gebhart/patrepeval huggingface dataset:
High affinity human IgE receptor (Fc epsilon RI). Analysis of functional domains of the alpha-subunit with monoclonal antibodies (1991)

The binding of IgE to the high affinity Fc epsilon receptor (Fc epsilon RI) on mast cells and basophils is mediated by the alpha-subunit of the tetrameric receptor complex. Based on sequence homologies, the 50-kDa alpha-subunit is a member of the immunoglobulin superfamily of proteins and has two predicted disulfide-bonded loops. Monoclonal antibodies specific for the human alpha-subunit have been identified and separated into two major classes: inhibitory and noninhibitory antibodies. Inhibitory antibodies (i.e. 15A5) block 125I-IgE binding to a recombinant chimeric alpha-subunit (ch-alpha-protein) expressed on Chinese hamster ovary cells and immunoprecipitate 125I-labeled purified ch-alpha-protein. Noninhibitory antibodies (i.e. 22E7) immunoprecipitate both 125I-labeled ch-alpha-protein and the soluble complex of 125I-IgE cross-linked to ch-alpha-protein but do not block 125I-IgE binding to the ch-alpha-protein expressed on Chinese hamster ovary cells. Both classes of antibodies bind to natural Fc epsilon RI present on human basophils and induce histamine release from these cells. Inhibitory antibody 15A5 specifically binds to a peptide corresponding to amino acids 125-140 of the putative second domain of the alpha-subunit sequence. All the inhibitory antibodies compete with 125I-15A5 for binding to the ch-alpha-protein, indicating that these antibodies recognize inhibitory epitopes that are either identical or sterically overlapping. Noninhibitory antibodies (i.e. 22E7) do not block 125I-15A5 binding to the ch-alpha-protein. These data suggest that antibodies binding to the predicted second domain of the alpha-subunit can inhibit IgE binding to the alpha-subunit, while antibodies binding at a distance from this site do not inhibit IgE binding. These inhibitory antibodies may block IgE binding to the ch-alpha-protein by direct overlap, steric inhibition, or induced conformational changes of the receptor contact points for IgE.
Statistical control of VLSI fabrication processes. II. A software system (1988)

For pt.I see ibid., vol.1, no.2, p.62-71, 1988. The algorithms used to implement the CMU-CAM statistical control system for VLSI integrated circuit fabrication are presented. The CMU-CAM system performs three major operations: modeling; quality control; and feed-forward control. In order to increase the efficiency of modeling and control, the problem is decomposed using statistical factorization techniques. Algorithms for process modeling and algorithms used in quality control and feed-forward control are described. The CMU-CAM system performs profit maximization through statistical process control. Its capabilities are illustrated by a number of computational examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein (1999)

The human endogenous retrovirus K (HERV-K) family of endogenous retroviruses consists of approximately 50 proviral copies per haploid human genome. Herein, the HERV-Ks are shown to encode a sequence-specific nuclear RNA export factor, termed K-Rev, that is functionally analogous to the HIV-1 Rev protein. Like HIV-1 Rev, K-Rev binds to both the Crm1 nuclear export factor and to a cis-acting viral RNA target to activate nuclear export of unspliced RNAs. Surprisingly, this HERV-K RNA sequence, which is encoded within the HERV-K long terminal repeat, is also recognized by HIV-1 Rev. These data provide surprising evidence for an evolutionary link between HIV-1 and a group of endogenous retroviruses that first entered the human genome approximately 30 million years ago.
Skeletal muscle hemojuvelin is dispensable for systemic iron homeostasis (2011)

