gebhart/patrepeval huggingface dataset:
Bioluminescence Hybridization Assays Using Recombinant Aequorin. Application to the Detection of Prostate-Specific Antigen mRNA (1996)

We developed microtiter well-based bioluminescence hybridization assays using the photoprotein aequorin as a reporter molecule. The target DNA was hybridized simultaneously with a capture probe and a detection probe. The capture probe was immobilized on the wells through digoxigenin/anti-digoxigenin interaction. The detection probe was biotinylated. The hybrids were determined by using aequorin covalently attached to streptavidin or complexes of biotinylated aequorin with streptavidin. The luminescence was then measured in the presence of excess Ca2+. The optimized protocols showed linearity in the range from 5 amol to 10 fmol of target DNA. In combination with reverse transcriptase polymerase chain reaction, the proposed assay was applied to the detection of the mRNA for prostate-specific antigen (PSA). PSA mRNA from a single cell, in the presence of one million cells that do not express PSA, was detected with a signal-to-background ratio of 2.5. Typical CVs obtained were 6%.
Cardioprotective actions of a monoclonal antibody against CD-18 in myocardial ischemia-reperfusion injury. (1993)

The administration of a specific anti-CD-18 monoclonal antibody, MAb R15.7, attenuates much of the PMN-mediated contractile dysfunction associated with this in vitro model of myocardial ischemia-reperfusion injury by limiting PMN accumulation. We conclude that CD-18-mediated adhesion may play a critical role in the pathogenesis of PMN-induced myocardial injury.
Dynamic interplay of flow and collagen stabilizes primary hepatocytes culture in a microfluidic platform (2014)

The creation of stable flow cultures of hepatocytes is highly desirable for the development of platforms for drug toxicity screening, bio-artificial liver support devices, and models for investigating liver physiology and pathophysiology. Given that hepatocytes cultured using the collagen overlay or in 'sandwich' configuration maintain a wide range of differentiated functions, we describe a simple method for adapting this culture configuration within a microfluidic device. The device design consists of a porous membrane sandwiched between two layers of PDMS resulting in a two-chambered device. In the bottom chamber, hepatocytes are cultured in the collagen sandwich configuration, while the top chamber is accessible for flow. We demonstrate that hepatocytes cultured under flow exhibit higher albumin and urea secretions and induce cytochrome P450 1A1 activity in comparison to static cultures. Furthermore, over two weeks, hepatocytes cultured under flow show a well-connected cellular network with bile canaliculi formation, whereas static cultures show formation of gaps in the cellular network that progressively increase over time. Although enhanced functional response of hepatocytes cultured under flow has been observed in multiple prior studies, the exact mechanism for this flow induced effect remains unknown. In our work, we identified that hepatocytes secrete a higher level of collagen in the flow cultures; inhibiting collagen secretion within the flow cultures reduced albumin secretion and restored the appearance of gaps in the cellular network similar to the static cultures. These results demonstrate the importance of the increased collagen secretion by hepatocytes cultured under flow as a mechanism to maintain a well-connected cellular network and a differentiated function.
Cellular regeneration strategies for macular degeneration: past, present and future (2018)

