gebhart/patrepeval huggingface dataset:
Moiré Topography (1970)

A technique observing contour lines of an object by the use of moiré is developed. Shadow of an equispaced plane grating is projected onto an object by a point source and observed through the grating. The resulting moiré is a contour line system showing equal depth from the plane of grating if the light source and the observing point lie on a plane parallel to the grating. A technique to wash away the unwanted aliasing moiré optimization of contour line spacing and visibility and the results of the application are described.
A postsynaptic role for single-stranded DNA-binding protein in recA protein-promoted DNA strand exchange. (1992)

The single-stranded DNA-binding protein (SSB protein) is required for efficient genetic recombination in vivo. One function for SSB protein in DNA strand exchange in vitro is to remove secondary structure from single-stranded DNA (ssDNA) and thereby aid in the formation of recA protein-saturated presynaptic complexes. In the preceding paper (Lavery, P. E., and Kowalczykowski, S. C. (1992) J. Biol. Chem. 267, 9307-9314) we demonstrated that DNA strand exchange can occur in the presence of volume-occupying agents at low magnesium ion concentration, where secondary structures are reduced. Our results suggest that SSB protein is not acting during presynapsis under these conditions, yet the DNA strand exchange reaction is stimulated by the addition of SSB protein. In this study we present biochemical evidence which suggests that SSB protein stimulates DNA strand exchange by binding to the ssDNA displaced from joint molecules, thereby stabilizing them and allowing branch migration to extend the region of heteroduplex DNA. Therefore, our results indicate dual roles for SSB protein at elevated magnesium ion concentration; it functions during presynapsis, removing secondary structure from ssDNA, as indicated previously, and it also functions postsynaptically, binding to the ssDNA displaced from joint molecules.
From RankNet to LambdaRank to LambdaMART: An Overview (2010)

LambdaMART is the boosted tree version of LambdaRank, which is based on RankNet. RankNet, LambdaRank, and LambdaMART have proven to be very successful algorithms for solving real world ranking problems: for example an ensemble of LambdaMART rankers won Track 1 of the 2010 Yahoo! Learning To Rank Challenge. The details of these algorithms are spread across several papers and reports, and so here we give a self-contained, detailed and complete description of them. 1
Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin (1985)

A photo-activatable analogue of biotin, N-(4-azido-2-nitrophenyl)-N'-(N-d-biotinyl-3-aminopropyl)-N'-methyl-1,3- propanediamine (photobiotin), has been synthesized and used for the rapid and reliable preparation of large amounts of stable, non-radioactive, biotin-labelled DNA and RNA hybridization probes. Upon brief irradiation with visible light, photobiotin formed stable linkages with single- and double-stranded nucleic acids yielding probes which were purified from excess reagent by 2-butanol extraction and ethanol precipitation. Using single-stranded phage M13 DNA probes chemically labelled with one biotin per 100-400 residues and dot-blot hybridization reactions on nitrocellulose, as little as 0.5 pg (6 X 10(-18) mol) of target DNA was detected colorimetrically by avidin or streptavidin complexes with acid or alkaline phosphatase from three commercial sources. The sensitivity of detection of target RNA in dot-blots and Northern blots was equivalent to that obtained with 32p-labelled DNA probes. Photobiotin was also used for the labelling of proteins with biotin.
Protein Kinase C Contains a Pseudosubstrate Prototope in Its Regulatory Domain (1987)

The regulatory domain of protein kinase C contains an amino acid sequence between residues 19 and 36 that resembles a substrate phosphorylation site in its distribution of basic residue recognition determinants. The corresponding synthetic peptide (Arg19-Phe-Ala-Arg-Lys-Gly-Ala25-Leu-Arg-Gln-Lys-Asn-Val-His -Glu-Val-Lys-Asn36) acts as a potent substrate antagonist with an inhibitory constant of 147 +/- 9 nM. It is a specific inhibitor of protein kinase C and inhibits both autophosphorylation and protein substrate phosphorylation. Substitution of Ala25 with serine transforms the pseudosubstrate into a potent substrate. These results demonstrate that the conserved region of the regulatory domain (residues 19 to 36) of protein kinase C has the secondary structural features of a pseudosubstrate and may be responsible for maintaining the enzyme in the inactive form in the absence of allosteric activators such as phospholipids.
Find Your Own Way: Weakly-Supervised Segmentation of Path Proposals for Urban Autonomy (2016)

