gebhart/patrepeval huggingface dataset:
Phage and Yeast Display (2015)

ABSTRACT Despite the availability of antimicrobial drugs, the continued development of microbial resistance—established through escape mutations and the emergence of resistant strains—limits their clinical utility. The discovery of novel, therapeutic, monoclonal antibodies (mAbs) offers viable clinical alternatives in the treatment and prophylaxis of infectious diseases. Human mAb-based therapies are typically nontoxic in patients and demonstrate high specificity for the intended microbial target. This specificity prevents negative impacts on the patient microbiome and avoids driving the resistance of nontarget species. The in vitro selection of human antibody fragment libraries displayed on phage or yeast surfaces represents a group of well-established technologies capable of generating human mAbs. The advantage of these forms of microbial display is the large repertoire of human antibody fragments present during a single selection campaign. Furthermore, the in vitro selection environments of microbial surface display allow for the rapid isolation of antibodies—and their encoding genes—against infectious pathogens and their toxins that are impractical within in vivo systems, such as murine hybridomas. This article focuses on the technologies of phage display and yeast display, as these strategies relate to the discovery of human mAbs for the treatment and vaccine development of infectious diseases.
The Cell Surface Proteome of Human Mesenchymal Stromal Cells (2011)

Collectively, our analytical methods not only provide a basis for further studies of mechanisms maintaining the multipotency of hMSCs within their niches and triggering their differentiation after signaling, but also a toolbox for a refined antibody-based identification of hMSC populations from different tissues and their isolation for therapeutic intervention.
Tissue inhibitor of metalloproteinases-2 (TIMP-2) mRNA expression in tumor cell lines and human tumor tissues. (1990)

Human tissue inhibitor of metalloproteinase-2 (TIMP-2) was cloned and sequenced from an A2058 human melanoma cell cDNA library. When the sequence was compared with that of human TIMP-1 at both the nucleotide and deduced amino acid levels, the homology appeared closer at the protein level than at the nucleotide level, suggesting that these inhibitors diverged early in the evolution of this gene family. Comparison of the deduced amino acid sequence for TIMP-2 with that of human TIMP-1 shows that there are two regions in which the similarity is below the overall average of 66%. It is postulated that these regions are responsible for the unique ability of TIMP-2 to bind to the latent form of the 72-kDa type IV collagenase. Polyclonal anti-TIMP-2 antisera recognized TIMP-2 but not TIMP-1 on immunoblotting. Northern blot analysis of RNA from A2058 human melanoma, HT-144 human melanoma, HT-1080 human fibrosarcoma, and WI-38 fetal lung fibroblast cell lines demonstrated two distinct transcripts of 1.0 and 3.5 kilobases (kb) for timp-2 mRNA. Both transcripts are down-regulated in response to transforming growth factor-beta but are unchanged in response to phorbol ester treatment. This is in contrast to the up-regulation of timp-1 transcripts by these agents and indicates that timp-2 and timp-1 are independently regulated in cell culture. Northern blot analyses of matched normal and tumor tissue samples from five cases of human colorectal carcinoma were performed. Normal and tumor tissues contain both the 1.0- and 3.5-kb transcripts. However, in the tissue samples the ratio of the 3.5-kb transcript to the 1.0-kb transcript was markedly elevated. No evidence of down-regulation of timp-2 transcript levels was noted in the tumor tissues. This is in contrast to the elevated timp-1 transcript levels seen in these tumor samples. Thus, timp-2 mRNA transcript levels are differentially regulated from timp-1 levels in vivo as well as in cell culture.
Activity of a Novel bcl-2/bcl-xL-Bispecific Antisense Oligonucleotide Against Tumors of Diverse Histologic Origins (2001)

The bcl-2/bcl-xL-bispecific antisense oligonucleotide 4625 merits further study as a novel compound for cancer therapy.
Deteriorating child health in countries with severe AIDS epidemics: forecasts and challenges. (1997)

