gebhart/patrepeval huggingface dataset:
Antigen Processing in the Endoplasmic Reticulum Is Monitored by Semi-Invariant αβ TCRs Specific for a Conserved Peptide–Qa-1b MHC Class Ib Ligand (2017)

Ag processing in the endoplasmic reticulum (ER) by the ER aminopeptidase associated with Ag processing (ERAAP) is central to presentation of a normal peptide-MHC class I (MHC I) repertoire. Alternations in ERAAP function cause dramatic changes in the MHC I-presented peptides, which elicit potent immune responses. An unusual subset of CD8<sup>+</sup> T cells monitor normal Ag processing by responding to a highly conserved FL9 peptide that is presented by Qa-1<sup>b</sup>, a nonclassical MHC Ib molecule (QFL) in ERAAP-deficient cells. To understand the structural basis for recognition of the conserved ligand, we analyzed the αβ TCRs of QFL-specific T cells. Individual cells in normal wild-type and TCRβ-transgenic mice were assessed for QFL-specific TCR α- and β-chains. The QFL-specific cells expressed a predominant semi-invariant TCR generated by DNA rearrangement of TRAV9d-3-TRAJ21 α-chain and TRBV5-TRBD1-TRBJ2-7 β-chain gene segments. Furthermore, the CDR3 regions of the α- as well as β-chains were required for QFL ligand recognition. Thus, the αβ TCRs used to recognize the peptide-Qa-1 ligand presented by ERAAP-deficient cells are semi-invariant and likely reflect a conserved mechanism for monitoring the fidelity of Ag processing in the ER.
Controlling the Galileo L1 OS Signal Emissions with Satellite Baseband Filters (2006)

Navigation satellites have a complex series of spectral emission requirement to meet. These range from controlling out- of-band energy to protect sensitive services, such as the radio astronomy band at approximately 1612MHz, just above the L1 RNSS frequencies, to controlling in-band emission profiles to prevent harmful interference between one signal and another. Whilst the out-of-band emissions can be controlled through the output filters connected between the high power amplifiers (HPA's) and antenna, this is not possible for spectral shaping within the transmission band. The technical challenge is increased by the need to transmit many signals within the same band, each carrying a different service. The current Galileo L1 signal proposals are a typical example, whereby 5 signals might be transmitted. These are PRS, BOC(1,1) and pilot OS component, and BCS((s);1) and pilot OS component. A similar situation is also likely to arise in the proposals for GPS3 whereby the signals could be CA code, P(Y), M-code, L1C and pilot signal. The method by which the signals are multiplexed onto the carrier also has a significant effect on the options for spectral control. Galileo will use a modified Interplex scheme to maintain a constant magnitude signal. The paper examines the various options for baseband spectral control through digital filters and proposes some practical options. One characteristic of such filters is the growth in the number of points in the output phase constellation. This growth poses real problems in the satellite payload design due to the precision of the amplitude control of the in-phase and quadrature carrier components. Examples are given showing that even a 2 pole filter may generate as many as 50 or more phase constellation states. The main body of the paper is concerned with the control and separation of the spectral from different services and signals. The filter method is shown to be more effective than other options (such as multi-level signal waveforms).
Natural antibodies against the immunoglobulin F(ab′)2 fragment cause elimination of antigens recognized by the F(ab′)2 from the circulation (1995)

A humanized monoclonal IgG1 antibody, designated hC4G1, recognizes the fibrinogen receptor glycoprotein (GP)IIb/IIIa on platelets and inhibits platelet aggregation. When the F(ab')2 fragment of hC4G1 (F(ab')2 hC4G1) was administered to cynomolgus monkeys, all the monkeys showed inhibition of platelet aggregation ex vivo. Unexpectedly, a significant decrease in platelet count was observed in 5 of 18 monkeys. Antibodies against F(ab')2 hC4G1 were detected in the plasma of these monkeys by ELISA. Antibody activity in the plasma of these monkeys was significantly correlated with the intensity of platelet decrease (r = 0.84). The natural monkey antibodies to F(ab')2 hC4G1 were directed against the C-terminal region of F(ab')2 fragment common to all human and humanized IgG antibodies. Natural homo-reactive antibodies were also detected in human plasma from 15 of 40 healthy volunteers. Specificity was closely similar to that of the monkey antibodies. Affinity-purified human homoreactive antibodies enhanced phagocytosis of platelets treated with the F(ab')2 hC4G1. Monkey plasma with high homo-reactive antibody activity was confirmed to decrease platelet count when administered together with F(ab')2 hC4G1 to a monkey with low antibody activity. These results suggest that F(ab')2 of humanized and human antibodies causes elimination of the corresponding antigens from the circulation by homo-reactive antibodies.
Conversion of 5-Hydroxytryptophan into Serotonin by Tryptophan Decarboxylase in Plants,Escherichia coli, and Yeast (2008)