We present a weakly-supervised approach to segmenting proposed drivable paths in images with the goal of autonomous driving in complex urban environments. Using recorded routes from a data collection vehicle, our proposed method generates vast quantities of labelled images containing proposed paths and obstacles without requiring manual annotation, which we then use to train a deep semantic segmentation network. With the trained network we can segment proposed paths and obstacles at run-time using a vehicle equipped with only a monocular camera without relying on explicit modelling of road or lane markings. We evaluate our method on the large-scale KITTI and Oxford RobotCar datasets and demonstrate reliable path proposal and obstacle segmentation in a wide variety of environments under a range of lighting, weather and traffic conditions. We illustrate how the method can generalise to multiple path proposals at intersections and outline plans to incorporate the system into a framework for autonomous urban driving.
Protection of mice and nude rats against toxoplasmosis by a multiple antigenic peptide construction derived from Toxoplasma gondii P30 antigen (1992)

The first part of this work presents the sequence of the first 20 NH2 terminus residues obtained from P30, the major surface Ag of Toxoplasma gondii, purified by HPLC. A synthetic peptide (P30 48-67) has been prepared both in linear form and as a multiple antigenic peptide (MAP) construct. Immunization of mice and rats with the P30 48-67 MAP in the presence of IFA induces high levels of IgG antibodies that recognize both the linear peptide and the MAP construct in ELISA, and P30 in Western blots of NP-40-extracted tachyzoite Ag. Because these sera are negative in immunofluorescence assays with whole tachyzoites, it seems that IgG antibodies induced by P30 48-67 MAP, although recognizing the denatured structure, are unable to recognize the native protein. However, the protective effect of both constructs has then been studied in mice and nude rats. Whereas immunization of mice with the monomeric peptide does not confer any protection against oral infection with 1200 cysts of T. gondii 76K strain (mortality within 11 days), 40% of mice immunized with the MAP construct survived up to 75 days after infection. Nude rats were passively transferred with 5 x 10(4) T lymphocytes from P30 48-67 MAP-immunized Fischer rats before infection with 5 x 10(4) RH strain tachyzoites. They survived up to 40 days after infection and raised an intense IgG antibody response against P30, whereas nude rats transferred with control lymphocytes died within 21 days. This shows that immunization with P30 48-67 MAP also induces an efficient T cell immune response. The present work confirms the recently demonstrated role of P30 in protective immunity and shows the interest of peptide octameric constructions as inducers of partially protective immune responses in toxoplasmosis, as already demonstrated in schistosomiasis.
Long-term Tumor Regression Induced by an Antibody–Drug Conjugate That Targets 5T4, an Oncofetal Antigen Expressed on Tumor-Initiating Cells (2012)

Antibody-drug conjugates (ADC) represent a promising therapeutic modality for the clinical management of cancer. We sought to develop a novel ADC that targets 5T4, an oncofetal antigen expressed on tumor-initiating cells (TIC), which comprise the most aggressive cell population in the tumor. We optimized an anti-5T4 ADC (A1mcMMAF) by sulfydryl-based conjugation of the humanized A1 antibody to the tubulin inhibitor monomethylauristatin F (MMAF) via a maleimidocaproyl linker. A1mcMMAF exhibited potent in vivo antitumor activity in a variety of tumor models and induced long-term regressions for up to 100 days after the last dose. Strikingly, animals showed pathologic complete response in each model with doses as low as 3 mg antibody/kg dosed every 4 days. In a non-small cell lung cancer patient-derived xenograft model, in which 5T4 is preferentially expressed on the less differentiated tumor cells, A1mcMMAF treatment resulted in sustained tumor regressions and reduced TIC frequency. These results highlight the potential of ADCs that target the most aggressive cell populations within tumors, such as TICs. In exploratory safety studies, A1mcMMAF exhibited no overt toxicities when administered to cynomolgus monkeys at doses up to 10 mg antibody/kg/cycle × 2 and displayed a half-life of 5 days. The preclinical efficacy and safety data established a promising therapeutic index that supports clinical testing of A1mcMMAF.
Stimulation through the TCR/CD3 complex up-regulates the CD2 surface expression on human T lymphocytes (1991)

Despite the well known interrelationship between the CD2- and CD3-mediated signal transduction pathways, it is not well established whether the CD2 surface expression can be regulated by triggering of TCR/CD3 complex. In this study we show that the stimulation of human PBMC with the Cris-7 (CD3) mAb, both in soluble and particulate form, results in hyperexpression of the CD2 surface Ag, as assessed by immunofluorescence and semi-quantitative immunoprecipitation assays. Similar effects on CD2 surface expression were obtained when different CD3 mAb (OKT3, RW2-8C8 and Leu-4) were tested. The CD3-mediated CD2 up-regulation was suppressed by cycloheximide and actinomycin D, indicating that it requires de novo protein and RNA synthesis. In agreement with this, increased CD2 RNA levels were observed after 3 h of stimulation, reaching a plateau at 24 h that was maintained for 72 h. The CD2 up-regulation was concomitant to other CD3-induced activation-related events such as induction of surface CD25 and CD71 and high RNA levels for c-myc, IL-2R alpha- and beta-chains, CD71, and IFN-gamma. CD2 up-regulation appeared to be elicited by a protein kinase C-dependent mechanism because it was abrogated by staurosporine, a potent protein kinase C inhibitor. Moreover, IL-2-dependent events may also help in enhancing CD2 hyper-expression because it was only partially inhibitable by cyclosporine, dexamethasone, or Mar-108 (CD25) mAb. In conclusion, our data suggest that CD2 up-regulation can be a relevant event in T cell activation triggered by the physiologic engagement of the TCR/CD3 complex.
Immune monitoring with iTAg™ MHC tetramers for prediction of recurrent or persistent cytomegalovirus (CMV) infection in allogeneic stem cell transplant (SCT) recipients: A prospective multicenter clinical trial (2006)

