gebhart/patrepeval huggingface dataset:
Recombinant Antibodies for the Generation of Antibody Arrays (2011)

Affinity proteomics, mainly represented by antibody microarrays, has in recent years been established as a powerful tool for high-throughput (disease) proteomics. The technology can be used to generate detailed protein expression profiles, or protein maps, of focused set of proteins in crude proteomes and potentially even high-resolution portraits of entire proteomes. The technology provides unique opportunities, for example biomarker discovery, disease diagnostics, patient stratification and monitoring of disease, and taking the next steps toward personalized medicine. However, the process of designing high-performing, high-density antibody micro- and nanoarrays has proven to be challenging, requiring truly cross-disciplinary efforts to be adopted. In this mini-review, we address one of these key technological issues, namely, the choice of probe format, and focus on the use of recombinant antibodies vs. polyclonal and monoclonal antibodies for the generation of antibody arrays.
Macrophage Depletion Diminishes Lesion Size and Severity in Experimental Choroidal Neovascularization (2003)

Macrophage depletion using CL(2)MDP-lip reduces size, cellularity, and vascularity of CNV. This observation supports the hypothesis that macrophages contribute to the severity of CNV lesions.
Ophthalmic Vehicles Containing Polymer-Solubilized Tropicamide: “In Vitro/In Vivo” Evaluation (2002)

Commercial 1.0% aqueous tropicamide (TR) eyedrops are buffered to pH 4.4-5.0 to produce sufficiently stable solutions of the weakly basic, poorly soluble drug. These acidic solutions, however, are irritants and may induce copious lachrimation, thus reducing the drug bioavailability. The aim of the present study was to evaluate some solubilizing agents for the preparation of 1.0% TR ophthalmic solutions adjusted at physiologically compatible pH, potentially showing increased eye tolerance, activity, and stability when compared with standard commercial eyedrops. The tested solubilizers were two non-ionic surfactants-Tyloxapol (TY) and Cremophor EL (CR) and one polymer, Pluronic P85 (PL). Four stable 1% TR formulations, containing 3% TY, 7.5% CR, 15% PL, or 5% CR + 10% PL were submitted to mydriatic activity tests in rabbits. They improved to a small but statistically significant extent the AUC for mydriatic effect of TR in the test animals when compared with commercial 1.0% TR eyedrops.
Inhibition of growth of prostatic cancer cell lines by peptide analogues of insulin-like growth factor 1. (1993)

We have investigated three prostatic cancer cell lines, PC-3, DU-145, and LNCa.FGC, and found that all three cell lines can grow in serum-free medium without the addition of exogenous growth factors. All three cell lines produce substantial amounts of insulin-like growth factor 1 (IGF-1) that is secreted in the medium and they all display constitutively autophosphorylated IGF-1 receptors; two of the cell lines overexpress IGF-1 receptor RNA. The growth of all three cell lines is inhibited by an antisense oligodeoxynucleotide to IGF-1 receptor RNA or by peptide analogues of IGF-1 that compete with IGF-1 binding to its receptor. Our results indicate that these three cell lines grow by an autocrine loop in which the overproduced IGF-1 activates its receptor. Interference with the activation of the receptor leads to cessation of growth.
Human corneal basement membrane heterogeneity: topographical differences in the expression of type IV collagen and laminin isoforms. (1995)

Type IV collagen controversy is the result of the shifts of isoforms in the limbus and conjunctiva. These shifts and the appearance of additional laminins in the limbus may be related to the differentiation state of corneal cells contributing to the EBM formation. Novel types of BM heterogeneity in the human cornea are described: regional (horizontal) in the EBM and vertical in the Descemet's membrane. The first one may be a common feature of converging complex epithelia, whereas the second one may be another unique property of the Descemet's membrane.
Längenmessung mit dem Laser / Using the Laser to measure length / Utilisation de Laser pour mesurage de longueur (1982)

Article Längenmessung mit dem Laser / Using the Laser to measure length / Utilisation de Laser pour mesurage de longueur was published on July 1, 1982 in the journal Materials Testing (volume 24, issue 7).
Possible Physiological Roles of Carboxylic Ester Hydrolases (1987)

(1987). Possible Physiological Roles of Carboxylic Ester Hydrolases. Drug Metabolism Reviews: Vol. 18, No. 4, pp. 379-439.
Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis. (1986)

