gebhart/patrepeval huggingface dataset:
Antigenic comparison of five species of mammalian zonae pellucidae (1987)

A comparison of glycoproteins of the zona pellucida (ZP) of five different mammalian species (cat, dog, rabbit, pig, and rat) has been made using polyclonal and monoclonal antibodies. In an enzyme-linked immunosorbent assay (ELISA), polyclonal antisera against total rabbit and pig ZP recognize their homologous ZP to the greatest extent but also detect crossreactive antigenic determinants in the ZP of all other species tested. Polyclonal antibodies against each of two purified rabbit ZP glycoproteins or one purified pig ZP glycoprotein also show some recognition of heterologous (pig, cat, and dog) ZP, but not rat ZP. Monoclonal antibodies (McR5-rabbit ZP protein determinant; McPSI-determinant associated with post-translational modifications of pig ZP proteins such as carbohydrates) further demonstrate that specific determinants are shared between some but not all of these mammalian species. For example, both of these antibodies recognize distinct determinants which are most abundant in pig and cat ZP. However, McR5 recognizes a determinant on all species of ZP except the rat, while McPSI does not recognize either the rabbit or rat ZP. Collectively, these studies suggest that the molecules of the pig, dog, and cat ZP are more closely related to each other than to those of the rabbit ZP, while there is little similarity with rat ZP molecules. Immunoblot analysis of ZP glycoproteins separated by two-dimensional polyacrylamide gel electrophoresis was used to identify antigenic relationships among four different species. The polyclonal antisera show that all of the major proteins of pig, rabbit, cat, and dog ZP are antigenically related.(ABSTRACT TRUNCATED AT 250 WORDS)
Niche‐based modelling as a tool for predicting the risk of alien plant invasions at a global scale (2005)

Predicting the probability of successful establishment of plant species by matching climatic variables has considerable potential for incorporation in early warning systems for the management of biological invasions. We select South Africa as a model source area of invasions worldwide because it is an important exporter of plant species to other parts of the world because of the huge international demand for indigenous flora from this biodiversity hotspot. We first mapped the five ecoregions that occur both in South Africa and other parts of the world, but the very coarse definition of the ecoregions led to unreliable results in terms of predicting invasible areas. We then determined the bioclimatic features of South Africa's major terrestrial biomes and projected the potential distribution of analogous areas throughout the world. This approach is much more powerful, but depends strongly on how particular biomes are defined in donor countries. Finally, we developed bioclimatic niche models for 96 plant taxa (species and subspecies) endemic to South Africa and invasive elsewhere, and projected these globally after successfully evaluating model projections specifically for three well-known invasive species (Carpobrotus edulis, Senecio glastifolius, Vellereophyton dealbatum) in different target areas. Cumulative probabilities of climatic suitability show that high-risk regions are spatially limited globally but that these closely match hotspots of plant biodiversity. These probabilities are significantly correlated with the number of recorded invasive species from South Africa in natural areas, emphasizing the pivotal role of climate in defining invasion potential. Accounting for potential transfer vectors (trade and tourism) significantly adds to the explanatory power of climate suitability as an index of invasibility. The close match that we found between the climatic component of the ecological habitat suitability and the current pattern of occurrence of South Africa alien species in other parts of the world is encouraging. If species' distribution data in the donor country are available, climatic niche modelling offers a powerful tool for efficient and unbiased first-step screening. Given that eradication of an established invasive species is extremely difficult and expensive, areas identified as potential new sites should be monitored and quarantine measures should be adopted.
Prognostic importance of flow cytometric immunophenotyping of 540 consecutive patients with B-cell chronic lymphocytic leukemia (1991)