AIDS is having a major adverse impact upon child health. UNAIDS estimated that by mid-1996, worldwide, there were 3 million HIV infections among children and 9 million maternal orphans due to AIDS. At least 30 million children living with HIV-positive parents will probably be orphaned over the next few years. The author discusses the direct and indirect impact of AIDS upon children, using estimates recently published by the US Bureau of the Census. Countries with severe HIV/AIDS epidemics are experiencing rising infant mortality rates; two-thirds of AIDS deaths among children occur among those aged 1-4 years; life expectancy has fallen due to AIDS in Zambia, Zimbabwe, Uganda, and Kenya; and the level of orphanhood will increase as HIV spreads and the prevalence of AIDS rises. Child health, poverty, and challenges in the context of AIDS are considered.
Vascular Endothelial Growth Factor Expression and Regulation of Murine Collagen-Induced Arthritis (2000)

We have examined the expression and function of the angiogenic factor, vascular endothelial growth factor (VEGF) during the evolution of type II collagen-induced arthritis (CIA). Biologically active VEGF was expressed along a time course that paralleled the expression of two specific VEGF receptors, Flk-1 and Flt-1, and the progression of joint disease. Moreover, levels of VEGF expression correlated with the degree of neovascularization, as defined by vWF levels, and arthritis severity. Macrophage- and fibroblast-like cells, which infiltrated inflamed sites and were then activated by other inflammatory mediators, are probably important sources of VEGF and may thus regulate angiogenesis during the development of CIA. Administration of anti-VEGF antiserum to CIA mice before the onset of arthritis delayed the onset, reduced the severity, and diminished the vWF content of arthritic joints. By contrast, administration of anti-VEGF antiserum after the onset of the disease had no effect on the progression or ultimate severity of the arthritis. These data suggest that VEGF plays a crucial role during an early stage of arthritis development, affecting both neovascularization and the progression of experimentally induced synovitis.
Where do triptans act in the treatment of migraine? (2005)

Migraine headache is a pervasive but poorly understood primary pain disorder.Sumatriptan and the 'triptan' class of serotonin receptor subtype-selective drugs have well-established efficacy in treating the pain of migraine.Although sumatriptan was originally selected to target vasoactive properties thought to be fundamental to the etiology of migraine, other studies point to an action of triptans at several levels of the nervous system.To this day, however, it is not clear whether the antimigraine activity of the triptans involves an action only in the periphery or in the CNS as well.Because sumatriptan is hydrophilic, it penetrates the blood-brain barrier poorly, suggesting a peripheral site of action.On the other hand, it has been proposed that the barrier is compromised in migraineurs, so a CNS site of action has not been ruled out.Finally, the basis for the apparent selectivity of triptans in the treatment of migraine pain but not other kinds of somatic pain is still not understood.Determining that mechanism of triptan action will likely provide important new insights into the unique and essential features of migraine.
ChemInform Abstract: Asynchronous Cycloaddition of the 1‐Dimethylamino‐2R‐isoindole System. (1989)

ChemInformVolume 20, Issue 24 Heterocyclic Compounds ChemInform Abstract: Asynchronous Cycloaddition of the 1-Dimethylamino-2R-isoindole System. V. A. KOVTUNENKO, V. A. KOVTUNENKO Kiev. univ.Search for more papers by this authorZ. V. VOITENKO, Z. V. VOITENKO Kiev. univ.Search for more papers by this authorA. K. TYLTIN, A. K. TYLTIN Kiev. univ.Search for more papers by this authorM. YU. KORNILOV, M. YU. KORNILOV Kiev. univ.Search for more papers by this authorF. S. BABICHEV, F. S. BABICHEV Kiev. univ.Search for more papers by this author V. A. KOVTUNENKO, V. A. KOVTUNENKO Kiev. univ.Search for more papers by this authorZ. V. VOITENKO, Z. V. VOITENKO Kiev. univ.Search for more papers by this authorA. K. TYLTIN, A. K. TYLTIN Kiev. univ.Search for more papers by this authorM. YU. KORNILOV, M. YU. KORNILOV Kiev. univ.Search for more papers by this authorF. S. BABICHEV, F. S. BABICHEV Kiev. univ.Search for more papers by this author First published: June 13, 1989 https://doi.org/10.1002/chin.198924159Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume20, Issue24June 13, 1989 RelatedInformation
Phase II Study of Irinotecan, 5-Fluorouracil and Leucovorin as First-line Therapy for Advanced Colorectal Cancer (2005)