Hepcidin, a hormone produced mainly by the liver, has been shown to inhibit both intestinal iron absorption and iron release from macrophages. Hemojuvelin, a glycophosphatidyl inositol-linked membrane protein, acts as a bone morphogenetic protein coreceptor to activate hepcidin expression through a SMAD signaling pathway in hepatocytes. In the present study, we show in mice that loss of hemojuvelin specifically in the liver leads to decreased liver hepcidin production and increased tissue and serum iron levels. Although it does not have any known function outside of the liver, hemojuvelin is expressed at very high levels in cardiac and skeletal muscle. To explore possible roles for hemojuvelin in skeletal muscle, we analyzed conditional knockout mice that lack muscle hemojuvelin. The mutant animals had no apparent phenotypic abnormalities. We found that systemic iron homeostasis and liver hepcidin expression were not affected by loss of hemojuvelin in skeletal muscle regardless of dietary iron content. We conclude that, in spite of its expression pattern, hemojuvelin is primarily important in the liver.
Bootstrapping language models for dialogue systems (2006)

We report results on rapidly building language models for dialogue systems. Our base line is a recogniser using a grammar network. We show that we can almost halve the word error rate (WER) by combining language models generated from a simple task grammar with a standard speech corpus and data collected from the web using a sentence selection algorithm based on relative perplexity. This model compares very well to a language model using “in-domain” data from a Wizard Of Oz (WOZ) collection. We strongly advocate the use of statistical language models (SLMs) in speech recognisers for dialogue systems and show that costly WOZ data collections are not necessary to build SLMs.
Medical Countermeasures against Nuclear Threats: Radionuclide Decorporation Agents (2008)

Exposure to radionuclides disseminated by a radiological dispersion device or deposited as fallout after a nuclear power plant accident or detonation of an improvised nuclear device could result in internal contamination of a significant number of individuals. Internalized radionuclides may cause both acute and chronic radiation injury and increase an individual's risk of developing cancer. This damage and risk can be mitigated by the use of decorporation agents that reduce internal contamination. Unfortunately, most effective agents decorporate only a limited range of radionuclides, and some are formulated in ways that would make administration in mass casualty situations challenging. There is a need for new radionuclide decorporation agents, reformulations of existing agents, and/or expansion of the labeled indications for existing treatments. Researchers developing novel or improved decorporation agents should also understand the regulatory pathway for these products. This workshop, the first in nearly half a century to focus exclusively on radionuclide decorporation, brought together researchers and scientific administrators from academia, government and industry as well as senior regulatory affairs officers and U.S. Food and Drug Administration personnel. Meeting participants reviewed recent progress in the development of decorporation agents and contemplated the future of the field.
Generation and in Vitro Differentiation of a Spermatogonial Cell Line (2002)

Spermatogenesis is the process by which spermatogonial stem cells divide and differentiate to produce sperm. In vitro sperm production has been difficult to achieve because of the lack of a culture system to maintain viable spermatogonia for long periods of time. Here we report the in vitro generation of spermatocytes and spermatids from telomerase-immortalized mouse type A spermatogonial cells in the presence of stem cell factor. This differentiation can occur in the absence of supportive cells. The immortalized spermatogonial cell line may serve as a powerful tool in elucidating the molecular mechanisms of spermatogenesis. Furthermore, through genomic modification and transplantation techniques, this male germ cell line may be used to generate transgenic mice and to develop germ cell gene therapy.
The mechanism of the stabilisation of glow plasma at atmospheric pressure (1990)

Some reasons are discussed for the stabilisation of a glow discharge at atmospheric pressure which was attained by controlling the following three conditions: the use of a high-frequency source, the use of He gas for dilution and the insertion of a dielectric plate between electrodes. The three conditions interact: the dielectric plate in a plasma forms the pulsed discharge from a low-frequency source, the fast duration of pulse current prevents a transition to an arc style discharge and a large volume of metastable atomic helium aids ionisation or dissociation near the electrode plate and in the flowing gas. The measurements of discharge-maintaining voltage at several hundred volts provide evidence that this is really a glow plasma at atmospheric pressure. The changes of the emission intensities of metastable helium prove indirectly that some dissociation occurs as a result of the action of the helium atom.
OpenSim: Open-Source Software to Create and Analyze Dynamic Simulations of Movement (2007)

Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.
Pharmacokinetics of Stavudine in Patients with AIDS or AIDS-Related Complex (1992)

The pharmacokinetics of stavudine (d4T; 2',3'-didehydro-3'-deoxythymidine) were studied in patients with AIDS-related complex or AIDS enrolled in a dose-ranging phase I/II study. Twenty-two patients were studied after the first oral dose of 0.67, 1.33, 2.67, or 4 mg/kg of body weight; 17 of them underwent an additional steady-state pharmacokinetic evaluation after thrice-daily dosing of the above doses. Stavudine absorption was rapid, with mean peak concentrations of 1.2-4.2 mg/L over the four dose levels studied. From 34% to 41% of an oral dose was excreted as unchanged drug in the urine. The mean values for plasma elimination half-life ranged from 1 to 1.6 h. The absolute bioavailability of a 4 mg/kg oral dose exceeded 80%. There was no change in pharmacokinetic parameters measured after the first dose and after chronic dosing. Stavudine is a new dideoxynucleoside with more complete and less variable oral absorption than existing nucleosides used for treatment of human immunodeficiency virus infection.
Synthesis of 2,3′-Diindolylmethanes and Substituted Indolo[3,2-b]carbazoles (2004)

Three different synthetic routes to substituted 2,3′-diindolylmethanes, and the syntheses of substituted indolo[3,2-b]carbazoles are described. The first rigid proof of an acylation in the 2-position of a 1,3-unsubstituted indole is also presented in the form of an X-ray structure.
Detection of the t(2;5)‐associated NPM/ALK fusion cDNA in peripheral blood cells of healthy individuals (1998)

The translocation t(2;5), which leads to the fusion of the nucleophosmin gene (NPM) on chromosome 5q35 to the receptor kinase ALK on chromosome 2p23, is found in CD30+ anaplastic large cell lymphomas and some cases of B-cell lymphoma. Hodgkin's disease (HD) is a malignant lymphoma characterized by large multinucleated tumour cells, Hodgkin and Reed-Sternberg (H&RS) cells, surrounded by a dense lymphohistiocytic infiltrate. Our group recently demonstrated NPM/ALK fusion cDNAs by single-cell RT-PCR in < 3% of CD30+ tumour cells in 2/9 cases of HD. To further delineate the relevance of this finding for HD, we studied the occurrence of NPM/ALK fusion genes in peripheral blood cells of healthy donors by RT-PCR. NPM/ALK fusion cDNAs were found by RT-PCR in 14/29 healthy individuals and confirmed by hybridization with a breakpoint-specific oligonucleotide. Due to the low rate of NPM/ALK-positive cells in the peripheral blood of positive individuals, an assignment to a defined cellular subpopulation was not possible. We conclude that NPM/ALK fusion genes are present in peripheral blood cells of healthy donors. After t(14;18) and t(9;22), t(2;5) represents the third example of tumour-associated translocation products in blood cells of apparently healthy donors. The implications of this finding are discussed.
Carboxyl-Terminal Parathyroid Hormone Fragments Stimulate Type-1 Procollagen and Insulin-Like Growth Factor-Binding Protein-5 mRNA Expression in Osteoblastic UMR-106 Cells. (1998)

The effects of carboxyl-terminal (C-) PTH fragments, (35-84), (53-84) and (69-84), on the proliferation and function of osteoblastic UMR-106 cells were compared with those of amino-terminal (N-) (1-34) and intact (I-) (1-84) PTH. I-PTH as well as N-PTH at 10(-8)M significantly inhibited [3H] thymidine incorporation and stimulated alkaline phosphatase activity in UMR-106 cells. No C-PTH fragments affected them. In contrast, the expression of type-1 procollagen mRNA in these cells was stimulated by all C-PTH fragments, inhibited by N-PTH and not affected by I-PTH. All C-PTH fragments except (69-84) as well as N-PTH and I-PTH stimulated IGFBP-5 mRNA expression. The present study suggests that the C-portion of the PTH molecule exercises biological activities in mRNA expression of type-1 procollagen as well as IGFBP-5 in osteoblasts, and that it might be involved in the anabolic action of PTH on bone in vivo.
Increased urinary excretion of orosomucoid is a risk predictor of diabetic nephropathy (2009)

