gebhart/patrepeval huggingface dataset:
The majority of human CD3 epitopes are conferred by the epsilon chain (1989)

Transgenic mouse T cells expressing the human CD3 epsilon chain bind the majority (29/36) of monoclonal antibodies (mAbs) specific for human CD3. A proportion of these mAbs are also able to recognize isolated CD3 epsilon in a soluble, recombinant form. Thus, CD3 epsilon can confer most CD3 epitopes on the TCR--CD3 complex, but many determinants may require assembly of the complex for their formation. A number of mAbs did not recognize epsilon-transgenic T cells and probably need other CD3 subunits for binding. CD3-specific mAbs from each of the three groups defined here, as well as mAbs directed against the TCR alpha beta heterodimer, are all able to activate T cells. Therefore mAb attachment at several different sites on the TCR--CD3 complex can give rise to activation signals. This suggests that the cross-linking function of mitogenic antibodies may be their most significant property, rather than the perturbation of a particular 'functional epitope'.
Feed-forward neural networks (1994)

One critical aspect neural network designers face today is choosing an appropriate network size for a given application. Network size involves in the case of layered neural network architectures, the number of layers in a network, the number of nodes per layer, and the number of connections. Roughly speaking, a neural network implements a nonlinear mapping of u=G(x). The mapping function G is established during a training phase where the network learns to correctly associate input patterns x to output patterns u. Given a set of training examples (x, u), there is probably an infinite number of different size networks that can learn to map input patterns x into output patterns u. The question is, which network size is more appropriate for a given problem? Unfortunately, the answer to this question is not always obvious. Many researchers agree that the quality of a solution found by a neural network depends strongly on the network size used. In general, network size affects network complexity, and learning time. It also affects the generalization capabilities of the network; that is, its ability-to produce accurate results on patterns outside its training set.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular Vibration Spectra by Electron Tunneling (1966)

The conductance of metal-metal oxide-metal tunneling junctions has been observed to increase at certain characteristic bias voltages. These voltages are identified with vibrational frequencies of molecules contained in the barrier.
Dendritic cells are the most efficient in presenting endogenous naturally processed self-epitopes to class II-restricted T cells. (1995)

Dendritic cells (DC) are potent APCs, able to induce efficiently primary T cell-mediated responses to foreign Ags. To assess the efficiency of DC, as compared with other APC types, in the in vivo presentation of self-Ags to CD4+ T cells, we analyzed processing and presentation to class II-restricted T cells of endogenous naturally processed self-epitopes constitutively expressed by mouse APC. Mouse beta 2-microglobulin (m beta 2-m) peptides corresponding to residues 26-39 and 24-36 are constitutively presented, in mice expressing m beta 2-m, by I-Ad and I-Ed molecules respectively, as demonstrated by activation of m beta 2-m-specific T cell hybridomas generated in BALB/c beta 2-m-deficient mice. These dominant, naturally processed self-epitopes of m beta 2-m are presented by APC from a variety of tissues, including the thymus. To analyze the relative efficiency of different APC populations in the presentation of self-beta 2-m, the ability of purified DC, macrophages, and large or small B cells to stimulate m beta 2-m-specific T cell hybridomas was tested. Naturally processed self-m beta 2-m epitopes are constitutively presented to T cells by any class II-positive APC tested, but with highest efficiency by splenic and thymic DC, followed by macrophages, large B cells, and small B cells. This hierarchy of self-beta 2-m presentation does not depend on differential processing capacity of these APC populations, and it correlates with expression of CTLA-4 ligands and ICAM-1 molecules, rather than with expression of class II molecules.
Ritanserin facilitates anxiety in a simulated public-speaking paradigm (1997)

The effects of ritanserin, a 5-HT2A/2C (5-hydroxytryptamine) antagonist, have been investigated in simulated public speaking with healthy volunteers. The aim was to investigate the role of 5-HT in subjective experimental anxiety. There were three experimental groups each comprising four or five males and 11 females. Subjects received placebo, ritanserin 2.5 or 10 mg, p.o. They rated themselves using the Spielberger State-Trait Anxiety Inventory and visual analogue scales factored into anxiety, sedation and discontentment scores. Autonomic measures included skin conductance and heart rate. Subjects were told, 75 min after drug or placebo ingestion, without prior warning, to prepare a 4-min speech. Measures were taken before, during and after the speech. Ritanserin prolonged the anxiety induced by the procedure on the subjective ratings but had minimal effect on autonomic responses to the procedure. The result contrasts with an anxiolytic-like effect of ritanserin on aversively conditioned autonomic responses. The present finding is compatible with animal behavioural evidence that 5-HT has distinct and opposing roles in modulating conditioned and unconditioned anxiety.
Off-Chip Coupling (2013)