We conclude that the modified Douillard regimen may be a practical and more tolerable treatment option in patients with advanced colorectal cancer.
ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function (2013)

Abstract Many mutations disappear from the population because they impair protein function and/or stability. Thus, amino acid positions that are essential for proper function evolve more slowly than others, or in other words, the slow evolutionary rate of a position reflects its importance. ConSurf ( http://consurf.tau.ac.il ), reviewed in this manuscript, exploits this to reveal key amino acid positions that are important for maintaining the native conformation(s) of the protein and its function, be it binding, catalysis, transport, etc. Given the sequence or 3D structure of the query protein as input, a search for similar sequences is conducted and the sequences are aligned. The multiple sequence alignment is subsequently used to calculate the evolutionary rates of each amino acid site, using Bayesian or maximum‐likelihood algorithms. Both algorithms take into account the evolutionary relationships between the sequences, reflected in phylogenetic trees, to alleviate problems due to uneven (biased) sampling in sequence space. This is particularly important when the number of sequences is low. The ConSurf‐DB, a new release of which is presented here, provides precalculated ConSurf conservation analysis of nearly all available structures in the Protein DataBank (PDB). The usefulness of ConSurf for the study of individual proteins and mutations, as well as a range of large‐scale, genome‐wide applications, is reviewed.
Three-dimensional man-machine interaction (1976)

The film accompanied by this paper illustrates an experimental system for real-time Computer-Aided Geometric Design of three-dimensional parametric surfaces. A detailed description of the system is given in another paper by the author(1). Its principle features are that it operates in real-time, all geometric interaction with the surfaces is accomplished with a 3-D Wand, the surfaces are viewed in 3-D using a head-mounted display, and the surfaces are mathematically represented using parametric spline surface patches.The two principle computing components of the system are a PDP-10 computer and an LDS-1 display computer. The PDP-10 acts as a host to the LDS-1. Its main tasks each 1/30 second are to compute the 3-D Wand and head-mounted display positions and to incrementally update the geometries of the surface patches being designed by the user. During the same time period, the LDS-1 loads its digital matrix multiplier with the room-to-head transformation matrix provided to it by the PDP-10, displays on the head-mounted display's CRT's a line drawn rendering of all of the parametric surface patches that are within the 40 degree field-of-view of the display and displays a small cube to represent the current position of the Wand.The user of the system initiates a design sequence by selecting a patch description file from the PDP-10's file system. He then puts on the head-mounted display and uses the 3-D Wand with its control buttons to grasp the patches, which appear to float before him in the room, and make appropriate changes to their geometry. After a design sequence he may save the new surfaces on the PDP-10 file system and select certain views of the surfaces to be rendered as a continuous-tone shaded picture with hidden-surfaces removed.The first part of the film described here shows the system in real-time operation. During this part, several free-form surfaces are manipulated as the camera records the action on a line-drawing monitor. The second part of the film illustrates a continuous-tone, shaded rendering of a design sequence. The continuous-tone rendering was produced "off-line" using pertinent viewpoint information that was saved during the design sequence. The final few minutes of the film depict the construction of a Klein-Bottle.
Femtosecond laser pulse generation with a fiber taper embedded in carbon nanotube/polymer composite (2007)