The L-tryptophan decarboxylase (TDC) gene of rice was heterologously expressed in various organisms. Transgenic rice overexpressing TDC showed accumulation of serotonin upon 5-hydroxytryptophan treatment, which was consistent with the in vitro 5-hydroxytryptophan decarboxylase enzyme activity of purified recombinant rice TDC in a pyridoxal phosphate-dependent manner. Recombinant yeast harboring TDC produced serotonin at the expense of the endogenous 5-hydroxytryptophan levels.
High average power diamond Raman laser (2011)

We report a pulsed Raman laser at 1193 nm based on synthetic diamond crystals with a record output power of 24.5 W and a slope efficiency of 57%. We compared the performance of an anti-reflection coated crystal at normal incidence with a Brewster cut sample. Raman oscillation was achieved at both room temperature and under cryogenic operation at 77 K. Modeling of these experiments allowed us to confirm the value of Raman gain coefficient of diamond, which was found to be 13.5 ± 2.0 cm/GW for a pump wavelength of 1030 nm.
Efficient implementations and alternative architectures for OFDM-OQAM systems (2001)

We derive new implementations for baseband and passband orthogonal frequency-division multiplexing based on offset QAM (OFDM-OQAM), which nearly halve the number of arithmetic operations required every symbol period by exploiting the symmetries in the transmitted sequences. We also propose a novel scheme, named conjugate, that employs two different filters being the time-reversed version of each other: one in the modulator for the even subchannels and in the demodulator for the odd ones, and the other in the modulator for the odd subchannels and in the demodulator for the even ones. We formulate both baseband and passband versions of this scheme in which the constraints for the filter design are loosened, requiring only amplitude tailoring of its frequency response. We derive efficient implementations for the conjugate scheme, which exhibit a significantly lower complexity than previous implementations of the traditional OFDM-OQAM scheme.
The origin of the first sharp diffraction peak in the structure factor of covalent glasses and liquids (1992)

It is proposed that the first sharp diffraction peak (FSDP) in the structure factor of network glasses and liquids is a pre-peak in the concentration-concentration structure factor due to the chemical ordering of interstitial voids around cation-centred clusters in the structure. This model can predict quantitatively the positions of the FSDP for a wide range of oxide and chalcogenide glasses and liquids, and can also successfully rationalize the anomalous temperature and pressure behaviour of the FSDP intensity, as well as the effect of the incorporation of network modifiers.
Common Structural Basis for Constitutive Activity of the Ghrelin Receptor Family (2004)

Three members of the ghrelin receptor family were characterized in parallel: the ghrelin receptor, the neurotensin receptor 2 and the orphan receptor GPR39. In transiently transfected COS-7 and human embryonic kidney 293 cells, all three receptors displayed a high degree of ligand-independent signaling activity. The structurally homologous motilin receptor served as a constitutively silent control; upon agonist stimulation, however, it signaled with a similar efficacy to the three related receptors. The constitutive activity of the ghrelin receptor and of neurotensin receptor 2 through the G(q), phospholipase C pathway was approximately 50% of their maximal capacity as determined through inositol phosphate accumulation. These two receptors also showed very high constitutive activity in activation of cAMP response element-driven transcription. GPR39 displayed a clear but lower degree of constitutive activity through the inositol phosphate and cAMP response element pathways. In contrast, GPR39 signaled with the highest constitutive activity in respect of activation of serum response element-dependent transcription, in part, possibly, through G(12/13) and Rho kinase. Antibody feeding experiments demonstrated that the epitope-tagged ghrelin receptor was constitutively internalized but could be trapped at the cell surface by an inverse agonist, whereas GPR39 remained at the cell surface. Mutational analysis showed that the constitutive activity of both the ghrelin receptor and GPR39 could systematically be tuned up and down depending on the size and hydrophobicity of the side chain in position VI:16 in the context of an aromatic residue at VII:09 and a large hydrophobic residue at VII:06. It is concluded that the three ghrelin-like receptors display an unusually high degree of constitutive activity, the structural basis for which is determined by an aromatic cluster on the inner face of the extracellular ends of TMs VI and VII.
Observation of a nonlocal Pancharatnam phase shift in the process of induced coherence without induced emission (1994)