Blood mononuclear cells from 540 newly diagnosed, unselected patients with B-cell chronic lymphocytic leukemia (CLL) were examined by immunofluorescence flow cytometry for a panel of surface membrane markers, including IgM and IgD, the monoclonal antibodies anti-CD3, -5, -20, -21, -22, -FMC7, and, for the final 125 patients, anti-CD23. There were 503 CD5+ and 37 CD5- cases. In the CD5+ cases, the cells typically expressed IgM, IgD, CD20, CD21, CD22, and CD23. In univariate analysis, age, clinical stage, IgM-fluorescence intensity, CD23, and FMC7 had significant prognostic importance, with high IgM-fluorescence intensity, high FMC7, and low CD23 expression being associated with a short survival. There was no significant difference in survival between 351 cases expressing IgMD and 55 cases expressing IgM without IgD, or between kappa and lambda light chain monoclonal cases. CD20, CD21, and CD22 had no prognostic importance. In Cox multiple regression analyses, age, CD23, IgM-fluorescence intensity, and clinical stage (International Workshop System) had independent prognostic importance. Thus, besides clinical variables, CD23 and IgM intensity might be useful prognostic markers in the management of CD5+, B-cell CLL. The survival of CD5- patients was on the borderline of being significantly shorter than that of CD5+ patients. The majority of the CD5- cases were FMC7+, CD23-, had strong IgM fluorescence, and had splenomegaly.
Role for the class A macrophage scavenger receptor in the phagocytosis of apoptotic thymocytes in vitro. (1996)

Numerous immature thymocytes undergo apoptosis and are rapidly engulfed by phagocytic thymic macrophages. The macrophage surface receptors involved in apoptotic thymocyte recognition are unknown. We have examined the role of the class A macrophage scavenger receptor (SR-A) in the engulfment of apoptotic thymocytes. Uptake of steroid-treated apoptotic thymocytes by thymic and inflammatory-elicited SR-A positive macrophages is partially inhibited by an anti-SR-A mAb and more completely by a range of scavenger receptor ligands. Thymic macrophages from mice with targeted disruption of the SR-A gene show a 50% reduction in phagocytosis of apoptotic thymocytes in vitro. These data suggest that SR-A may play a role in the clearance of dying cells in the thymus.
CD34+ hematopoietic stem-progenitor cell microRNA expression and function: A circuit diagram of differentiation control (2007)

MicroRNAs (miRNAs) are a recently identified class of epigenetic elements consisting of small noncoding RNAs that bind to the 3' untranslated region of mRNAs and down-regulate their translation to protein. miRNAs play critical roles in many different cellular processes including metabolism, apoptosis, differentiation, and development. We found 33 miRNAs expressed in CD34+ hematopoietic stem-progenitor cells (HSPCs) from normal human bone marrow and mobilized human peripheral blood stem cell harvests. We then combined these data with human HSPC mRNA expression data and with miRNA-mRNA target predictions, into a previously undescribed miRNA:mRNA interaction database called the Transcriptome Interaction Database. The in silico predictions from the Transcriptome Interaction Database pointed to miRNA control of hematopoietic differentiation through translational control of mRNAs critical to hematopoiesis. From these predictions, we formulated a model for miRNA control of stages of hematopoiesis in which many of the genes specifying hematopoietic differentiation are expressed by HSPCs, but are held in check by miRNAs until differentiation occurs. We validated miRNA control of several of these target mRNAs by demonstrating that their translation in fact is decreased by miRNAs. Finally, we chose miRNA-155 for functional characterization in hematopoiesis, because we predicted that it would control both myelopoiesis and erythropoiesis. As predicted, miRNA-155 transduction greatly reduced both myeloid and erythroid colony formation of normal human HSPCs.
Selective induction of immune responses by cytokines coexpressed in recombinant fowlpox virus (1994)