It is interesting to note that the fantastic growth in semiconductor electronics is based on only a few concepts. The rst transistor was made from germanium (Ge) because of its rather low processing temperatures in comparison to silicon (Si). What was considered a disadvantage turned out to become the unbeatable lead of Si technology since silicon dioxide and related materials allow fabrication techniques such as parallel and planar processing (Grimmeiss and Kasper, 2009). Dramatic shrinkage in feature sizes and a corresponding increase in transistor numbers led to integrated circuits (IC), which are now, with their incredibly high complexity, the undisputed backbone of microelectronics. The indirect semiconductors Si and Ge suffered in their potential for optoelectronics from low radiative emission efciency and low absorption at the indirect band gap. The direct semiconductors, mainly from group III/V, were strong in that respect and they started to dominate optoelectronics with clear band gap emission, light emission diodes (LED) of high quantum efciency, and laser diodes with low threshold currents even at room temperature. This had a strong impact on many areas including long-distance information transmission via optical ber cables. With more mature fabrication technology, highpower lasers and LEDs entered manufacturing applications and lighting in vehicles and homes. Although optoelectronic integrated circuits (OEIC) are familiar on group III/V substrates, their integration complexity is much lower than that of their IC counterparts.
Periplasmic glycerophosphodiester phosphodiesterase of Escherichia coli, a new enzyme of the glp regulon. (1983)

The promoter-proximal gene (glpT) of the glpT-glpQ operon of Escherichia coli encodes a membrane permease responsible for active transport of sn-glycerol 3-phosphate. Promoter-distal glpQ encodes a periplasmic protein which is not required for active transport of sn-glycerol 3-phosphate (Larson, T.J., Schumacher, G., and Boos, W. (1982) J. Bacteriol. 152, 1008-1021). This periplasmic protein has now been identified as a phosphodiesterase which hydrolyzes glycerophosphodiesters into sn-glycerol 3-phosphate plus alcohol. The enzyme exhibited broad substrate specificity with respect to the alcohol moiety; sn-glycerol 3-phosphate was released from glycerophosphoethanolamine, glycerophosphocholine, glycerophosphoglycerol, and bis(glycerophospho)glycerol. The enzyme was specific for glycerophosphodiesters; bis(p-nitrophenyl)phosphate, a substrate for other phosphodiesterases, was not hydrolyzed. In a coupled spectrophotometric assay utilizing sn-glycerol 3-phosphate dehydrogenase and NAD, apparent activity was optimal at pH 9 and was stimulated by Ca2+. The substrates of the phosphodiesterase had no affinity for the glpT-encoded active transport system. Thus, the glpQ gene product expands the catabolic capability of the glp regulon to include a variety of glycerophosphodiesters.
Nuclear magnetic resonance using a high temperature superconducting quantum interference device (1997)

In this letter, we present results of experiments in which nuclear magnetic resonance (NMR) signals were detected using an untuned pickup coil coupled to a high temperature superconductor (HTS) based superconducting quantum interference device (SQUID). We were able to operate the HTS SQUID in the presence of static fields of up to 500 Gauss and radio frequency fields of up to 6 Gauss. The ability of a HTS SQUID to detect NMR signals opens up the possibility of using a sensitive detector for practical applications involving NMR that require a broad detection bandwidth.
Total intravenous anaesthesia using propofol, gamma-hydroxybutyrate or midazolam in combination with sufentanil for patients undergoing coronary artery bypass surgery (1997)

