gebhart/patrepeval huggingface dataset:
Myasthenia gravis. CD4+ T epitopes on the embryonic gamma subunit of human muscle acetylcholine receptor. (1992)

In myasthenia gravis (MG) an autoimmune response against muscle acetylcholine receptor (AChR) occurs. Embryonic muscle AChR contains a gamma subunit, substituted in adult muscle by a homologous epsilon subunit. Antibodies and CD4+ cells specific for embryonic AChR have been demonstrated in MG patients. We identified sequence segments of the human gamma subunit forming epitopes recognized by four embryonic AChR-specific CD4+ T cell lines, propagated from MG patients' blood by stimulation with synthetic peptides corresponding to the human gamma subunit sequence. Each line had an individual epitope repertoire, but two 20-residue sequence regions were recognized by three lines of different HLA haplotype. Most T epitope sequences were highly diverged between the gamma and the other AChR subunits, confirming the specificity of the T cells for embryonic AChR. These T cells may have been sensitized against AChR expressed by a tissue other than innervated skeletal muscle, possibly the thymus, which expresses an embryonic muscle AChR-like protein, containing a gamma subunit. Several sequence segments forming T epitopes are similar to regions of microbial and/or mammalian proteins unrelated to the AChR. These findings are consistent with the possibility that T cell cross-reactivity between unrelated proteins ("molecular mimicry"), proposed as a cause of autoimmune responses, is not a rare event.
Phased-array wavelength demultiplexer withflattened wavelength response (1994)

A four-channel phased-array wavelength demultiplexer with a flattened wavelength response has been realised for the first time in InP/InGaAsP at 1.54 µm by employing multimode output waveguides. The device has 2 nm channel spacing and a flat response (within 1 dB) of 1 nm.
Cloning, characterization, and chromosomal mapping of human aquaporin of collecting duct. (1994)

We recently cloned a cDNA of the collecting duct apical membrane water channel of rat kidney, which is important for the formation of concentrated urine (Fushima, K., S. Uchida, Y. Hara, Y. Hirata, F. Marumo, and S. Sasaki. 1993. Nature [Lond.]. 361:549-552). Since urine concentrating ability varies among mammalian species, we examined whether an homologous protein is present in human kidney. By screening a human kidney cDNA library, we isolated a cDNA clone, designated human aquaporin of collecting duct (hAQP-CD), that encodes a 271-amino acid protein with 91% identity to rat AQP-CD. mRNA expression of hAQP-CD was predominant in the kidney medulla compared with the cortex, immunohistochemical staining of hAQP-CD was observed only in the collecting duct cells, and the staining was dominant in the apical domain. Functional expression study in Xenopus oocytes confirmed that hAQP-CD worked as a water channel. Western blot analysis of human kidney medulla indicated that the molecular mass of hAQP-CD is 29 kD, which is the same mass expected from the amino acid sequence. Chromosomal mapping of the hAQP-CD gene assigned its location to chromosome 12q13. These results could be important for future studies of the pathophysiology of human urinary concentration mechanisms in normal and abnormal states.
A Hypoxia-Regulated Adeno-Associated Virus Vector for Cancer-Specific Gene Therapy (2001)

The presence of hypoxic cells in human brain tumors is an important factor leading to resistance to radiation therapy. However, this physiological difference between normal tissues and tumors also provides the potential for designing cancer-specific gene therapy. We compared the increase of gene expression under anoxia (<0.01% oxygen) produced by 3, 6, and 9 copies of hypoxia-responsive elements (HRE) from the erythropoietin gene (Epo), which are activated through the transcriptional complex hypoxia-inducible factor 1 (HIF-1). Under anoxic conditions, nine copies of HRE (9XHRE) yielded 27- to 37-fold of increased gene expression in U-251 MG and U-87 MG human brain tumor cell lines. Under the less hypoxic conditions of 0.3% and 1% oxygen, gene activation by 9XHRE increased expression 11- to 18-fold in these cell lines. To generate a recombinant adeno-associated virus (rAAV) in which the transgene can be regulated by hypoxia, we inserted the DNA fragment containing 9XHRE and the LacZ reporter gene into an AAV vector. Under anoxic conditions, this vector produced 79- to 110-fold increase in gene expression. We believe this hypoxia-regulated rAAV vector will provide a useful delivery vehicle for cancer-specific gene therapy.
Hierarchy of Notch–Delta interactions promoting T cell lineage commitment and maturation (2007)