Avipoxviruses have recently been studied as potential vectors for the delivery of heterologous vaccine antigen. Because these viruses abortively infect mammalian cells yet still effectively present encoded foreign genes to the host immune system, they offer a safer but effective alternative to other live virus vectors. We have examined the effect of coexpressing the cytokine interleukin-6 or gamma interferon on immune responses to a recombinant fowlpox virus expressing influenza virus hemagglutinin. The encoded cytokine was expressed for prolonged periods in infected cell culture with little cytopathic effect due to the abortive nature of the infection. In mice, vector-expressed cytokine dramatically altered immune responses induced by the coexpressed hemagglutinin antigen. Expression of interleukin-6 augmented both primary systemic and mucosal antibody responses and primed for enhanced recall responses. In contrast, expression of gamma interferon markedly inhibited antibody responses without affecting the generation of cell-mediated immunity. The safety of these constructs was demonstrated in mice with severe combined immunodeficiency, and no side effects due to cytokine expression were observed. In summary, fowlpox virus vectors encoding cytokines represent a safe and effective vaccine strategy which may be used to selectively manipulate the immune response.
Interleukin 1 and poly(rI) · poly(rC) induce production of a hybridoma growth factor by human fibroblasts (1987)

Cultures of normal diploid fibroblasts and of a human osteosarcoma cell line (MG-63) are shown to be able to produce a factor which promotes the growth of B cell hybridomas (hybridoma growth factor, HGF). The induction is stimulated by treatment of the cells with interleukin 1 (IL 1) (alpha or beta) or polyriboinosinic-polyribocytidylic acid [poly(rI).poly(rC)]. Combined treatment with cycloheximide and actinomycin D also stimulates production and enhances production induced by IL 1 or poly(rI).poly(rC). Extremely small doses of IL 1 (0.1 units/ml) are active as inducer of HGF. Also, under optimal conditions the yield of HGF can attain as much as 10(4) units/ml. Tumor necrosis factor (TNF-alpha), which otherwise shares various properties with IL 1, is a weak inducer of HGF. Although there is a superficial resemblance between induction of HGF and that of interferon-beta, the two activities are serologically distinct and conditions for their induction are quite different. In fact, conditions for induction of HGF are indistinguishable from those described for the induction of the mRNA of the so-called 26-kDa protein (also known as interferon-beta 2). Finally, the HGF derived from IL 1- or poly(rI).poly(rC)-treated fibroblasts is serologically not distinguishable from that produced by mitogen-stimulated peripheral blood leukocytes.
In vitro lymphocyte cytotoxicity II. Unstable lymphotoxins (β-LT) secreted and inactivated by mitogen-stimulated human lymphocytes (1976)

Supernatants from phytohemagglutinin (PHA)-activated human lymphocytes contain two major classes of cytotoxins (α-LT and β-LT). While α-LT appears to be stable, and the major component in 5-day culture supernatants, the majority of cytolytic activity at earlier intervals in these cultures is due to a “family” of highly unstable cytotoxins which are both secreted and destroyed at a rapid rate. The inactivation of the unstable LT molecules appears to be due to: (a) inherent instability o β-LT molecules, and (b) a lymphocyte-mediated inactivation mechanism(s) which involves serum.
Evaluation of natural diatomaceous earth deposits from south‐eastern Europe for stored‐grain protection: the effect of particle size (2009)

Deposits from south-eastern Europe appeared to be very effective against the tested species, and therefore this region should be further evaluated as a source of development of commercial products. Particle size is a physical property that should always be taken into account during the DE manufacturing process, as it can strongly influence the insecticidal action of a given product.
Tumor angiogenesis correlates with metastasis in invasive prostate carcinoma. (1993)

Tumor growth and metastasis require angiogenesis; and microvessel density, a measure of tumor angiogenesis, correlates with metastasis in breast and lung carcinoma. To determine how microvessel density correlated with metastasis in prostate carcinoma, we counted microvessels within the initial invasive carcinomas of 74 patients (29 with metastasis, 45 without). Microvessels were highlighted by immunostaining endothelial cells for factor VIII-related antigen. Without knowledge of the patient's cancer stage, microvessels were counted in a 200 field (0.739 mm2) in the most active areas of neovascularization. The mean microvessel count in tumors from patients with metastases was 76.8 microvessels per 200 field (median, 66; standard deviation, 44.6). The counts within carcinomas from patients without metastasis were significantly lower, 39.2 (median, 36; standard deviation, 18.6) (P < 0.0001). Microvessel counts increased with increasing Gleason's score (P < 0.0001), but this increase was present predominantly in the poorly differentiated tumors. Although Gleason's score also correlated with metastasis (P = 0.01), multivariate analysis showed that Gleason's score added no additional information to that provided by microvessel count alone. Assay of microvessel density within invasive tumors may prove valuable in selecting patients for aggressive adjuvant therapies in early prostate carcinoma.
The Vrml 2.0 Handbook: Building Moving Worlds on the Web (1996)