Background: CMV infection is an important cause of morbidity and mortality in SCT recipients despite the introduction of routine post-transplant virologic monitoring and the use of potent antiviral agents. This prospective multicenter study evaluated the use of tetramers in monitoring CMV-specific T cell recovery following allogeneic SCT to predict patients at risk for CMV-related complications. Methods: Patients were tested every 2 weeks and monitored for up to 1 year post-transplant. iTAg™ MHC Tetramers (Beckman Coulter, San Diego) were used to enumerate CMV-specific CD8+ T cells by flow cytometry using a single-platform absolute counting method. The following tetramers were included: pp50: A0101 VTEHDTLLY; pp65: A0201 NLVPMVATV, B0702 TPRVTGGGAM, B3501 IPSINVHHY; IE-1: B0801 ELRRKMMYM. All patients underwent weekly surveillance by pp65 antigenemia or DNAemia with preemptive antiviral therapy. Results: Data were analyzed for 83 CMV-seropositive recipients with 3 or more tetramer values. Median follow-up was 9 months (range 2–12). Delayed recovery of CMV-specific CD8+ T cells (<7 cells/mL in all blood samples during the first 65 days post-transplant) predisposes patients to CMV-related complications (Table 1). These patients are 2.6 times more likely to develop recurrent or persistent CMV infection, 4.8 times more likely to develop CMV disease, 2.4 times more likely to develop fatal complications, and 2.2 times more likely to develop one of more of these outcomes than patients showing rapid recovery. Rapid recovery (≥7 cells/mL in any blood sample during the first 65 days post-transplant) was associated with protection from CMV-related complications. Inter- and intraassay variability of the assay was ≤8% and ≤8%, and results were available in 3 hours. Conclusions: CMV tetramer-based immune monitoring, in conjunction with virologic monitoring, can be an important new tool that permits clinicians to assess the period of risk of CMV-related complications and to make appropriate preemptive therapeutic choices in managing allogeneic SCT patients. For high-risk patients with delayed immunologic recovery, virologic monitoring, CMV tetramer monitoring, and other preemptive strategies should be continued beyond 100 days post-transplant. For low-risk patients (≥7 tetramer-positive cells/mL), studies are needed to determine how long virologic monitoring should be continued or if preemptive therapy may be modified or instituted at higher viral load levels (Table 1).Table 1Relative RiskRecurrent or Persistent CMV InfectionCMV DiseaseTransplant-Related MortalityComposite (one or More of These Outcomes)Delayed recovery of CMV-specific CD8+ cells (< 7 cells/uL)2.64.82.42.2P = .02P = .09P = .12P = .01 Open table in a new tab
Multiple consequences of human growth hormone expression in transgenic mice. (1989)

Transgenic mice harbouring growth hormone gene constructs have been produced by DNA microinjection into pronuclei of fertilized oocytes. We examined transgenic mice carrying a mouse metallothionein I-human growth hormone (mMT I-hGH) fusion gene. Here, we present our results concerning gene integration, gene expression, and phenotypical, clinical and pathomorphological alterations found in mice expressing the hGH transgene. Body and organ growth was significantly increased in transgenic mice, whereas fertility was found to be reduced. The life-span was markedly shortened indicating detrimental side-effects of the high levels of circulating hGH. Lesions of kidneys, liver and heart were the predominant pathological findings. Our own results are compared with those obtained by other authors who have investigated mice carrying rat, bovine or ovine growth hormone fusion genes. GH-transgenic mice may serve as a model system to investigate ectopic expression of hormone genes thus circumventing endogenous feedback control mechanisms in complex hormonal cascades.
2,6-bis(N-pyrazolyl)pyridines: the convenient synthesis of a family of planar tridentate N3 ligands that are terpyridine analogs (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2,6-bis(N-pyrazolyl)pyridines: the convenient synthesis of a family of planar tridentate N3 ligands that are terpyridine analogsDonald L. Jameson and Kenneth A. GoldsbyCite this: J. Org. Chem. 1990, 55, 17, 4992–4994Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/jo00304a007https://doi.org/10.1021/jo00304a007research-articleACS PublicationsRequest reuse permissionsArticle Views2438Altmetric-Citations140LEARN 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
Optical Spectrum Analysis of Large Space Bandwidth Signals (1966)