Notch1 (N1) receptor signaling is essential and sufficient for T cell development, and recently developed in vitro culture systems point to members of the Delta family as being the physiological N1 ligands. We explored the ability of Delta1 (DL1) and DL4 to induce T cell lineage commitment and/or maturation in vitro and in vivo from bone marrow (BM) precursors conditionally gene targeted for N1 and/or N2. In vitro DL1 can trigger T cell lineage commitment via either N1 or N2. N1- or N2-mediated T cell lineage commitment can also occur in the spleen after short-term BM transplantation. However, N2-DL1-mediated signaling does not allow further T cell maturation beyond the CD25(+) stage due to a lack of T cell receptor beta expression. In contrast to DL1, DL4 induces and supports T cell commitment and maturation in vitro and in vivo exclusively via specific interaction with N1. Moreover, comparative binding studies show preferential interaction of DL4 with N1, whereas binding of DL1 to N1 is weak. Interestingly, preferential N1-DL4 binding reflects reduced dependence of this interaction on Lunatic fringe, a glycosyl transferase that generally enhances the avidity of Notch receptors for Delta ligands. Collectively, our results establish a hierarchy of Notch-Delta interactions in which N1-DL4 exhibits the greatest capacity to induce and support T cell development.
Effect of Carbon-4 and Carbon-5 Volatile Fatty Acids on Growth of Mixed Rumen Bacteria In Vitro (1984)

Mixed ruminal bacteria (400 mg cells/liter) were incubated in artificial media containing ammonia, sodium carbonate, macrominerals, vitamins, sulfide, microminerals, acetate, propionate, and butyrate. When mixed carbohydrates (equal parts glucose, maltose, sucrose, cellobiose, and soluble starch) were added at 155 mg/liter per h for 10 h, average bacterial growth rate was slow, and dry weight yield was greater than 23%. Additions of isobutyrate, valerate, isovalerate, and 2 methylbutyrate had little influence on synthesis of bacterial dry weight, deoxyribonucleic acid, ribonucleic acid, or carbohydrate. When a timothy hay inoculum was used, isovalerate and 2 methyl-butyrate increased protein synthesis by 11.2 and 16.4%, but isobutyrate and valerate alone were without effect. All four acids combined increased bacterial protein by 18.7%. Responses with an inoculum of 60% concentrate and mixed hay were smaller and not statistically different from control incubations. Low concentrations of Trypticase (less than 250 mg/liter) improved efficiency of microbial protein synthesis from organic matter, but more was associated with decreased efficiency and utilization of extracellular ammonia.
Statistical evaluation of the coding capacity of complementary DNA strands (1984)

Two independent methods are used to evaluate the protein-coding information content in different classes of DNA sequences. The first method allows to evaluate the statistical relevance of finding unidentified reading frames, longer than 100 codons, on both DNA strands of: a) 117 DNA sequences that code for 142 nuclear proteins; b) 39 stable RNA coding sequences and c) 36 other DNA sequences which include regulatory and as yet unknown function sequences. The finding of 50 reading frames longer than 100 codons (complementary inverted proteins or c.i.p. genes) located on the DNA strand complementary to the protein-coding one is drastically in excess of the number predicted by chance alone. An independent method (testcode) applied to c.i.p. gene sequences, which assigns the probability of coding to a given sequence, predicts that more than 50% of these genes are translated in a functional product. These analyses indicate the existence of a new class of protein-coding genes, located on the DNA sequences complementary to the protein-coding DNA strand.
Data intensive analysis on the gordon high performance data and compute system (2011)

The Gordon data intensive computing system was designed to handle problems with large memory requirements that cannot easily be solved using standard workstations or distributed memory supercomputers. We describe the unique features of Gordon that make it ideally suited for data mining and knowledge discovery applications: memory aggregation using the vSMP software solution from ScaleMP, I/O nodes containing 4 TB of low-latency flash memory, and a high performance parallel file system with 4 PB capacity. We also demonstrate how a number of standard data mining tools (e.g. Matlab, WEKA, R) can be used effectively on Dash, an early prototype of the full Gordon system.
Style Tokens: Unsupervised Style Modeling, Control and Transfer in End-to-End Speech Synthesis (2018)