Total intravenous anaesthesia (TIVA) using propofol, gamma-hydroxybutyrate (GHB) or midazolam in combination with sufentanil was investigated in 45 patients undergoing coronary artery bypass grafting (CABG). Anaesthesia was induced with sufentanil, etomidate and pancuronium. After endotracheal intubation, anaesthesia was continued with sufentanil (2 μg kg−1 h−1) for all patients. Patients were randomized to receive supplementary propofol (2 mg kg−1 h−1, n=15), gamma-hydroxybutyrate (20 mg kg−1 h−1, n=15) or midazolam (0.06 mg kg−1 h−1, n=15). Haemodynamic measurements were performed after induction and at various times in the pre-bypass period. In the propofol group, a significant decrease in heart rate (HR 12%±3%), cardiac index (CI 23%±4%), mean arterial pressure (MAP 16%±3%) and left ventricular stroke work index (LVSWI 17%±4%) occurred until sternotomy was performed. With the exception of cardiac index, both midazolam and gamma-hydroxybutyrate produced similar haemodynamic effects: cardiac index was temporarily decreased (19%±4%) by midazolam and remained unchanged after gamma-hydroxybutyrate. In both groups, sternotomy was followed by temporary hypertension, associated with a significant rise in systemic vascular resistance. No electrocardiographical signs of ischaemia were observed in any patient. In the case of propofol and midazolam, gamma-hydroxybutyrate showed adequate haemodynamic stability especially after induction of anaesthesia and may also be a suitable agent for total intravenous anaesthesia in patients with coronary artery disease. However, during sternotomy, supplementary administration of opioids was required.
Diuretic and Natriuretic Actions of Melanin Concentrating Hormone in Conscious Sheep (1996)

Melanin concentrating hormone (MCH) is a 19 amino-acid peptide expressed in high concentrations within the dorso-lateral hypothalamus of rats, sheep and man. MCH regulates skin colour and ACTH release in teleost fish, however, its physiological relevance in mammals is unclear. The present study examined the cardiovascular and metabolic actions of intracerebroventricular (i.c.v.) infusion of MCH, and the pro-MCH derived peptide Neuropeptide-E-I (NEI), in conscious, chronically instrumented sheep. Human MCH (1-19) or NEI (1-13) was infused i.c.v. for 24 h into 6 sheep, and measurements were made every 10 min of arterial pressure, heart rate, cardiac output, stroke volume and peripheral blood flow/conductance. Recordings of water intake (H2Oin), urine volume (Uv), urinary Na (UNaV) and K excretion (UKV) were made, as well as hematocrit, plasma Na, K, osmolality, protein, glucose, ACTH, vasopressin, renin, endothelin, ANF, cortisol and aldosterone concentrations. After 24 h of infusion at 10 microg/h, MCH produced a significant increase in Uv from 0.8 +/- 0.2 to 1.4 +/- 0.3 l/day, together with an increase in UNaV from 56 +/- 8 to 107 +/- 14 mmol/day, and in UKV from 202 +/- 18 to 369 +/- 38 mmol/day. H2Oin was unchanged. Similar renal changes were observed during i.c.v. infusion of NEI. There was no change in any cardiovascular parameter, although hematocrit showed a large decrease with infusion of both peptides after 24 h infusion. Plasma osmolality increased from 291 +/- 1 to 295 +/- 1 mOsm/kg during MCH infusion, whereas total protein and plasma Na and K were unchanged. MCH increased plasma glucose from 3.4 +/- 0.2 to 3.8 +/- 0.2 mmol/l. Plasma aldosterone exhibited a 30-40% decrease following MCH or NEI infusion, whereas all other plasma concentrations remained unchanged. This study has shown that i.c.v. infusion of MCH or NEI can produce diuretic, natriuretic and kaliuretic changes in conscious sheep, triggered by a possible increase in plasma volume as indicated by the changes in hematocrit. These results, together with anatomical data reporting the presence of MCH/NEI in fluid regulatory areas of the brain, indicate that MCH/NEI may be an important peptide involved in the central control of fluid homeostasis in mammals.
Expression and Functional Significance of HtrA1 Loss in Endometrial Cancer (2010)

Collectively, these data indicate loss of HtrA1 may contribute to the aggressiveness and metastatic ability of endometrial tumors.
Combinations of Oseltamivir and T-705 Extend the Treatment Window for Highly Pathogenic Influenza A(H5N1) Virus Infection in Mice (2016)