A Pancharatnam phase shift, which is similar to Berry's topological phase, is introduced into the idler path between two down-converters in an experiment on induced coherence without induced emission. Although the idler beams in such an experiment do not take part in interference, the Pancharatnam phase shift is observable in the interference of the signal beams. This is clearly a nonlocal manifestation of Pancharatnam's phase.
A Common Site of the Fc Receptor γ Subunit Interacts with the Unrelated Immunoreceptors FcαRI and FcϵRI (2006)

The transmembrane (TM) region of the Fc receptor-gamma (FcRgamma) chain is responsible for the association of this ubiquitous signal transduction subunit with many immunoreceptor ligand binding chains, making FcRgamma key to a number of leukocyte activities in immunity and disease. Some receptors contain a TM arginine residue that interacts with Asp-11 of the FcRgamma subunit, but otherwise the molecular basis for the FcRgamma subunit interactions is largely unknown. This study reports residues in the TM region of the FcRgamma subunit are important for association with the high affinity IgE receptor FcepsilonRI and a leukocyte receptor cluster member, the IgA receptor FcalphaRI. FcRgamma residue Leu-21 was essential for surface expression of FcepsilonRIalpha/gamma2 and Tyr-8, Leu-14, and Phe-15 contributed to expression. Likewise, detergent-stable FcRgamma association with FcalphaRI was also dependent on Leu-14 and Leu-21 and in addition required residues Tyr-17, Tyr-25, and Cys-26. Modeling the TM regions of the FcRgamma dimer indicated these residues interacting with both FcalphaRI and FcepsilonRI are near the interface between the two FcRgamma TM helices. Furthermore, the FcRgamma residues interacting with FcalphaRI form a leucine zipper-like interface with mutagenesis confirming a complementary interface comprising FcalphaRI residues Leu-217, Leu-220, and Leu-224. The dependence of these two nonhomologous receptor interactions on FcRgamma Leu-14 and Leu-21 suggests that all the associated Fc receptors and the activating leukocyte receptor cluster members interact with this one site. Taken together these data provide a molecular basis for understanding how disparate receptor families assemble with the FcRgamma subunit.
Erhardorina n. g., Ascogregarina polynesiensis n. sp., Eimeria golemanskii n. sp., Isospora tamariscini n. sp., Gregarina kazumii n. nom., New Combinations and Emendations in the Names of Apicomplexan Protozoa1 (1985)

On the basis of a review of the approximately 4300 species of apicomplexan protozoa, the following new species, new names, new combinations, and emendations are given: NEW GENUS, Erhardovina; NEW SPECIES, Ascogregarina polynesiensis, Eimeria golemanskii, Isospora tamariscini; NEW NAME, Gregarina kazumii; NEW COMBINATIONS, Ascogregarina brachyceri (Purrini, 1980), Erhardovina euzeti (Lipa, 1981), E. scutovertexi (Erhardová, 1955), Haemorhormidium batrachi (Chaudhuri & Choudhury, 1983); EMENDATIONS, Selenidium francianum (Arvy, 1952) Tuzet & Ormières, 1965, Pyxinioides bolitoides D. P. Henry, 1938, P. japonicus H. Hoshide, 1951, P. kamenote H. Hoshide, 1951, P. kurofuji H. Hoshide, 1951, P. oshoroensis H. Hoshide, 1951, P. pugetensis D. P. Henry, 1938, Gregarina levinei Haldar & Sarkar, 1980, Retractocephalus halticae Haldar, Chakraborty & Kundu, 1982, Cnemidospora schizophylli Tuzet & Guerin, 1947, Grebneckiella indica (Merton, 1911) Watson, 1916, Quadruspinospora atractomorphae Haldar & Chakraborty, 1978, Haemogregarina acipenseri Nawrotzky, 1914, H. lobianci Yakimov & Kohl-Yakimov, 1912, H. yakimovikohlae Wladimiroff, 1910, Hepatozoon luehi (Sambon, 1909) Pessoa, Cavalheiro & de Souza, 1970, Eimeria beyerae Ovezmukhammedov, 1977, E. (?) gigantea (Labbé, 1896) Reichenow, 1921, E. (?) labbei Hardcastle, 1943, E. rufi Prasad, 1960, E. (?) scylii (Drago, 1902) Levine & Becker, 1933, Isospora corvi Ray, Shivnani, Oommen & Bhaskaran, 1952, I. melopsittaci Bhatia, Chauhan, Arora & Agrawal, 1973, I. seicerci Ray, Shivnani, Oommen & Bhaskaran, 1952, I. stomatici Chakravarty & Kar, 1944, I. triffitae Nukerbaeva & Svanbaev, 1973, Wenyonella mackinnonae Misra, 1947, Octosporella sanguinolentae Ovezmukhammedov, 1975, Lankesterella millani Alvarez Calvo, 1975, Sarcocystis woodhousei Dogel', 1916, Haemoproteus lari Yakunin, 1972, Babesia ninakohlyakimovae (Yakimoff & Shokhor, 1916), Theileria ninakohlyakimovae (Yakimov, 1916) Krylov, 1974, Haemohormidium batrachi (Chaudhuri & Choudhury, 1983).
Novel therapeutic targets along the Th17 pathway (2009)