Despite considerable effort and significant therapeutic advances, age-related macular degeneration (AMD) remains the commonest cause of blindness in the developed world. Progressive late-stage AMD with outer retinal degeneration currently has no proven treatment. There has been significant interest in the possibility that cellular treatments may slow or reverse visual loss in AMD. A number of modes of action have been suggested, including cell replacement and rescue, as well as immune modulation to delay the neurodegenerative process. Their appeal in this enigmatic disease relate to their generic, non-pathway-specific effects. The outer retina in particular has been at the forefront of developments in cellular regenerative therapies being surgically accessible, easily observable, as well as having a relatively simple architecture. Both the retinal pigment epithelium (RPE) and photoreceptors have been considered for replacement therapies as both sheets and cell suspensions. Studies using autologous RPE, and to a lesser extent, foetal retina, have shown proof of principle. A wide variety of cell sources have been proposed with pluripotent stem cell-derived cells currently holding the centre stage. Recent early-phase trials using these cells for RPE replacement have met safety endpoints and hinted at possible efficacy. Animal studies have confirmed the promise that photoreceptor replacement, even in a completely degenerated outer retina may restore some vision. Many challenges, however, remain, not least of which include avoiding immune rejection, ensuring long-term cellular survival and maximising effect. This review provides an overview of progress made, ongoing studies and challenges ahead.
The Effects of DNA Covalent Adducts on <i>in Vitro</i> Transcription (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Effects of DNA Covalent Adducts on in Vitro TranscriptionMarek Gniazdowski and Cinzia CeraView Author Information Department of General Chemistry, Medical University of Lodz, ul.Lindleya 6, 90-131 Lodz, Poland, and Department of Pharmaceutical Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy Cite this: Chem. Rev. 1996, 96, 2, 619–634Publication Date (Web):March 28, 1996Publication History Received14 November 1994Revised22 January 1996Published online28 March 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/cr940049lhttps://doi.org/10.1021/cr940049lresearch-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views502Altmetric-Citations35LEARN 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:Adducts,Genetics,Lesions,Nucleic acid structure,Peptides and proteins Get e-Alerts
Prostaglandin E1 Versus Mixture of Prostaglandin E1, Papaverine and Phentolamine in Nonresponders to High Papaverine Plus Phentolamine Doses (1996)

The 3-drug mixture may be regarded as more effective than prostaglandin E1 alone in inducing an erectile response with a decreased incidence of pain.
A Study of Gain Dynamics of Erbium-Doped Fiber Amplifiers for Burst Optical Signals (2002)

We analyze the transient response of Erbium-Doped Fiber Amplifiers (EDFAs) that amplify burst optical signals. Furthermore, we propose and evaluate a technique for suppressing the optical signal distortion induced by the EDFA's characteristics.
Ontogeny‐based immunogens for the induction of V2‐directed <scp>HIV</scp> broadly neutralizing antibodies (2017)

The development of a preventative HIV vaccine able to elicit broadly neutralizing antibodies (bNAbs) remains a major challenge. Antibodies that recognize the V2 region at the apex of the HIV envelope trimer are among the most common bNAb specificities during chronic infection and many exhibit remarkable breadth and potency. Understanding the developmental pathway of these antibodies has provided insights into their precursors, and the viral strains that engage them, as well as defined how such antibodies mature to acquire breadth. V2-apex bNAbs are derived from rare precursors with long anionic CDR H3s that are often deleted in the B cell repertoire. However, longitudinal studies suggest that once engaged, these precursors contain many of the structural elements required for neutralization, and can rapidly acquire breadth through moderate levels of somatic hypermutation in response to emerging viral variants. These commonalities in the precursors and mechanism of neutralization have enabled the identification of viral strains that show enhanced reactivity for V2 precursors from multiple donors, and may form the basis of germline targeting approaches. In parallel, new structural insights into the HIV trimer, the target of these quaternary antibodies, has created invaluable new opportunities for ontogeny-based immunogens designed to select for rare V2-bNAb precursors, and drive them toward breadth.
Measurements of Phagocytosis and Phagosomal Maturation (2004)

Phagocytosis is an essential component of the innate immune response. Invading microorganisms are engulfed by neutrophils and macrophages, and subsequently killed by a complex series of reactions that require fusion of the phagocytic vacuole with multiple endomembrane organelles. This vacuolar remodeling process, known as phagosomal maturation, is often the target of intracellular parasites that evade killing by the host immune system. This unit describes detailed protocols for the assessment of phagosome formation and maturation. Particular attention is given to Fc- and complement-receptor mediated phagocytosis, but the protocols provided can be readily adapted to other types of phagocytic processes.
50대 만학도 여성의 생애사 연구 :삶의 영역, 전환점과 적응을 중심으로 (2014)