Urinary orosomucoid is a DN-related biomarker, which is associated with the development and progression of DN. Furthermore, increased UOER is an independent risk factor of DN.
Poly(Ethylene Oxide)/Organosolv Lignin Blends:  Relationship between Thermal Properties, Chemical Structure, and Blend Behavior (2004)

Blends of poly(ethylene oxide) with organosolv lignin (Alcell) were prepared by thermal blending. Excellent fiber spinning was achieved over the entire blend ratio. The good thermal properties of the Alcell lignin arise from its unique chemical structure. HMQC 2D NMR analysis revealed the presence of alkoxyl chains at the Cα and Cγ positions of the Alcell lignin side chain structure acting as internal plasticizers and enhancing the thermal mobility of the lignin. The addition of a small amount of Alcell lignin to PEO resulted in an increase of the PEO crystalline domain size. However, both PEO crystallinity and crystalline domain size decreased with lignin incorporation beyond 25 wt %. A negative polymer−polymer interaction energy density “B” was calculated on the basis of the melting point depression of PEO and a negative deviation of Tg from the weighted average values observed. Good prediction of the Tg-composition behavior was obtained indicating the presence of favorable interactions between blend components. FT-IR analysis revealed the formation of a strong hydrogen-bonding system between Alcell lignin and PEO, supporting that hydrogen-bonding interactions are an important factor in the formation of miscible lignin-based polymer blends.
Targeting CD19 with genetically modified EBV-specific human T lymphocytes. (2002)

Human Epstein-Barr virus-specific T cells were genetically modified to express chimeric receptors specific for human CD19, which is expressed on the cell surface of most B cell malignancies. The receptor-modified EBV-specific T cells can be expanded and maintained long term in the presence of EBV-infected B cells. They recognize autologous EBV-infected targets through their conventional T cell receptor, and allogeneic EBV-infected targets and tumor targets through their chimeric receptor. They efficiently lyse both EBV and CD19-positive tumor targets in the absence of background cytotoxicity against CD19-negative targets. Donor-derived EBV-specific T cells expressing chimeric anti-tumor receptors may represent a source of effector cells that could be safely administered to leukemia patients to eradicate minimal residual disease after allogeneic bone marrow transplantation.
Anaplastic lymphoma kinase in human cancer (2011)

The receptor tyrosine kinases (RTKs) play a critical role, controlling cell proliferation, survival, and differentiation of normal cells. Their pivotal function has been firmly established in the pathogenesis of many cancers as well. The anaplastic lymphoma kinase (ALK), a transmembrane RTK, originally identified in the nucleophosmin (NPM)-ALK chimera of anaplastic large cell lymphoma, has emerged as a novel tumorigenic player in several human cancers. In this review, we describe the expression of the ALK-RTK, its related fusion proteins, and their molecular mechanisms of activation. Novel tailored strategies are briefly illustrated for the treatment of ALK-positive neoplasms.
Industry (1998)

Apart from table D1, which gives indices of aggregate industrial production, and table D13, showing the number of cotton spindles, all the tables in this section consist of physical output and external trade volume statistics for major commodities which possess an adequate degree of homogeneity to allow aggregation and meaningful comparisons between countries. Inevitably these are mostly basic commodities rather than finished goods—yarn and cloth rather than clothing, metals rather than machinery. The picture they give of industrial development is necessarily biased and partial. However, until very recent times there is little that could be added to them in the way of continuous statistical series for industries making finished products.
MLbase: A Distributed Machine-learning System (2013)