A DNA double-strand break can be efficiently repaired in Escherichia coli if an oligodeoxyribonucleotide is provided to direct the repair. The oligonucleotide must be at least 20 residues long and have a sequence identical to sequences flanking the break. The phenomenon can be used to introduce defined mutations into DNA in the area of a double-strand break. To obtain mutants, the oligonucleotide that carries a mutation and the denatured linearized plasmid DNA are introduced into E. coli by transformation. No enzymatic manipulation in vitro is required. The mutants can constitute up to 98% of the total number of transformants obtained. The efficiency of mutagenesis decreases as the distance between the mutation and the plasmid cleavage site increases. The universality of the method was tested by introducing mutations into four genes, using four plasmids and three E. coli strains, as well as eight restriction enzymes to linearize DNA. Several models of the oligonucleotide-directed DNA double-strand break repair are discussed.
Functional Characterization of the Multidomain F Plasmid TraI Relaxase-Helicase (2011)

TraI, a bifunctional enzyme containing relaxase and helicase activities, initiates and drives the conjugative transfer of the Escherichia coli F plasmid. Here, we examined the structure and function of the TraI helicase. We show that TraI binds to single-stranded DNA (ssDNA) with a site size of ∼25 nucleotides, which is significantly longer than the site size of other known superfamily I helicases. Low cooperativity was observed with the binding of TraI to ssDNA, and a double-stranded DNA-binding site was identified within the N-terminal region of TraI 1-858, outside the core helicase motifs of TraI. We have revealed that the affinity of TraI for DNA is negatively correlated with the ionic strength of the solution. The binding of AMPPNP or ADP results in a 3-fold increase in the affinity of TraI for ssDNA. Moreover, TraI prefers to bind ssDNA oligomers containing a single type of base. Finally, we elucidated the solution structure of TraI using small angle x-ray scattering. TraI exhibits an ellipsoidal shape in solution with four domains aligning along one axis. Taken together, these data result in the assembly of a model for the multidomain helicase activity of TraI.
Sequential Multiplexed Analyte Quantification Using Peptide Immunoaffinity Enrichment Coupled to Mass Spectrometry (2011)

Peptide immunoaffinity enrichment coupled to selected reaction monitoring (SRM) mass spectrometry (immuno-SRM) has emerged as a technology with great potential for quantitative proteomic assays. One advantage over traditional immunoassays is the tremendous potential for concurrent quantification of multiple analytes from a given sample (i.e. multiplex analysis). We sought to explore the capacity of the immuno-SRM technique for analyzing large numbers of analytes by evaluating the multiplex capabilities and demonstrating the sequential analysis of groups of peptides from a single sample. To evaluate multiplex analysis, immuno-SRM assays were arranged in groups of 10, 20, 30, 40, and 50 peptides using a common set of reagents. The multiplex immuno-SRM assays were used to measure synthetic peptides added to plasma covering several orders of magnitude concentration. Measurements made in large multiplex groups were highly correlated (r(2) ≥ 0.98) and featured good agreement (bias ≤ 1%) compared with single-plex assays or a 10-plex configuration. The ability to sequentially enrich sets of analyte peptides was demonstrated by enriching groups of 10 peptides from a plasma sample in a sequential fashion. The data show good agreement (bias ≤ 1.5%) and similar reproducibility regardless of enrichment order. These significant advancements demonstrate the utility of immuno-SRM for analyzing large numbers of analytes, such as in large biomarker verification experiments or in pathway-based targeted analysis.
Hard drive failure prediction using non-parametric statistical methods (2003)

We present a case study of a difficult real-world pattern recognition problem: predicting hard drive failure using attributes monitored internally by individual drives. We compare the performance of support vector machines (SVMs), unsupervised clustering, and non-parametric sta- tistical tests (rank-sum and reverse arrangements). Some- what surprisingly, the rank-sum method outperformed the other methods, including SVMs. We also show the utility of using non-parametric tests for feature set selection.
Paint selection (2009)

In this paper, we present Paint Selection, a progressive painting-based tool for local selection in images. Paint Selection facilitates users to progressively make a selection by roughly painting the object of interest using a brush. More importantly, Paint Selection is efficient enough that instant feedback can be provided to users as they drag the mouse. We demonstrate that high quality selections can be quickly and effectively "painted" on a variety of multi-megapixel images.
Some monaural and binaural facets of median plane localization (1973)

Recent studies, together with others dating back as far as 1851, leave little doubt that the cavities and convolutions of the pinnae play an important role in the localization of signals that originate in the median plane. Less clearly understood, however, is the nature of the clues that are utilized in arriving at a localization decision. Results of the present study indicate that, insofar as localization in the anterior sector of the median plane is concerned, clues associated with the cavities of the pinna have an important monaural component. Binaural reception also plays a significant role including confining the apparent location of the resultant image within, or near, the median plane. Such a centralizing influence is an essential requirement for optimizing this type of localization. Clues of a secondary nature were found to be associated with the range of frequencies between about 0.7 and 3.5 kHz.
Comparative Evaluation of Virus Transmission Inhibition by Dual-Acting Pyrimidinedione Microbicides Using the Microbicide Transmission and Sterilization Assay (2008)