We propose and demonstrate a new saturable absorber based on a fiber taper embedded in a carbon nanotube/polymer composite. Greater than a 10% reduction in absorption (due to saturation) is directly measured for our saturable absorber. Using an embedded fiber-taper saturable absorber, we built an all-fiber mode-locked ring laser, which produces 594 fs/1.7 nJ pulses with a repetition rate of 13.3 MHz.
Phagocytosis of particulate activators of the human alternative complement pathway through monocyte beta-glucan receptors. (1989)

Human monocytes phagocytose particulate activators of the alternative complement pathway through beta-glucan receptors in the absence of opsonins. Recognition of soluble beta-glucans by monocytes selectively inhibits ingestion of particulate activators and has no effect on responses mediated by monocyte receptors for Fc-IgG, complement, or fibronectin. The smallest ligand unit recognized by monocyte beta-glucan receptors is an acid-resistant heptaglucoside present in yeast cell walls. Mouse monoclonal anti-beta-glucan antibodies have been prepared, one of which completely neutralizes the inhibitory capacity of the HPLC-purified heptaglucoside. This antibody has been used as immunogen for the preparation of an anti-Id. The pretreatment of monocytes with low concentrations of anti-Id inhibits monocyte ingestion of zymosan particles but not EsIgG, suggesting that this antibody has specificity for monocyte beta-glucan receptors and is a powerful probe for further receptor studies. Other receptors with specificities for carbohydrates are also present on mononuclear phagocytes. Receptors for mannose/fucose and those for galactose have been isolated and cloned. The development of probes, such as structural analogs of the active heptaglucoside and the anti-Id, will bring the beta-glucan receptors to a similar stage of definition. A major factor that adds a considerable degree of difficulty to studies of the beta-glucan receptors and is not shared by the other receptors for carbohydrates is the requirement for structural conformations provided by the alignment of several glucose units rather than the recognition of a hexose residue in, for example, a glycoconjugate. The designation of these receptors as beta-glucan receptors has inadvertently taken us into a new area of nonimmune defense. Animal studies indicate that beta-glucans with 1,3- and/or 1,6-linkages are active pharmacologic agents that rapidly confer protection to a normal host against a variety of biologic insults. The beta-glucan receptors provide a mechanism by which a heightened state of host responsiveness is initiated.
Indoor Semantic Segmentation using depth information (2013)

This work addresses multi-class segmentation of indoor scenes with RGB-D\ninputs. While this area of research has gained much attention recently, most\nworks still rely on hand-crafted features. In contrast, we apply a multiscale\nconvolutional network to learn features directly from the images and the depth\ninformation. We obtain state-of-the-art on the NYU-v2 depth dataset with an\naccuracy of 64.5%. We illustrate the labeling of indoor scenes in videos\nsequences that could be processed in real-time using appropriate hardware such\nas an FPGA.\n
Estradiol in elderly men (2002)

The role of estrogens in male physiology has become more evident, as a consequence of the discovery of human models of estrogen deficiency such as estrogen resistance or aromatase deficiency. In males, testosterone is the major source of plasma estradiol, the main biologically active estrogen, only 20% of which is secreted by the testes. Plasma estrone, 5% of which is converted to plasma estradiol, originates from tissue aromatization of, mainly adrenal, androstenedione. The plasma concentration of estradiol in males is 2-3 ng/dl and its production rate in blood is 25-40 micrograms/24 h; both of these values are significantly higher than in postmenopausal women. Plasma levels of estradiol do not necessarily reflect tissue-level activity as peripherally formed estradiol is partially metabolized in situ; thus, not all enters the general circulation, with a fraction remaining only locally active. Of the factors influencing plasma estradiol levels, plasma testosterone is a major determinant. However, the age-associated decrease in testosterone levels is scarcely reflected in plasma estradiol levels, as a result of increasing aromatase activity with age and the age-associated increase in fat mass. Free and bioavailable estradiol levels do decrease modestly with age as does the ratio of free testosterone to free estradiol, the latter testifying to the age-associated increased aromatization of testosterone. Estradiol levels are highly significantly positively related to body fat mass and more specifically to subcutaneous abdominal fat, but not to visceral (omental) fat. Indeed, aromatase activity in omental fat is only one-tenth of the activity in gluteal fat. Estrogens in males play an important role in the regulation of the gonadotropin feedback, several brain functions, bone maturation, regulation of bone resorption and in lipid metabolism. Moreover, they affect skin metabolism and are an important factor determining sex interest in man.
Capillary zone electrophoresis of derivatized acidic monosaccharides (1994)