In this work, we propose "global style tokens" (GSTs), a bank of embeddings that are jointly trained within Tacotron, a state-of-the-art end-to-end speech synthesis system. The embeddings are trained with no explicit labels, yet learn to model a large range of acoustic expressiveness. GSTs lead to a rich set of significant results. The soft interpretable "labels" they generate can be used to control synthesis in novel ways, such as varying speed and speaking style - independently of the text content. They can also be used for style transfer, replicating the speaking style of a single audio clip across an entire long-form text corpus. When trained on noisy, unlabeled found data, GSTs learn to factorize noise and speaker identity, providing a path towards highly scalable but robust speech synthesis.
Novel Photoacid Generators for Photodirected Oligonucleotide Synthesis (2003)

Photodirected oligonucleotide synthesis uses either direct or indirect light-dependent 5'-deprotection. Both have been reported to give lower stepwise synthetic yields than conventional methods. The deficiency appears to be due to incomplete deprotection at the oligonucleotide 5'-position and, additionally in the case where photodirection is indirect and uses photogenerated photoacid to effect 5'-detritylation, the depurinating effects of strong acid. We have developed novel photosensitive-2-nitrobenzyl esters that on irradiation with near UV light generate alpha-chloro-substituted acetic acids, such as trichloroacetic acid, which are widely and successfully used in conventional solid-phase oligonucleotide synthesis. alpha-Phenyl-4,5-dimethoxy-2-nitrobenzyltrichloroacetate and alpha-phenyl-4,5-dimethoxy-2,6-dinitrobenzyltrichloroacetate showed appropriate photochemical characteristics and were used for photodirected synthesis of a variety of oligonucleotides, including (T)(5), TATAT, TGTGT, (T)(10), (AT)(5), (CT)(5) (GT)(5), and (TGCAT)(2) on a modified Millipore Expedite DNA synthesizer. The outcomes were compared with those obtained by use of directly added trichloroacetic acid (conventional synthesis). The stepwise yields for the two methods were essentially identical.
Glucose autoxidation and protein modification. The potential role of ‘autoxidative glycosylation’ in diabetes (1987)

Monosaccharide autoxidation (a transition metal-catalysed process that generates H2O2 and ketoaldehydes) appears to contribute to protein modification by glucose in vitro. The metal-chelating agent diethylenetriaminepenta-acetic acid (DETAPAC), which inhibits glucose autoxidation, also reduces the covalent attachment of glucose to bovine serum albumin. A maximal 45% inhibition of covalent attachment was observed, but this varied with glucose and DETAPAC concentrations in a complex fashion, suggesting at least two modes of attachment. The extent of inhibition of the metal-catalysed pathway correlated with the extent of inhibition of glycosylation-associated chromo- and fluorophore development. DETAPAC also inhibited tryptophan fluorescence quenching associated with glycosylation. Conversely, ketoaldehydes analogous to those produced by glucose autoxidation, but generated by 60Co irradiation, bound avidly to albumin and accelerated browning reactions. It is therefore suggested that a component of protein glycosylation is dependent upon glucose autoxidation and subsequent covalent attachment of ketoaldehydes. The process of glucose autoxidation, or ketoaldehydes derived therefrom, appear to be important in chromophoric and fluorophoric alterations. It is noted, consistent with these observations, that the chemical evidence for the currently accepted 'Amadori' product derived from the reaction of glucose with protein amino groups is consistent also with the structure expected for the attachment of a glucose-derived ketoaldehyde to protein. The concept of 'autoxidative glycosylation' is briefly discussed in relation to oxidative stress in diabetes mellitus.
Clinical and biological consequences of transmetallation induced by contrast agents for magnetic resonance imaging: a review (2006)