The recent discovery of IL-17-producing CD4(+) Th subset significantly revised the Th1/Th2 dichotomy model proposed by Mosmann and Coffman almost two decades ago. Th17 cells are involved in the pathogenesis of many human autoimmune diseases. Th17 cells, their developmental pathways and their effector functions, therefore, provide novel therapeutic targets.
Epigenetic Regulation of Immune Checkpoints: Another Target for Cancer Immunotherapy? (2016)

Epigenetic changes in oncogenes and tumor-suppressor genes contribute to carcinogenesis. Understanding the epigenetic and genetic components of tumor immune evasion is crucial. Few cancer genetic mutations have been linked to direct correlations with immune evasion. Studies on the epigenetic modulation of the immune checkpoints have revealed a critical interaction between epigenetic and immune modulation. Epigenetic modifiers can activate many silenced genes. Some of them are immune checkpoints regulators that turn on immune responses and others turn them off resulting in immune evasion. Many forms of epigenetic inheritance mechanisms may play a role in regulation of immune checkpoints including: covalent modifications, noncoding RNA and histone modifications. In this review, we will show how the potential interaction between epigenetic and immune modulation may lead to new approaches for specific epigenome/immunome-targeted therapies for cancer.
MLL fusion proteins link transcriptional coactivators to previously active CpG-rich promoters (2014)

Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show that only two functional modules are necessary and sufficient for target recognition: those that bind to non-methylated CpGs and di-/tri-methylated histone H3 lysine 36 (H3K36me2/3). An artificial protein composed of the two targeting modules and an interaction domain for AF4-family coactivators can functionally substitute for MLL fusion proteins. Because H3K36me2/3 markers are indicative of active transcription, MLL fusion proteins target previously active CpG-rich genes and activate transcription by recruiting coactivators thereto. Our results indicate that such chromatin context-dependent gene activation is the fundamental mechanism by which MLL fusion proteins maintain the expression of the cellular memory/hematopoietic stem cell program genes.
Cytokines and Nitric Oxide in Islet Inflammation and Diabetes (1996)

Cytokines released by both T lymphocytes and activated macrophages, in particular interleukin-1 (IL-1), have been implicated as immunological effector molecules that both inhibit insulin secretion from the pancreatic beta cell and induce beta-cell destruction. Recent findings have demonstrated that production of the free radical nitric oxide (NO), resulting from the expression of the cytokine-inducible isoform of NO synthase (iNOS), mediates these deleterious effects. The cellular mechanism responsible for inhibition of beta-cell function and destruction by NO involves, in part, inactivation of enzymes specifically localized to the beta-cell mitochondria that contain iron- sulfur centers or clusters. Intraislet release of IL-1 also inhibits beta-cell function by this same cellular mechanism involving the overproduction of NO. In addition, the cytokine, IL-1, induces the co-expression of both iNOS and the cytokine-inducible isoform of cyclooxygenase, COX-2. The expression of COX-2 results in the overproduction of the proinflammatory prostaglandins and thromboxanes. Furthermore, NO produced by iNOS directly stimulates the activities of both constitutive and inducible isoforms of COX, further augmenting the overproduction of these proinflammatory mediators, NO and prostaglandins, which may be important in initiating or maintaining the inflammatory response and destruction of the beta cell associated with autoimmune diabetes.
DNA sequences from the str operon of Escherichia coli. (1980)