Current anti-influenza therapy depends on administering drugs soon after infection, which is often impractical. We assessed whether combinations of oseltamivir (a neuraminidase inhibitor) and T-705 (a nonspecific inhibitor of viral polymerases) could extend the window for treating lethal infection with highly pathogenic A(H5N1) influenza virus in mice. Combination therapy protected 100% of mice, even when delayed until 96 h postinoculation. Compared to animals receiving monotherapy, mice receiving combination therapy had reduced viral loads and restricted viral spread in lung tissues, limited lung damage, and decreased inflammatory cytokine production. Next-generation sequencing showed that virus populations in T-705-treated mice had greater genetic variability, with more frequent transversion events, than did populations in control and oseltamivir-treated mice, but no substitutions associated with resistance to oseltamivir or T-705 were detected. Thus, combination therapy extended the treatment window for A(H5N1) influenza infection in mice and should be considered for evaluation in a clinical setting.
Quantum Computations with Cold Trapped Ions (1995)

A quantum computer can be implemented with cold ions confined in a linear trap and interacting with laser beams. Quantum gates involving any pair, triplet, or subset of ions can be realized by coupling the ions through the collective quantized motion. In this system decoherence is negligible, and the measurement (readout of the quantum register) can be carried out with a high efficiency.
Purification and properties of a major, low molecular weight protein released by the trophoblast of sheep blastocysts at Day 13–21 (1982)

Sheep blastocysts (Day 13-21) incubated in a modified Minimum Essential Medium released proteins into the medium at an approximately linear rate over a 24-h period. Single Day-16 blastocysts converted 2-8% of the radioactivity supplied (100 muCi L-[3H]leucine) into non-dialysable macromolecules which were released into the medium. Two-dimensional polyacrylamide gel electrophoresis revealed that at Day 13 there was only one major product (Protein X), consisting of three closely similar isoelectric species of (pI of denatured polypeptides about 5.5), each with molecular weights of 17 000. Between Days 14 and 21 additional proteins were detected. One of these was of high molecular weight (greater than 660 000) and did not appear on the two-dimensional gels, but Protein X continued to predominate until Day 23 when it could not be detected. Explants of chorion from Day 30 of pregnancy failed to secrete Protein X. Protein X was released in significant quantities (50-100 micrograms per 24 h) by the trophoblast but not the yolk sac of Day-14 and Day-16 conceptuses, but was present in very low amounts in the tissues. Protein X from the incubation medium of Day-14 and Day-16 conceptuses was purified by successive DEAE ion exchange and Sephacryl S-200 gel chromatography. Because Protein X and some of the other proteins are produced transiently between Days 13 and 21, it is possible that they may play a role in maternal recognition of pregnancy in sheep.
The Prevention of Thymic Lymphomas in Transgenic Mice by Human O 6 -Alkylguanine-DNA Alkyltransferase (1993)

Nitrosoureas form O6-alkylguanine-DNA adducts that are converted to G to A transitions, the mutation found in the activated ras oncogenes of nitrosourea-induced mouse lymphomas and rat mammary tumors. These adducts are removed by the DNA repair protein O6-alkylguanine-DNA alkyltransferase. Transgenic mice that express the human homolog of this protein in the thymus were found to be protected from developing thymic lymphomas after exposure to N-methyl-N-nitrosourea. Thus, transgenic expression of a single human DNA repair gene is sufficient to block chemical carcinogenesis. The transduction of DNA repair genes in vivo may unravel mechanisms of carcinogenesis and provide therapeutic protection from known carcinogens.
A Framework for Text Mining Services (2004)

The growth of online scientific literature, coupled with the growing maturity of text pro-cessing technology, has boosted the importance of text mining as a potentially crucial tool. However, there are several challenges to be addressed before sophisticated text mining services can be deployed within emerging workflow environments. Our work contributes at two levels. At the invocation level, we have developed a flexible XML-based pipeline architecture which allows non-XML processors to be readily integrated. At the descrip-tion/discovery level, we have developed a broker for service composition, and an accom-panying domain ontology, that leverage the OWL-S approach to service profiles. 1
Planen und Auswerten von Versuchen (1968)