In the absence of a fully effective human immunodeficiency virus (HIV) vaccine, topical microbicides represent an important strategy for preventing the transmission of HIV through sexual intercourse, the predominant mode of HIV transmission worldwide. Although a comprehensive understanding of HIV transmission has not yet emerged in the microbicide field, it is likely the result of rapid infection of monocyte-derived cells in the vaginal mucosa by CCR5-tropic viruses. Inhibition of HIV transmission requires agents that prevent entry, fusion, reverse transcription, or other preintegrative replication events or agents which directly inactivate HIV or modulate the target cells to render them uninfectible. In vitro assays typically used to evaluate the ability of a microbicide to prevent virus transmission use epithelial or human osteosarcoma-derived cells or immune cells more relevant to the development of anti-HIV therapeutic agents and quantify virus production at short time intervals following infection. We have developed a microbicide transmission and sterilization assay (MTSA) to more sensitively and quantitatively evaluate virus transmission in cell culture in the presence of microbicidal compounds. Results obtained with the MTSA demonstrate that the inhibitory capacity of microbicides is often overestimated in short-term transmission inhibition assays, while some compounds yield equivalent inhibitory results, indicating a biological relevance for the MTSA-based evaluations to identify superior potent microbicides. The MTSA defines the concentration of the microbicide required to totally suppress the transmission of virus in cell culture and may thus help define the effective concentration of the microbicide required in a formulated microbicide product.
Design of a wide-angle, lightweight head-mounted display using free-form optics tiling (2011)

We present a concept of a wide-angle, lightweight, optical see-through head-mounted display (HMD) using free-form optics tiling. Free-form optics tiling can potentially address several critical problems in existing tiled HMD designs that use rotationally symmetric optics. The optical design of our tiled optical see-through HMD achieves a field of view (FOV) of 56° × 45° and an angular resolution of 3.2 arcmin with two display channels. We demonstrate a proof-of-concept prototype and present some of its manufacturing details. The FOV can be further enlarged by tiling more display channels together at their bottom and side surfaces.
Forces involved in bacterial adhesion to hydrophilic and hydrophobic surfaces (2008)

Using a parallel-plate flow chamber, the hydrodynamic shear forces to prevent bacterial adhesion (F(prev)) and to detach adhering bacteria (F(det)) were evaluated for hydrophilic glass, hydrophobic, dimethyldichlorosilane (DDS)-coated glass and six different bacterial strains, in order to test the following three hypotheses. 1. A strong hydrodynamic shear force to prevent adhesion relates to a strong hydrodynamic shear force to detach an adhering organism. 2. A weak hydrodynamic shear force to detach adhering bacteria implies that more bacteria will be stimulated to detach by passing an air-liquid interface (an air bubble) through the flow chamber. 3. DLVO (Derjaguin, Landau, Verwey, Overbeek) interactions determine the characteristic hydrodynamic shear forces to prevent adhesion and to detach adhering micro-organisms as well as the detachment induced by a passing air-liquid interface. F(prev) varied from 0.03 to 0.70 pN, while F(det) varied from 0.31 to over 19.64 pN, suggesting that after initial contact, strengthening of the bond occurs. Generally, it was more difficult to detach bacteria from DDS-coated glass than from hydrophilic glass, which was confirmed by air bubble detachment studies. Calculated attractive forces based on the DLVO theory (F(DLVO)) towards the secondary interaction minimum were higher on glass than on DDS-coated glass. In general, all three hypotheses had to be rejected, showing that it is important to distinguish between forces acting parallel (hydrodynamic shear) and perpendicular (DLVO, air-liquid interface passages) to the substratum surface.
Code generation in the polyhedral model is easier than you think (2004)

Many advances in automatic parallelization and optimization have been achieved through the polyhedral model. It has been extensively shown that this computational model provides convenient abstractions to reason about and apply program transformations. Nevertheless, the complexity of code generation has long been a deterrent for using polyhedral representation in optimizing compilers. First, code generators have a hard time coping with generated code size and control overhead that may spoil theoretical benefits achieved by the transformations. Second, this step is usually time consuming, hampering the integration of the polyhedral framework in production compilers or feedback-directed, iterative optimization schemes. Moreover, current code generation algorithms only cover a restrictive set of possible transformation functions. This paper discusses a general transformation framework able to deal with nonunimodular, noninvertible, nonintegral or even nonuniform functions. It presents several improvements to a state-of-the-art code generation algorithm. Two directions are explored: generated code size and code generator efficiency. Experimental evidence proves the ability of the improved method to handle real-life problems.
Cytochrome P-450 in Plant/Insect Interactions: Geraniol 10-Hydroxylase and the Biosynthesis of Iridoid Monoterpenoids (1995)