A new and specific precolumn derivatization reaction for acidic monosaccharides was introduced and evaluated in the separation and sensitive detection of carbohydrates by capillary electrophoresis. The derivatization reaction involved the attachment of sulfanilic acid (a UV absorbing tag) or 7-amino-naphthalene-1,3-disulfonic acid (a UV absorbing and fluorescing tag) via a condensation reaction between the amino group of the derivatizing agent and the carboxyl group of the sugar in the presence of a water-soluble carbodiimide. The derivatization reaction replaced the weak carboxylic acid of the sugar by a strong sulfonic acid, which is fully ionized at all pH. This allowed the electrophoresis of the sugar derivatives over a wide pH range and permitted the determination of acidic carbohydrates at very low femtomole levels by UV and fluorescence detection.
Comparative Study of the Solid-Matrix Luminescence Properties of Perdeuterated Phenanthrene and Phenanthrene Adsorbed on Several Solid Matrices (1996)

Temperature was varied over a wide range to determine its effect on the luminescence properties of deuterated phenanthrene and phenanthrene adsorbed on a number of solid matrices. Not only were insights into the effects of temperature and solid matrices on the luminescence properties acquired but also the deuterium isotope effect revealed unique information about the role played by the solid matrix in the luminescence of the model compounds. In addition, comparisons of nonradiative rate constants and the efficiencies of intersystem crossing revealed important differences among the solid matrices in altering these parameters. The perdeuterated phenanthrene and phenanthrene proved to be useful probes for investigating the effects of solid matrices on the excited triplet state of phosphors because the excited singlet state of the lumiphor was affected very little by the solid matrices, and the rate constants of phosphorescence for the two phosphors are essentially the same.
Non-invasive assessment of cardiac contractility on a weighing scale (2009)

Myocardial contractility, the intrinsic ability of the heart muscle to produce force, has been difficult to quantify non-invasively. Pre-ejection-period (PEP), the time the ventricles spend in isovolumetric contraction, is widely accepted as a way to measure contractility. This work presents a way by which the ballistocardiogram - a readily accessible non-invasive cardiovascular signal - can be used in tandem with the electrocardiogram to obtain a parameter highly correlated to PEP and thus to myocardial contractility. This parameter is the delay from the electrocardiogram R-wave to the peak (the J-wave) of the ballistocardiogram. In this work, we showed that this delay, the RJ interval, was correlated to PEP (r(2) = 0.75) for 709 heartbeats across 4 subjects, with a slope of 1.11, and a y-intercept of 151 ms. This suggests that the RJ interval can be used in place of the PEP for a reliable, practical, and non-invasive assessment of myocardial contractility.
Elastomer Surfaces with Directionally Dependent Adhesion Strength and Their Use in Transfer Printing with Continuous Roll‐to‐Roll Applications (2012)

In this paper we present mechanics and materials aspects of elastomeric stamps that have angled features of relief on their surfaces, designed to enable control of adhesion strength by peeling direction, in a way that can be exploited in schemes for deterministic assembly by transfer printing. Detailed mechanics models capture the essential physics of interface adhesion in this system. Experiments with cylindrical stamps that have this design demonstrate their potential for use in a continuous, roller mode of operation.
A new surgical technique for deep stromal, anterior lamellar keratoplasty (1999)

With this technique a deep stromal anterior lamellar keratoplasty can be performed with the donor to recipient interface just anterior to the posterior corneal surface. The technique has the advantage that the dissection can be completed in the event of inadvertent microperforation, or that the procedure can be aborted to perform a planned penetrating keratoplasty.