chromosomal localization of a gene frequently deleted in human liver cancer (DLC-1) homologous to rat RhoGAP. (1998)

The isolation of genes involved in cancer development is critical for uncovering the molecular basis of cancer. We report here the isolation of the full-length cDNA and chromosomal localization of a new gene frequently deleted in liver cancer (DLC-1) that was identified by representational difference analysis. Loss of heterozygosity was detected for DLC-1 in 7 of 16 primary hepatocellular carcinomas (HCCs) and in 10 of 11 HCC cell lines. Although mRNA for DLC-1 was expressed in all normal human tissues, it was not expressed in 4 of 14 HCC cell lines. Full-length cDNA for DLC-1 of 3800 bp encodes a protein of 1091 amino acids, has 86% homology with rat p122 RhoGAP gene, and was localized by fluorescence in situ hybridization on chromosome 8 at bands p21.3-22. Deletions on the short arm of chromosome 8 are recurrent in liver, breast, lung, and prostate cancers, suggesting the presence of tumor suppressor genes. DLC-1 may be a tumor suppressor gene in liver cancer as well as in other cancers.
Tethered Bilayer Membranes Containing Ionic Reservoirs:  Selectivity and Conductance (2003)

Ion channels, such as gramicidin A, selectively facilitate the transport of ions across biological and synthetic membranes. The conductance properties of ion channels are frequently characterized in synthetic bilayer lipid membranes (BLMs). The instability of BLMs has seriously limited the range of applications for these structures, and tethered bilayer lipid membranes (tBLMs) have addressed the problem through tethering many of the membrane components to a solid surface. In the present study, thin gold substrates have been used to tether thiol- and disulfide-terminated membrane components to form a tBLM electrode to provide a reservoir for ions. This study reports on the ion selectivity and apparent permeability of gramicidin channels in such tethered bilayer membranes. The investigations using electrical impedance spectroscopy indicated that the magnitude of ionic conductance varies substantially in reservoirs with different chemical structures. This study addressed the effect of changing ionic concentration, the effect of changing the species in the bulk solution above the membrane, and the influence of the chemical structure of the reservoir tethers. The effect of two-dimensional packing on membrane conductance was also investigated. The present observations suggested that (a) the reservoir region resistivity has a major influence on the overall conductivity of the membrane and in some instances can dominate conduction, (b) the conduction behavior is nonlinear and exhibits saturation with increasing electrolyte concentration, and (c) that ion pairing in the reduced dielectric (ε ∼50) reservoir region is the likely basis for the latter effect. The inferred limiting ionic mobilities of alkali chloride species in the membrane reservoir regions were 3−4 orders of magnitude less than in aqueous solution, indicating that the reservoirs resembled hydrated polymer gels.
Glycoprotein C-independent binding of herpes simplex virus to cells requires cell surface heparan sulphate and glycoprotein B (1994)

Previous studies have shown that the initial interaction of herpes simplex virus (HSV) with cells is binding to heparan sulphate and that HSV-1 glycoprotein C (gC) is principally responsible for this binding. Although gC-negative viral mutants are impaired for binding and entry, they retain significant infectivity. The purpose of the studies reported here was to explore the requirements for infectivity of gC-negative HSV-1 mutants. We found that absence or alteration of cell surface heparan sulphate significantly reduced the binding of gC-negative mutant virus and rendered cells resistant to infection, as shown previously for the wild-type virus. We isolated a recombinant double-mutated HSV strain that produces virions devoid of both of the known heparin-binding glycoproteins, gB and gC. The drastically impaired binding of these mutant virions to cells, relative to gC-negative and wild-type virions, indicates that gB mediates the binding of gC-negative virions to cells. Thus at least two HSV glycoproteins can independently mediate the binding of HSV to cell surface heparan sulphate to start the process of viral entry into cells.
Circumvention of Normal Constraints on Granule Protein Gene Expression in Peripheral Blood Neutrophils and Monocytes of Patients with Antineutrophil Cytoplasmic Autoantibody–Associated Glomerulonephritis (2004)

Granulopoiesis-related genes are distinctively upregulated in peripheral leukocytes of patients with antineutrophil cytoplasmic autoantibodies (ANCA)-associated glomerulonephritis. Affymetrix microarrays identified the upregulation of nine neutrophilic primary granule genes, including myeloperoxidase (MPO) and proteinase 3 (PR3), plus five secondary granule genes. Coordinate expression of granulocyte maturation marker CD35, measured by TaqMan PCR, and positive in situ staining for PR3 transcripts in polymorphic neutrophils and monocytes indicate that these genes are expressed in "mature" cells. Increased transcripts correlated with disease activity and absolute neutrophil values but not with "left shift," drug regimen, cytokine levels, hematuria, proteinuria, ANCA titer, serum creatinine, gender, or age. Upregulation of PR3 and MPO transcripts was specifically associated with ANCA disease (n = 56) as these changes were not detected in patients with ESRD (n = 25) or systemic lupus erythematosus (n = 17), as determined by TaqMan PCR. This is the first report of this phenomenon in nonneoplastic cells. The data raise the hypothesis that, in addition to the presence of anti-MPO or anti-PR3 autoantibodies, a second critical component in the cause of this disease is the reactivation of once-silenced genes leading to increased antigen availability.