https://works.swarthmore.edu/alum-books/1512/thumbnail.jpg
Requirement for Atm in Ionizing Radiation-Induced Cell Death in the Developing Central Nervous System (1998)

Ataxia telangiectasia (AT) is characterized by progressive neurodegeneration that results from mutation of the ATM gene. However, neither the normal function of ATM in the nervous system nor the biological basis of the degeneration in AT is known. Resistance to apoptosis in the developing central nervous system (CNS) of Atm-/- mice was observed after ionizing radiation. This lack of death occurred in diverse regions of the CNS, including the cerebellum, which is markedly affected in AT. In wild-type, but not Atm-/- mice, up-regulation of p53 coincided with cell death, suggesting that Atm-dependent apoptosis in the CNS is mediated by p53. Further, p53 null mice showed a similar lack of radiation-induced cell death in the developing nervous system. Atm may function at a developmental survival checkpoint that serves to eliminate neurons with excessive DNA damage.
Diameter-Selective Raman Scattering from Vibrational Modes in Carbon Nanotubes (1997)

Single wall carbon nanotubes (SWNTs) that are found as close-packed arrays in crystalline ropes have been studied by using Raman scattering techniques with laser excitation wavelengths in the range from 514.5 to 1320 nanometers. Numerous Raman peaks were observed and identified with vibrational modes of armchair symmetry (n, n) SWNTs. The Raman spectra are in good agreement with lattice dynamics calculations based on C-C force constants used to fit the two-dimensional, experimental phonon dispersion of a single graphene sheet. Calculated intensities from a nonresonant, bond polarizability model optimized for sp2 carbon are also in qualitative agreement with the Raman data, although a resonant Raman scattering process is also taking place. This resonance results from the one-dimensional quantum confinement of the electrons in the nanotube.
Stereo vision and rover navigation software for planetary exploration (2003)

NASA's Mars Exploration Rover (MER) missions will land twin rovers on the surface of Mars in 2004. These rovers will have the ability to navigate safely through unknown and potentially hazardous terrain, using autonomous passive stereo vision to detect potential terrain hazards before driving into them. Unfortunately, the computational power of currently available radiation hardened processors limits the amount of distance (and therefore science) that can be safely achieved by any rover in a given time frame. We present overviews of our current rover vision and navigation systems, to provide context for the types of computation that are required to navigate safely. We also present baseline timing results that represent a lower bound in achievable performance (useful for systems engineering studies of future missions), and describe ways to improve that performance using commercial grade (as opposed to radiation hardened) processors. In particular, we document speedups to our stereo vision system that were achieved using the vectorized operations provided by Pentium MMX technology. Timing data were derived from implementations on several platforms: a prototype Mars rover with flight-like electronics (the Athena Software Development Model (SDM) rover), a RAD6000 computing platform (as will be used in the 2003 MER missions), and research platforms with commercial Pentium III and Sparc processors. Finally, we summarize the radiation effects analysis that suggests that commercial grade processors are likely to be adequate for Mars surface missions, and discuss the level of speedup that may accrue from using these instead of radiation hardened parts.
Conformational Stability of Collagen Relies on a Stereoelectronic Effect (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTConformational Stability of Collagen Relies on a Stereoelectronic EffectLynn E. Bretscher, Cara L. Jenkins, Kimberly M. Taylor, Michele L. DeRider, and Ronald T. RainesView Author Information Departments of Biochemistry and Chemistry and Graduate Program in Biophysics, University of Wisconsin−Madison, Madison, Wisconsin 53706 Cite this: J. Am. Chem. Soc. 2001, 123, 4, 777–778Publication Date (Web):January 3, 2001Publication History Received22 August 2000Published online3 January 2001Published inissue 1 January 2001https://pubs.acs.org/doi/10.1021/ja005542vhttps://doi.org/10.1021/ja005542vrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views3667Altmetric-Citations395LEARN 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 SUBJECTS:Biopolymers,Conformational stability,Frustrated Lewis pairs,Organic compounds,Peptides and proteins Get e-Alerts
pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2012)