Abstract Für das Auffinden optimaler Reaktionsbedingungen mit Hilfe mathematisch statistischer Methoden muß man die Größe des Versuchsfehlers ermitteln können sowie wissen, ob und wie sich die verschiedenen Versuchsparameter auf das Ergebnis auswirken. Hier werden einige der wichtigsten Prinzipien aufgezeigt, wie man mit wenigen gezielten Messungen rasch zu eindeutigen Ergebnissen gelangt.
NuMA: an unusually long coiled-coil related protein in the mammalian nucleus. (1992)

A bank of 892 autoimmune sera was screened by indirect immunofluorescence on mammalian cells. Six sera were identified that recognize an antigen(s) with a cell cycle-dependent localization pattern. In interphase cells, the antibodies stained the nucleus and in mitotic cells the spindle apparatus was recognized. Immunological criteria indicate that the antigen recognized by at least one of these sera corresponds to a previously identified protein called the nuclear mitotic apparatus protein (NuMA). A cDNA which partially encodes NuMA was cloned from a lambda gt11 human placental cDNA expression library, and overlapping cDNA clones that encode the entire gene were isolated. DNA sequence analysis of the clones has identified a long open reading frame capable of encoding a protein of 238 kD. Analysis of the predicted protein sequence suggests that NuMA contains an unusually large central alpha-helical domain of 1,485 amino acids flanked by nonhelical terminal domains. The central domain is similar to coiled-coil regions in structural proteins such as myosin heavy chains, cytokeratins, and nuclear lamins which are capable of forming filaments. Double immunofluorescence experiments performed with anti-NuMA and antilamin antibodies indicate that NuMA dissociates from condensing chromosomes during early prophase, before the complete disintegration of the nuclear lamina. As mitosis progresses, NuMA reassociates with telophase chromosomes very early during nuclear reformation, before substantial accumulation of lamins on chromosomal surfaces is evident. These results indicate that the NuMA proteins may be a structural component of the nucleus and may be involved in the early steps of nuclear reformation during telophase.
Breast cancer detection using symmetrical antenna array (2007)

In this paper we present the results of breast cancer detection using a symmetrical antenna array. This new antenna array is built on a curved surface and can be used with realistic three-dimensional breast models, as well as with real breast cancer patients. The complete measurement setup and post-reception focusing algorithm is described in this contribution. The system performance is verified experimentally and results of detection of small spherical tumours are presented.
Joint aperture detection for speckle reduction and increased collection efficiency in ophthalmic MHz OCT (2013)

Joint-aperture optical coherence tomography (JA-OCT) is an angle-resolved OCT method, in which illumination from an active channel is simultaneously probed by several passive channels. JA-OCT increases the collection efficiency and effective sensitivity of the OCT system without increasing the power on the sample. Additionally, JA-OCT provides angular scattering information about the sample in a single acquisition, so the OCT imaging speed is not reduced. Thus, JA-OCT is especially suitable for ultra high speed in-vivo imaging. JA-OCT is compared to other angle-resolved techniques, and the relation between joint aperture imaging, adaptive optics, coherent and incoherent compounding is discussed. We present angle-resolved imaging of the human retina at an axial scan rate of 1.68 MHz, and demonstrate the benefits of JA-OCT: Speckle reduction, signal increase and suppression of specular and parasitic reflections. Moreover, in the future JA-OCT may allow for the reconstruction of the full Doppler vector and tissue discrimination by analysis of the angular scattering dependence.
Contextual domain classification in spoken language understanding systems using recurrent neural network (2014)

In a multi-domain, multi-turn spoken language understanding session, information from the history often greatly reduces the ambiguity of the current turn. In this paper, we apply the recurrent neural network (RNN) to exploit contextual information for query domain classification. The Jordan-type RNN directly sends the vector of output distribution to the next query turn as additional input features to the convolutional neural network (CNN). We evaluate our approach against SVM with and without contextual features. On our contextually labeled dataset, we observe a 1.4% absolute (8.3% relative) improvement in classification error rate over the non-contextual SVM, and 0.9% absolute (5.5% relative) improvement over the contextual SVM.
Selective Immobilization of Proteins onto Solid Supports through Split‐Intein‐Mediated Protein Trans‐Splicing (2006)

Without a trace: The immobilization of biologically active proteins onto a solid support through split-intein-mediated protein trans-splicing reactions requires only very dilute samples. Not only is this process traceless but it does not require purification of the protein, thereby making possible the direct immobilization of proteins from complex mixtures such as cell lysates. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z503475_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.