본 연구의 목적은 만학도 여성들의 생애사 연구를 통해 그들의 환경적 특성과 만학의 의미, 그리고 그들의 삶의 변화 과정을 분석하는 것이다. 이러한 연구목적을 위해, 현재 전문대학 사회복지학과에 다니는 50대 만학도 여성들 7명을 대상으로 심층면접을 하여 자료를 수집하였다. 자료 분석 과정에서는 Mandelbaum이 제시한 삶의 영역, 전환점, 적응의 3가지 개념 틀에 따라 공통의 범주와 개념이 도출되었다. 연구결과, 추출된 범주들은 삶의 영역에서는 ‘원가족’, ‘결혼 후 가족’, ‘학교’, 전환점에서는 ‘진학 좌절’, ‘취업’, ‘결혼’, ‘학부모됨’, ‘중년기 위기’, ‘학교 입학’, 적응에서는 ‘상황에 대한 수용’, ‘자신의 기대 충족’, ‘가족관계의 변화’, ‘새로운 정체감의 형성’, ‘미래에 대한 전망’ 이었다. 본 연구에서는 만학도 여성들이 대학공부를 통해 자존감이 높아지고 자아정체성을 찾았으며 가족관계가 더욱 향상된 것으로 나타났다. 본 연구는 그동안 사회적 존재가 드러나지 않았던 50대 만학도 여성들의 생애 경험을 추적하여 그들의 문제를 가시화함으로써 늦은 나이의 학습활동이 자아실현을 이룰 수 있게 할 뿐 아니라 연장된 노년기를 보다 건강하고 의미 있게 보낼 수 있는 긍정적인 방안이 될 수 있음을 밝혔다는 데 의의가 있다.
IL-12 enhances Th1-type responses in human <i>Leishmania donovani</i> infections. (1995)

IL-12 is a pluripotent cytokine that interacts with NK and T cells to play a central role in the initiation and maintenance of Th1 responses and IFN-gamma production. Because of the interactive relationship between IL-12 and IFN-gamma response to infectious organisms, a study was undertaken to examine the role of IL-12 in the immune regulation of human visceral leishmaniasis (VL). Human (Hu) VL is associated with immune dysfunction and the appearance of IL-10 mRNA, not present in healed individuals. We found that PBMC from treated VL patients produced both IL-12 p40 and IFN-gamma in response to in vitro stimulation with Leishmania donovani. The production of both IL-12 p40 and IFN-gamma were interdependent and were abrogated by the addition of exogenous Hu rIL-10. In contrast, PBMC from active VL patients did not produce IL-12 p40 or IFN-gamma in response to L. donovani lysate. Neutralizing anti-IL-10 mAb led to the enhancement of IFN-gamma production by active VL PBMC cultured with L. donovani lysate, and this enhanced IFN-gamma production was blocked by anti-IL-12 mAb. The addition of exogenous Hu rIL-12 to PBMC from active VL patients resulted in the augmentation of IFN-gamma in response to L. donovani lysate. Therefore, treatment of active VL patient PBMC with anti-IL-10 or IL-12 shifted the response toward a Th1-type response with the production of IFN-gamma. These results indicate that IL-12 may play an important role in the regulation of the cellular immune responses in Hu VL.
Runx1 Regulation of Pu.1 Corepressor/Coactivator Exchange Identifies Specific Molecular Targets for Leukemia Differentiation Therapy (2014)

Gene activation requires cooperative assembly of multiprotein transcription factor-coregulator complexes. Disruption to cooperative assemblage could underlie repression of tumor suppressor genes in leukemia cells. Mechanisms of cooperation and its disruption were therefore examined for PU.1 and RUNX1, transcription factors that cooperate to activate hematopoietic differentiation genes. PU.1 is highly expressed in leukemia cells, whereas RUNX1 is frequently inactivated by mutation or translocation. Thus, coregulator interactions of Pu.1 were examined by immunoprecipitation coupled with tandem mass spectrometry/Western blot in wild-type and Runx1-deficient hematopoietic cells. In wild-type cells, the NuAT and Baf families of coactivators coimmunoprecipitated with Pu.1. Runx1 deficiency produced a striking switch to Pu.1 interaction with the Dnmt1, Sin3A, Nurd, CoRest, and B-Wich corepressor families. Corepressors of the Polycomb family, which are frequently inactivated by mutation or deletion in myeloid leukemia, did not interact with Pu.1. The most significant gene ontology association of Runx1-Pu.1 co-bound genes was with macrophages, therefore, functional consequences of altered corepressor/coactivator exchange were examined at Mcsfr, a key macrophage differentiation gene. In chromatin immunoprecipitation analyses, high level Pu.1 binding to the Mcsfr promoter was not decreased by Runx1 deficiency. However, the Pu.1-driven shift from histone repression to activation marks at this locus, and terminal macrophage differentiation, were substantially diminished. DNMT1 inhibition, but not Polycomb inhibition, in RUNX1-translocated leukemia cells induced terminal differentiation. Thus, RUNX1 and PU.1 cooperate to exchange corepressors for coactivators, and the specific corepressors recruited to PU.1 as a consequence of RUNX1 deficiency could be rational targets for leukemia differentiation therapy.
Evidence for the superconducting proximity effect in junctions between the surfaces of YBa2Cu3O<i>x</i> thin films (1989)