Coherent optical spectrum analyzers are available for determining the frequency content of many analog signals written simultaneously on film. The space bandwidth product of each signal must not exceed one thousand for a typical 35 mm system. By sacrificing the multichannel capability of such a computer, single signals with space bandwidth products greater than one million (10(6)) can be analyzed. Two optical systems are described. The first analyzes long signals but maintains the frequency resolution of the multichannel system (one part in one thousand). The second system yields frequency resolution of at least one part in one million. Near real-time, continuous spectrum analysis of analog signals is within the current state of the art. A breadboard system is being built.
An empirical comparison of supervised learning algorithms (2006)

A number of supervised learning methods have been introduced in the last decade. Unfortunately, the last comprehensive empirical evaluation of supervised learning was the Statlog Project in the early 90's. We present a large-scale empirical comparison between ten supervised learning methods: SVMs, neural nets, logistic regression, naive bayes, memory-based learning, random forests, decision trees, bagged trees, boosted trees, and boosted stumps. We also examine the effect that calibrating the models via Platt Scaling and Isotonic Regression has on their performance. An important aspect of our study is the use of a variety of performance criteria to evaluate the learning methods.
Transforming growth factor-beta inhibits human vascular smooth muscle cell growth and migration. (1993)

TGF-beta inhibits both migration and proliferation of human SMC. This inhibitory effect is not mediated through protein kinase C, mitogen-activated protein kinase, or tyrosine kinases.
An Evening with Berferd In Which a Cracker is Lured, Endured, and Studied (1991)

On 7 January 1991 a cracker, believing he had discovered the famous sendmail DEBUG hole in our Internet gateway machine, attempted to obtain a copy of our password file. I sent him one. For several months we led this cracker on a merry chase in order to trace his location and learn his techniques. This paper is a chronicle of the cracker&amp;apos;s &amp;quot;successes&amp;quot; and disappointments, the bait and traps used to lure and detect him, and the chroot &amp;quot;Jail&amp;quot; we built to watch his activities. We concluded that our cracker had a lot of time and persistence, and a good list of security holes to use once he obtained a login on a machine. With these holes he could often subvert the uucp and bin accounts in short order, and then root. Our cracker was interested in military targets and new machines to help launder his connections. 1. Introduction Our secure Internet gateway was firmly in place by the spring of 1990[1]. With the castle gate in place, I wondered how often the lock was tried. I knew there were b...
Antisense phosphorothioate oligonucleotides: selective killing of the intracellular parasite Leishmania amazonensis. (1994)

We targeted the mini-exon sequence, present at the 5' end of every mRNA of the protozoan parasite Leishmania amazonensis, by phosphorothioate oligonucleotides. A complementary 16-mer (16PS) was able to kill amastigotes--the intracellular stage of the parasite--in murine macrophages in culture. After 24 hr of incubation with 10 microM 16PS, about 30% infected macrophages were cured. The oligomer 16PS acted through antisense hybridization in a sequence-dependent way; no effect on parasites was observed with noncomplementary phosphorothioate oligonucleotides. The antisense oligonucleotide 16PS was a selective killer of the protozoans without any detrimental effect to the host macrophage. Using 16PS linked to a palmitate chain, which enabled it to complex with low density lipoproteins, improved the leishmanicidal efficiency on intracellular amastigotes, probably due to increased endocytosis. Phosphorothioate oligonucleotides complementary to the intron part of the mini-exon pre-RNA were also effective, suggesting that antisense oligomers could prevent trans-splicing in these parasites.
Isolation of Differentially Expressed Genes by Combining Representational Difference Analysis (RDA) and cDNA Library Arrays (1998)

The difference products (DP) of representational difference analyses (RDA) were used as hybridization probes on cDNA arrays. The effectivity of RDA products obtained with increasing driver/tester ratios (DP 1 = 100:1, DP 2 = 800:1 and DP 3 = 400,000:1) to isolate differentially expressed genes was compared with the effectivity of conventional differential hybridizations. Pacreatic cancer and control tissues were used as a test system to isolate differentially expressed genes. The use of RDA products as hybridization probes showed two major advantages: (i) a reliable identification of true differential signals; and (ii) only one autoradiograph had to be analyzed, which eliminated the need for a laborious subtraction of signal intensities obtained with different cDNA probes. Increasing driver/tester ratios in iterative rounds of RDA delivered more specific results, though the total yield of differential clones was gradually reduced. In this situation, the intermediate RDA product DP 2 provided the best compromise.