Machine learning (ML) and statistical techniques are key to transforming big data into actionable knowledge. In spite of the modern primacy of data, the complexity of existing ML algorithms is often overwhelming—many users do not understand the trade-offs and challenges of parameterizing and choosing between different learning techniques. Furthermore, existing scalable systems that support machine learning are typically not accessible to ML researchers without a strong background in distributed systems and low-level primitives. In this work, we present our vision for MLbase, a novel system harnessing the power of machine learning for both end-users and ML researchers. MLbase provides (1) a simple declarative way to specify ML tasks, (2) a novel optimizer to select and dynamically adapt the choice of learning algorithm, (3) a set of high-level operators to enable ML researchers to scalably implement a wide range of ML methods without deep systems knowledge, and (4) a new run-time optimized for the data-access patterns of these high-level operators. 1.
DELIVERY OF SUBSTANCES INTO CELLS AND TISSUES USING A PARTICLE BOMBARDMENT PROCESS (1987)

ABSTRACT Biologists commonly wish to introduce a wide range of substances into living cells. Such substances include biological stains, proteins (antibodies or enzymes), and genetic material (either RNA or DNA). The cell membrane and, in the case of plant ceils, the cell wall pose formidable barriers which exclude many macromolecules. The concept of particle bombardment has been put forward as a universal mechanism for transporting substances into any living cell. An acceleration device has been designed and constructed which can accelerate small tungsten particles (1 to 4 urn in diameter) to velocities of about 1,000 to 2,000 ft/sec. We have found that these particles can penetrate cell walls and membranes and enter cells in a nonlethal manner. Thousands of cells can be penetrated simultaneously, in situ, as they occur in tissues. Particle bombardment has been shown to be effective in delivering foreign substances into a variety of plant species, including onion, tobacco, corn, and rice. This new method of delivering macromolecules into living cells and tissues should have diverse scientific applications.
Blind Image Blur Identification in Cepstrum Domain (2007)

The type and extent of blur affect image quality and therefore its evaluation. This paper presents an accurate method for blur identification and parameter estimation from one image without a priori knowledge. The key idea of the proposed method is to perform Fourier transform of logarithm spectrum to detect the periodic blur pattern in cepstrum domain instead of spectral nulls. Accordingly, the estimation of blur parameters is more accurate and robust to noise. The experimental results validate the accuracy of the proposed method.
CD8+ Cytotoxic T Lymphocyte Activation by Soluble Major Histocompatibility Complex-Peptide Dimers (2005)

CD8+ cytotoxic T lymphocyte (CTL) can recognize and kill target cells that express only a few cognate major histocompatibility complex class I-peptide (pMHC) complexes. To better understand the molecular basis of this sensitive recognition process, we studied dimeric pMHC complexes containing linkers of different lengths. Although dimers containing short (10-30-A) linkers efficiently bound to and triggered intracellular calcium mobilization and phosphorylation in cloned CTL, dimers containing long linkers (> or = 80 A) did not. Based on this and on fluorescence resonance energy transfer experiments, we describe a dimeric binding mode in which two T cell receptors engage in an anti-parallel fashion two pMHC complexes facing each other with their constant domains. This binding mode allows integration of diverse low affinity interactions, which increases the overall binding and, hence, the sensitivity of antigen recognition. In proof of this, we demonstrated that pMHC dimers containing one agonist and one null ligand efficiently activate CTL, corroborating the importance of endogenous pMHC complexes in antigen recognition.
Robust phosphorescent platinum(ii) complexes with tetradentate O∧N∧C∧N ligands: high efficiency OLEDs with excellent efficiency stability (2013)

The Pt(II) complexes (1-3) bearing tetradentate O^N^C^N ligands display high emission quantum yields (0.76-0.90) and good thermal stability (T(d) > 400 °C). Complex is an excellent green phosphorescence dopant for OLEDs with excellent efficiency and low efficiency roll-off (η(L), η(Ext)(max) = 66.7 cd A(-1), 18.2%; η(L), η(Ext) (1000 cd m(-2)) = 65.1 cd A(-1), 17.7%).