We have used the squeezable electron tunneling junction technique for testing the electrical properties of the surfaces of YBa2Cu3Ox (YBCO) thin-film electrodes. As deposited and annealed, the surfaces of the electrodes were insulating at 4 K. Several methods were used to improve the electrical properties of the electrodes’ surfaces including rapid thermal annealing, oxygen sputter etching, and thin Ag coating treatments. The greatest improvement occurred after a deposition of a 5 nm Ag coating and subsequent rapid thermal anneal of one set of YBCO films. Under these conditions it was possible to make a superconducting Josephson point contact between the surfaces of the electrodes. We think that the Ag acts as a normal-metal proximity layer effectively shunting the degraded electrodes’ surfaces.
Herbal Interventions in Asthma and Allergy (1999)

This paper reviews the role of herbal-based medicines in the treatment of asthma and allergic rhinitis. A comprehensive literature search was performed of relevant English-language papers and abstracts were identified through a MEDLINE search and from bibliographies of the identified papers. Papers and studies pertaining to the use of medicinal plants in the treatment of asthma and allergic rhinitis were identified. They were then analyzed according to design, inclusion and exclusion criteria, population studied, variables tested, method of treatment (i.e., specific medicinal plants or herbal combinations), and results. The data have been reviewed and divided on the basis of culture and the effects of medicinal plants in asthma and allergy. A number of studies were found that support the use of some herbal medicines in asthma and allergy. Various derivatives from specific medicinal plants were identified as the antiasthma components and some mechanisms of action were explored. The results show positive effects of these herbs on bronchodilation, pulmonary function tests, and antagonism of asthma mediators such as histamine and platelet activating factor, corticosteroid levels, and clearance of mucus. Improved symptoms were also seen in patients with allergic rhinitis specifically on histamine-induced reactions, e.g., rhinorrhea, sneezing, and itching. From the review, there has been a role for some herbal medicines in the treatment of asthma and allergic rhinitis. Usage of herbal medicines has increased in recent years. Many of these medicinal plants provided relief of symptoms equal to allopathic medicines used. Specific chemical derivatives have been isolated from many of these plant products which act on the mechanisms and mediators that cause asthma and allergies. The amount of research on these products, especially in the United States, is limited. There is a lack of control of quantity and quality of the components in these remedies. Yet, many have fewer side effects than current therapy. Throughout the history of medicine, drugs have been developed from traditional medicine. By continuing to investigate how some of these herbal interventions work, we may be able to find additional effective medicines to treat asthma and allergies.
Knowledge-based middleware for future home networks (2009)

Humans are lazy. They want to get as much support and assistance in their daily life as possible. To provide sophisticated digital butler functionality a system has to monitor the humans and their environment to understand their desires. It has to control all devices to translate the deduced wills into actions. To provide an integrated intelligent environment to the residents it is necessary to overcome the borders of different manufacturers, devices and access technologies. A management and control middleware is needed that shields users as well as high level management services from the technical details of the network of devices by providing a standardized, resilient and secure communication channel. We present a knowledge-based middleware as base for that purpose in this paper. The novel approach is the transparent connection of highly heterogeneous home devices by requiring only very limited functionality per device. Our design allows the desired high autonomicity in a secure and efficient way.
A Parallel Data Mining Toolbox Using MatlabMPI (2004)