Gadolinium-based contrast agents (CAs) are widely used to enhance the contrast of images in magnetic resonance imaging procedures. Two categories of gadolinium chelates exist: the macrocyclic molecules where Gd3+ is caged in the pre-organized cavity of the ligand and the linear molecules. Gadolinium chelates differ in their thermodynamic stability constants and in their kinetic stability. In general, macrocyclic chelates such as Gd-DOTA or Gd-HP-DO3A are more stable than linear molecules. Even among linear agents, differences can be found. There is increasing evidence that transmetallation can be found in vivo, in the case of certain CAs (especially linear chelates), with body cations such as zinc, calcium or iron. Furthermore, analytical interference with colorimetric determination of calcium has been clinically evidenced with two linear chelates, Gd-DTPA-BMA and Gd-DTPA-BMEA. Clinical cases of spurious hypocalcaemia have been reported with these molecules. Such interference with some colorimetric assays for calcium is clinically relevant in that it can lead to unnecessary and potentially harmful treatment for hypocalcaemia.
Evaluation Update of the Red Light Camera Program in Fairfax County, VA (2006)

The Red Light Camera (RLC) program in Fairfax County, VA, had 13 cameras in operation in year 2003. This update study is conducted to evaluate the Fairfax County RLC program after 2 years of operation. The results of the violation analysis indicate that the RLC program did reduce the violation rate by up to 63% in the 22nd- to 27th-month period of its operation. The results also show that the increase of the intersection amber time combined with RLC produced a higher reduction of up to 72% in violation rate. The reduction in violation rate was found to be statistically significant. The accident rate was reduced by 27% after 2 years of RLC operation. However, the reduction in accidents was not found to be statistically significant at this point in time
EphB Receptor-binding Peptides Identified by Phage Display Enable Design of an Antagonist with Ephrin-like Affinity (2005)

The Eph receptor tyrosine kinases are overexpressed in many pathologic tissues and have therefore emerged as promising drug target candidates. However, there are few molecules available that can selectively bind to a single Eph receptor and not other members of this large receptor family. Here we report the identification by phage display of peptides that bind selectively to different receptors of the EphB class, including EphB1, EphB2, and EphB4. Peptides with the same EphB receptor specificity compete with each other for binding, suggesting that they have partially overlapping binding sites. In addition, several of the peptides contain amino acid motifs found in the G-H loop of the ephrin-B ligands, which is the region that mediates high-affinity interaction with the EphB receptors. Consistent with targeting the ephrin-binding site, the higher affinity peptides antagonize ephrin binding to the EphB receptors. We also designed an optimized EphB4-binding peptide with affinity comparable with that of the natural ligand, ephrin-B2. These peptides should be useful as selective inhibitors of the pathological activities of EphB receptors and as targeting agents for imaging probes and therapeutic drugs.
Named Entity Recognition from Diverse Text Types (2001)

Current research in Information Extraction tends to be focused on application-specific systems tailored to a particular domain. The Muse system is a multi-purpose Named Entity recognition system which aims to reduce the need for costly and time-consuming adaptation of systems to new applications, with its capability for processing texts from widely di#ering domains and genres. Although the system is still under development, preliminary results are encouraging, showing little degradation when processing texts of lower quality or of unusual types. The system currently averages 93% precision and 95% recall across a variety of text types.
Asymptotic Minimax Character of the Sample Distribution Function and of the Classical Multinomial Estimator (1956)

This paper is devoted, in the main, to proving the asymptotic minimax character of the sample distribution function (d.f.) for estimating an unknown d.f. in $\mathscr{F}$ or $\mathscr{F}_c$ (defined in Section 1) for a wide variety of weight functions. Section 1 contains definitions and a discussion of measurability considerations. Lemma 2 of Section 2 is an essential tool in our proofs and seems to be of interest per se; for example, it implies the convergence of the moment generating function of $G_n$ to that of $G$ (definitions in (2.1)). In Section 3 the asymptotic minimax character is proved for a fundamental class of weight functions which are functions of the maximum deviation between estimating and true d.f. In Section 4 a device (of more general applicability in decision theory) is employed which yields the asymptotic minimax result for a wide class of weight functions of this character as a consequence of the results of Section 3 for weight functions of the fundamental class. In Section 5 the asymptotic minimax character is proved for a class of integrated weight functions. A more general class of weight functions for which the asymptotic minimax character holds is discussed in Section 6. This includes weight functions for which the risk function of the sample d.f. is not a constant over $\mathscr{F}_c.$ Most weight functions of practical interest are included in the considerations of Sections 3 to 6. Section 6 also includes a discussion of multinomial estimation problems for which the asymptotic minimax character of the classical estimator is contained in our results. Finally, Section 7 includes a general discussion of minimization of symmetric convex or monotone functionals of symmetric random elements, with special consideration of the "tied-down" Wiener process, and with a heuristic proof of the results of Sections 3, 4, 5, and much of Section 6.
Lignin Biosynthesis (2003)