The str operon at 72 min on the Escherichia coli chromosome contains genes for ribosomal proteins (r-proteins) S12 (str or rpsL) and S7 (rpsG) and elongation factors G (fus) and Tu (tufA). The sequence of the entire S12 gene, the S12-S7 intercistronic region, and the beginning of the S7 gene is reported. Also, the sequence of the end of the S7 gene, the S7-G intercistronic region, and the beginning of the elongation fractor G gene is reported. The S12-S7 intercistronic region is 96 base pairs long, in contrast to other intercistronic regions in r-protein operons which have been found to vary from 3 to 66 base pairs. The S7-G intercistronic region is only 27 bases long, supporting the previous conclusion that r-protein and elongation factor genes are co-transcribed. A comparison of translation initiation sites of the S12 and S7 genes, and other examples of co-transcribed r-protein genes, reveals no obvious features that could account for equimolar synthesis of all r-proteins. The codon usage in the S12 and S7 genes follows the pattern observed in other r-protein genes; that is, there is a highly preferential usage of codons recognized by the most abundant of isoaccepting tRNA species. This pattern could reflect the cell's need for efficient translation or minimal errors, or both, in r-protein synthesis.
INTERLEUKIN-17 ANTAGONISM INHIBITS ACUTE BUT NOT CHRONIC VASCULAR REJECTION1 (2001)

These findings support a role for IL-17 in the immunopathogenesis of acute vascular rejection and demonstrate the potential of IL-17 antagonism for therapy. By contrast, IL-17 antagonism does not appear to prevent ensuing chronic graft vascular disease, in particular neointimal formation.
Depressed low frequency power of heart rate variability as an independent predictor of sudden death in chronic heart failure (2000)

Depressed heart rate variability has independent prognostic value in patients with chronic heart failure; spectral analysis identifies an increased risk for sudden death in these patients.
Reduction of 2,3-Dihydroisoxazoles to β-Amino Ketones and β-Amino Alcohols (2005)

[chemical reaction: see text]. We report the reduction of 2,3-dihydroisoxazoles to beta-amino ketones and beta-amino alcohols. The latter are obtained in high diastereoselectivity with preference for the syn isomer.
Performance Characteristics of Four Automated Natriuretic Peptide Assays (2005)

Measurement of circulating B-type natriuretic peptide (BNP) and N-terminal proBNP (NT-proBNP) can identify patients with heart failure and guide therapy. The limit of detection, linearity, imprecision, method comparison, analytic concordance, and reference intervals of the Access 2 BNP (Biosite, San Diego, CA), ADVIA Centaur BNP (Bayer Diagnostics, Tarrytown, NY), AxSYM BNP (Abbott Diagnostics, Abbott Park, IL), and E170 NT-proBNP (Roche Diagnostics, Indianapolis, IN) methods were evaluated. The Triage meter BNP assay (Biosite) was the comparison method. Imprecision testing showed total coefficients of variation of 4.1%, 4.4%, 5.5%, and 0.8% for the Access 2, ADVIA Centaur, AxSYM, and E170, respectively. Relative to the Triage meter, method comparison revealed a slope of 0.96 and r = 0.95, a slope of 0.77 and r = 0.92, a slope of 1.13 and r = 0.94, and a slope of 8.8 and r = 0.80 for the Access 2, ADVIA Centaur, AxSYM, and E170, respectively. Overall analytic concordance values with the Triage meter were 95.9%, 92.9%, 92.4%, and 84.3% for the Access 2, ADVIA Centaur, AxSYM, and E170, respectively. All automated natriuretic peptide methods showed acceptable analytic performance.
RACIAL DIFFERENCES IN TUMOR VOLUME AND PROSTATE SPECIFIC ANTIGEN AMONG RADICAL PROSTATECTOMY PATIENTS (1999)

Racial difference in PSA persists, despite rigorous covariate adjustment, and further study is needed to explain this PSA difference.
Remote Oblivious Storage: Making Oblivious RAM Practical (2011)

Remote storage of data has become an increasingly attractive and advantageous option, especially due to cloud systems. While encryption protects the data, it does not hide the access pattern to the data. A natural solution is to access remote storage using an Oblivious RAM (ORAM) which provably hides all access patterns. While ORAM is asymptotically efficient, the best existing scheme (Pinkas and Reinman, Crypto'10) still has considerable overhead for a practical implementation: for M stored items, it stores 4 times and sometimes 6 times more items remotely, requires O(log2 M) round trips to storage server per request, and periodically blocks all data requests to shuffle all storage (which is a lengthy process). In this paper, we first define a related notion to ORAM, oblivious storage (OS), which captures more accurately and naturally the security setting of remote storage. Then, we propose a new ORAM/OS construction that solves the practicality issues just outlined: it has a storage constant of ~ 1, achieves O(1) round trips to the storage server per request, and allows requests to happen concurrently with shuffle without jeopardizing security. Our construction consists of a new organization of server memory into a flat main part and a hierarchical shelter, a client-side index for rapidly locating identifiers at the server, a new shelter serving requests concurrent with the shuffle, and a data structure for locating items efficiently in a partially shuffled storage.