The ready availability of vast quantities of data has driven the need for data mining algorithms that can discover patterns, correlations and changes in the data. The amount and high dimensionality of the data make data mining an important application for high performance computing [Joshi, 2002]. The mathematical and interactive nature of many of the data mining algorithm, makes it natural to use a language like MATLAB both to design algorithms and for post-processing of the results. Recently, Kepner [2002] has developed a system, called MatlabMPI, which implements the six basic functions of the Message Passing Interface (MPI) standard in MATLAB, and thus allows any Matlab program to exploit multiple processors. This has motivated us to develop a parallel data mining toolbox that is based on MatlabMPI. Implementations of a parallel clustering algorithm and a parallel classification algorithm have been completed, and other functions are currently under development. We present two parallel implementations of K-Means clustering using MatlabMPI in this poster. 1. Master-Slave Method. In this approach there is a main node (Master) that performs data distribution, convergence check and centroid update. The slave processors are used only to calculate the centroids of their own local data. The algorithm is as follows:
Parallel beamforming using synthetic transmit beams (2005)

Ultrasound images generated using conventional parallel beamforming contains stationary stripes due to beam-to-beam variations across adjacent beams. Such an imaging system is thus shift variant. This paper investigates a method which eliminates this flaw and restores the shift invariant property. The beam-to-beam variations occur because the transmit and receive beams are not aligned. The underlying idea is then to generate additional synthetic transmit beams (STB) through interpolation of the received, unfocused signal at each array element prior to beamforming. Now each of the parallel receive beams can be aligned perfectly with a transmit beam-synthetic or real-thus eliminating the distortion caused by misalignment. To investigate the performance of the method a simulation study has been conducted. The simulations were done with parameters similar to a standard cardiac examination. Using the proposed method the variation was reduced to 1.5 dB. The simulations were confirmed by results front in vitro experiments where vertical line artifacts were unnoticeable when using the proposed method.
From the discovery of Vascular Endothelial Growth Factor to the introduction of Avastin in clinical trials - an interview with Napoleone Ferrara (2011)

Napoleone Ferrara and his colleagues at Genentech were the first to isolate and clone vascular endothelial growth factor (VEGF) in 1989. His laboratory has investigated many aspects of VEGF biochemistry and molecular biology. In 1993, Ferrara reported that inhibition of VEGF-induced angiogenesis by specific monoclonal antibodies resulted in dramatic suppression of the growth of a variety of tumors in vivo. These findings provided an important evidence that inhibition of angiogenesis may suppress tumor growth and blocking VEGF action could have therapeutic value for a variety of malignancies. A further development was the design in a rational fashion in 1997 of a humanized anti-VEGF monoclonal antibody (Avastin), now in clinical trials as a treatment for several solid tumors and also outside of cancer, in the treatment of age-related macular degeneration (AMD). Ferrara's work is revolutionizing quality of life for many of the estimated 1.2 million individuals in the US who have wet AMD. Upwards of a million AMD patients worldwide have already received anti-VEGF antibody therapy.
Memorial design : considerations for Christchurch (2012)

In the wake of a series of devastating earthquakes, Christchurch, New Zealand is faced with a long, complicated mourning and memorialisation process. The initial intention of this research was to comparatively examine memorial design theory with popular memorial sentiment as expressed in Christchurch City Council's 'Share an Idea' initiative. The outcome of such an investigation was hypothesized to reveal conflicting perspectives which may potentially be reconciled by the development of a series of schematic models for memorial design. As the research was carried out, it became clear that any attempt to develop such models is counter-intuitive. This position is reinforced by the literature reviewed and the data examined. Subsequently, a fundamentally different approach to memorialisation focused on an active participation process is suggested.
An approach to reachability analysis for feed-forward ReLU neural networks (2017)

We study the reachability problem for systems implemented as feed-forward neural networks whose activation function is implemented via ReLU functions. We draw a correspondence between establishing whether some arbitrary output can ever be outputed by a neural system and linear problems characterising a neural system of interest. We present a methodology to solve cases of practical interest by means of a state-of-the-art linear programs solver. We evaluate the technique presented by discussing the experimental results obtained by analysing reachability properties for a number of benchmarks in the literature.