The lignin biosynthetic pathway has been studied for more than a century but has undergone major revisions over the past decade. Significant progress has been made in cloning new genes by genetic and combined bioinformatics and biochemistry approaches. In vitro enzymatic assays and detailed analyses of mutants and transgenic plants altered in the expression of lignin biosynthesis genes have provided a solid basis for redrawing the monolignol biosynthetic pathway, and structural analyses have shown that plant cell walls can tolerate large variations in lignin content and structure. In some cases, the potential value for agriculture of transgenic plants with modified lignin structure has been demonstrated. This review presents a current picture of monolignol biosynthesis, polymerization, and lignin structure.
Realistic Ray Tracing (2003)

Concentrating on the "nuts and bolts" of writing ray tracing programs, this new and revised edition emphasizes practical and implementation issues and takes the reader through all the details needed to write a modern rendering system. Most importantly, the book adds many C++ code segments, and adds new details to provide the reader with a better intuitive understanding of ray tracing algorithms.
Binding of cytokines to pharmaceutically prepared human immunoglobulin. (1993)

Pharmaceutically prepared IgG, pooled from sera of over 2,000 normal individuals, contained both monomeric and dimeric IgG. Each type of IgG bound 125I-labeled interleukin (IL)-1 alpha, IL-1 beta, IL-6, and tumor necrosis factor (TNF)-alpha. Increased binding to IgG was observed if 125I-IL-1 beta was denatured by heating to 39 degrees C. However, the binding of both nondenatured and denatured 125I-IL-1 beta was not inhibited by unlabeled IL-1 beta. In contrast, binding of 125I-IL-1 alpha, 125I-IL-6, and 125I-TNF alpha was inhibited by the corresponding unlabeled cytokine. Papain-digestion of IgG abolished binding of 125I-TNF alpha but failed to influence the displaceable binding of 125I-IL-1 alpha and 125I-IL-6. 125I-TNF alpha was a mixture of trimeric and monomeric forms, the latter being the predominant form at lower concentrations. The apparent saturability of 125I-TNF alpha was explained by a higher nonspecific binding of monomeric than of trimeric 125I-TNF alpha to IgG. The amounts of cytokine antibodies in IgG preparations would contribute approximately 2 micrograms anti-IL-1 alpha IgG and 1 microgram anti-IL-6 IgG per kg body wt during high dose immune globulin therapy. In conclusion, pharmaceutical preparations of human IgG contain specific and neutralizing, high affinity antibodies against IL-1 alpha and IL-6, but not against TNF alpha or IL-1 beta. There are significant methodological pitfalls that hamper detection of IgG autoantibodies against cytokines.
Survival analysis of adverse effects data in the Beta-Blocker Heart Attack Trial (1987)

Monitoring for adverse effects in an integral part of controlled clinical trials. Traditionally the results of monitoring are reported as either cumulative percentages at the end of the study or cross-sectional percentages at a given time in the study. These results are likely to underestimate the true number of complaints because participants may be withdrawn (e.g., deaths, losses to follow-up, and refusals) before they ever complain of an adverse effect. However, survival analysis methods can be used to compare the distributions of "time to first complaint" in the active and placebo treatment groups, taking into account withdrawals. Participants in the Beta-Blocker Heart Attack Trial were monitored for possible adverse effects. On each follow-up visit they were asked whether they had had any of four conditions (blacking out, fatigue, depression, and bronchospasm) since their previous visit about 3 months earlier. The patients were followed for up to 30 months. For fatigue and bronchospasm, the complaint-free time was significantly longer in the placebo vs. active (propranolol) treatment group (P less than 0.005).