The interactions between plant secondary metabolites (particularly monoterpenes) and insects are discussed. Such metabolites are likely to have influenced the evolution of cyt P450-linked detoxification systems in animals, through animal/plant coevolution. The biosynthesis of many classes of plant secondary metabolites involves cyt P450 enzymes. Of these, one of the best characterised is the geraniol/nerol 10-hydroxylase which catalyses a key step in the biosynthesis of the iridoid class of plant terpenes. It would appear that these monoterpenoids are synthesised (via cyt P450 hydroxylation) from different precursors in different plant species, namely geraniol, its isomer nerol, or the related monoterpenoid, citronellol. We show that cyt P450 from the plants Catharanthus roseus and Nepeta racemosa are capable of hydroxylating geraniol, nerol and citronellol, and thus do not impose precursor specificity on iridoid biosynthesis in plants.
An artificial crystalline DDT‐binding polypeptide (1983)

A hydrophobic 24‐residue polypeptide that could potentially form a four‐stranded antiparallel β‐pleated sheet and bind the insecticide DDT was designed and synthesized. The synthetic peptide aggregated in 1 M acetic acid but was monomeric in aqueous 50% ethanol. In the latter solvent the 24‐residue polypeptide and DDT formed a complex with an apparent dissociation constant of ≈2 × 10 −5 M. The DDT binding of an analogue of this peptide possessing the same amino acid residues in a random sequence was more than 2 orders of magnitude and that of bovine serum albumin at least 3 orders of magnitude weaker. The designed polypeptide could be crystallized.
CHEMICAL HYDROXYLATION OF 12a-DEOXYTETRACYCLINE (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCHEMICAL HYDROXYLATION OF 12a-DEOXYTETRACYCLINEChester E. Holmlund, William W. Andres, and Anthony J. ShayCite this: J. Am. Chem. Soc. 1959, 81, 17, 4748–4749Publication Date (Print):September 1, 1959Publication History Published online1 May 2002Published inissue 1 September 1959https://pubs.acs.org/doi/10.1021/ja01526a078https://doi.org/10.1021/ja01526a078research-articleACS PublicationsRequest reuse permissionsArticle Views48Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Beta‐cell replacement strategies for diabetes (2017)

Diabetes is characterized by elevated levels of blood glucose as a result of insufficient production of insulin from loss or dysfunction of pancreatic islet β-cells. Here, we review several approaches to replacing β-cells that were recently discussed at a symposium held in Kyoto, Japan. Transplant of donor human islets can effectively treat diabetes and eliminate the need for insulin injections, supporting research aimed at identifying abundant supplies of cells. Studies showing the feasibility of producing mouse islets in rats support the concept of generating pigs with human pancreas that can serve as donors of human islets, although scientific and ethical challenges remain. Alternatively, in vitro differentiation of both human embryonic stem cells and induced pluripotent stem cells is being actively pursued as an islet cell source, and embryonic stem cell-derived pancreatic progenitor cells are now in clinical trials in North America in patients with diabetes. Macro-encapsulation devices are being used to contain and protect the cells from immune attack, and alternate strategies of immune-isolation are being pursued, such as islets contained within long microfibers. Recent advancements in genetic engineering tools offer exciting opportunities to broaden therapeutic strategies and to probe the genetic involvement in β-cell failure that contributes to diabetes. Personalized medicine might eventually become a possibility with genetically edited patient-induced pluripotent stem cells, and the development of simplified robust differentiation protocols that ideally become standardized and automated. Additional efforts to develop a safe and effective β-cell replacement strategy to treat diabetes are warranted.
Prospective identification of parasitic sequences in phage display screens (2013)

Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10(9) random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the 'parasites'), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 'parasites'. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼ 10(6) diverse clones prevents the biased selection of parasitic clones.
Polynorbornene: synthesis, properties and simulations (1996)

Abstract The vinylic polymerization of norbornenes upon catalysis with Pd 2+ complexes with norbornylnitrile as ligands is reported. The polynorbornenes ( M̄ w = 10 6 ) display a set of unique properties including a dense packing in the amorphous state, high glass transition temperatures, large refractive index, low birefringence and significant brittleness. To test the concept that these properties can be traced back to the conformational constraints of the polymer chains, we performed ab initio calculations, semi‐empirical quantum mechanical calculations and force‐field calculations employing a force field developed by us for polynorbornenes.