De novo peptide sequencing is the only tool for extracting peptide sequences directly from tandem mass spectrometry (MS) data without any protein database. However, neither the accuracy nor the efficiency of de novo sequencing has been satisfactory, mainly due to incomplete fragmentation information in experimental spectra. Recent advancement in MS technology has enabled acquisition of higher energy collisional dissociation (HCD) and electron transfer dissociation (ETD) spectra of the same precursor. These spectra contain complementary fragmentation information and can be collected with high resolution and high mass accuracy. Taking these advantages, we have developed a new algorithm called pNovo+, which greatly improves the accuracy and speed of de novo sequencing. On tryptic peptides, 86% of the topmost candidate sequences deduced by pNovo+ from HCD + ETD spectral pairs matched the database search results, and the success rate reached 95% if the top three candidates were included, which was much higher than using only HCD (87%) or only ETD spectra (57%). On Asp-N, Glu-C, or Elastase digested peptides, 69-87% of the HCD + ETD spectral pairs were correctly identified by pNovo+ among the topmost candidates, or 84-95% among the top three. On average, it takes pNovo+ only 0.018 s to extract the sequence from a spectrum or spectral pair on a common personal computer. This is more than three times as fast as other de novo sequencing programs. The increase of speed is mainly due to pDAG, a component algorithm of pNovo+. pDAG finds the k longest paths in a directed acyclic graph without the antisymmetry restriction. We have verified that the antisymmetry restriction is unnecessary for high resolution, high mass accuracy data. The extensive use of HCD and ETD spectral information and the pDAG algorithm make pNovo+ an excellent de novo sequencing tool.
Electrocatalytic generation of C2 and C3 compounds from carbon dioxide on a cobalt complex-immobilized dual-film electrode (1993)

The electrocatalytic reduction of CO2 on a Prussian blue–polyaniline dual film electrode on platinum including immobilized 2-hydroxy-1-nitrosonaphthalene-3,6-disulfonatocobalt(II) in aqueous solution leads to the formation of lactic acid, ethanol, acetone and methanol at a low overpotential (–0.6 V vs. standard calomel electrode) under ambient conditions.
Life history and histopathology of ultraviolet light-induced skin tumors. (1978)

The life history and histopathology of UV light-induced skin tumors were studied in NMR rats, outbred female Swiss mice, and Syrian golden hamsters. High intensity UV light of medium wavelengths produced hyperplasia and papillomas, as well as a dysplastic, intermediary solar keratosis-like stage, with distinct cellular atypia leading to several types of squamous cell carcinomas. High doses of UV irradiation of short duration caused scars, which developed into fibromas and fibrosarcomas composed of "light" and "dark" cells. Carcinomas with neoplastic squamous and fibrous components were uncommon; however, collision tumors with two components were occasionally seen. Angiomas and angiosarcomas with a proliferating endothelial structure were observed, but adnexal tumors, with follicular or sebaceous differentiation, and basal cell carcinomas were infrequent. Pigment cell tumors were found only rarely. The number of tumors and tumor-bearing animals at different stages of the experiment were also studied. Tumors were compared with lesions induced by chemical carcinogens in different systems. UV carcinogenesis was characterized by many tumor-bearing animals, but with a low total tumor count and a high mortality, thereby decreasing the number of animals-at-risk. The tumor types, their progression from on type to another, and the distribution of certain biologic characteristics were also analyzed. We concluded that UV irradiation is an effective tumor inducer in animal skin, and the type of tumor, its behavior, and location depend on the experimental conditions.