gebhart/patrepeval huggingface dataset:
Improved renal function in mouse kidney allografts lacking MHC class I antigens. (1993)

The immunological responses that lead to rejection of organ and tissue transplants are triggered by the recognition of proteins encoded within the MHC. The relative contributions of responses directed toward MHC class I compared with class II in the loss of functional integrity of vascularized organ grafts have been difficult to define. The recent development of technologies which allow the generation of mice in which specific genes have been altered by gene targeting offers a new approach to addressing this question. We examine here the rejection of kidney allografts from mice lacking native MHC class I Ag. These mice were obtained from embryonic stem cells in which the beta 2 microglobulin (beta 2m) gene had been disrupted by homologous recombination. We found a significant improvement in function of renal allografts from MHC class I-deficient donors compared with allografts from donors with normal MHC class I expression. Surprisingly, the improved function of the MHC class I-deficient grafts was not associated with differences in mononuclear inflammatory cell infiltration of these grafts nor in differences in alloreactive proliferative or cytotoxic T cell responses. However, we did find differences in alloantibody response between the groups. Recipients of control allografts produced antibodies against both donor MHC class I and II, whereas recipients of MHC class I-deficient grafts formed alloantibodies primarily against donor MHC class II Ag. These studies confirm that immune responses directed toward donor MHC class I alloantigens contribute to kidney transplant dysfunction in this model. Also, these findings suggest that, at least for renal transplants, genetic manipulations which reduce MHC class I expression may be effective in overcoming some of the effects of MHC incompatibility.
Monte Carlo vs Molecular Dynamics for Conformational Sampling (1996)

A comparison study has been carried out to test the relative efficiency of Metropolis Monte Carlo and molecular dynamics simulations for conformational sampling. The test case that has been examined is liquid hexane. OPLS potential functions have been used with sampling of external motions and internal angle bending and torsions. The BOSS 3.6 and AMBER 4.0 programs were used to perform the internal-coordinate Monte Carlo and Cartesian molecular dynamics simulations, respectively, for samples of 267 molecules in the NPT ensemble at 25 °C and 1 atm with periodic boundary conditions. The initial configurations of the system were equilibrated with the hexane molecules in the all trans configuration. The major findings are (1) the Monte Carlo and molecular dynamics results for thermodynamic properties and conformer populations are in accord, (2) the conformer populations reach equilibrium in ca. 107 Monte Carlo configurations or 100 ps of molecular dynamics, and (3) the molecular dynamics calculations require 1.6−3.8 times more computer time to achieve the same level of convergence as the Monte Carlo simulations. The viability of internal-coordinate Monte Carlo methodology contrasts with earlier notions on the inefficiency of Cartesian Monte Carlo methods. Monte Carlo sampling in related contexts such as for side-chain torsional motion in proteins appears promising.
Increased intragraft IL‐15 mRNA expression after liver transplantation (1998)

To study T-cell/macrophage interactions at the molecular level in clinical allograft rejection, we measured intragraft mRNA expression of the T-cell derived cytokine IL-2 and the macrophage derived chemokine IL-15, a novel cytokine associated with T-cell activation, in post-transplant liver biopsies (n = 33) and in non-transplanted control liver tissue by reverse transcriptase-polymerase chain reaction (RT-PCR). We analyzed biopsies without evidence of rejection (n = 12), with spontaneously resolving histological rejection (n = 10), or with histological rejection accompanied with clinical rejection (n = 11) defined by rising serum bilirubin and aspartate amino transaminase levels. IL-15 mRNA expression was present in the majority of post-transplant liver biopsies (91%, 30/33) and was significantly upregulated as compared with non-transplanted liver tissue (p = 0.005). However, the increased intragraft IL-15 mRNA level was not indicative for rejection. In contrast to intragraft IL-15 mRNA expression, IL-2 mRNA transcription was measured in the minority of the post-transplant liver biopsies (15%, 5/33) and not detectable in control specimens. In addition, IL-2 mRNA was almost specifically measured in rejection biopsies concurrent with graft dysfunction (36%, 4/11 versus 1/22 without clinical rejection; p = 0.03). No relation between intragraft IL-2 and IL-15 mRNA expression was found. The IL-15 mRNA expression levels were not higher in the IL-2 negative rejections compared with those in IL-2 positive rejections. To conclude, in contrast to IL-2, the function of IL-15 in T-cell mediated rejection remains unclear. The overall high IL-15 mRNA levels in sites of immune responses suggests that the macrophage-derived mediator IL-15 is involved in a constant flow of T-cells from the circulation into the graft.
A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. (1996)

A polymorphic C-->T transition located on the human Y chromosome was found by the systematic comparative sequencing of Y-specific sequence-tagged sites by denaturing high-performance liquid chromatography. The results of genotyping representative global indigenous populations indicate that the locus is polymorphic exclusively within the Western Hemisphere. The pre-Columbian T allele occurs at > 90% frequency within the native South and Central American populations examined, while its occurrence in North America is approximately 50%. Concomitant genotyping at the polymorphic tetranucleotide microsatellite DYS19 locus revealed that the C-->T mutation displayed significant linkage disequilibrium with the 186-bp allele. The data suggest a single origin of linguistically diverse native Americans with subsequent haplotype differentiation within radiating indigenous populations as well as post-Columbian European and African gene flow. The mutation may have originated either in North America at a very early time during the expansion or before it, in the ancestral population(s) from which all Americans may have originated. The analysis of linkage of the DYS199 and the DYS19 tetranucleotide loci suggests that the C-->T mutation may have occurred around 30,000 years ago. We estimate the nucleotide diversity over 4.2 kb of the nonrecombining portion of the Y chromosome to be 0.00014. compared to autosomes, the majority of variation is due to the smaller effective population size of the Y chromosome rather than selective sweeps. There begins to emerge a pattern of pronounced geographical localization of Y-specific nucleotide substitution polymorphisms.
Official ARPA-Internet protocols (1985)

This RFC identifies the documents specifying the official protocols
used in the ARPA-Internet. Annotations identify any revisions or
changes planned. This memo is an official status report on the
protocols used in the DARPA research community. See RFC-991.
Human Progesterone Receptor Displays Cell Cycle-Dependent Changes in Transcriptional Activity (2005)

The human progesterone receptor (PR) contains multiple Ser-Pro phosphorylation sites that are potential substrates for cyclin-dependent kinases, suggesting that PR activity might be regulated during the cell cycle. Using T47D breast cancer cells stably transfected with an mouse mammary tumor virus (MMTV) chloramphenicol acetyltransferase reporter (Cat0) synchronized in different phases of the cell cycle, we found that PR function and phosphorylation is remarkably cell cycle dependent, with the highest activity in S phase. Although PR expression was reduced in the G2/M phase, the activity per molecule of receptor was markedly reduced in both G1 and G2/M phases compared to the results seen with the S phase of the cell cycle. Although PR is recruited to the MMTV promoter equivalently in the G1 and S phases, recruitment of SRC-1, SRC-3, and, consequently, CBP is reduced in G1 phase despite comparable expression levels of SRC-1 and SRC-3. In G2/M phase, site-specific phosphorylation of PR at Ser162 and at Ser294, a site previously reported to be critical for transcriptional activity and receptor turnover, was abolished. Treatment with the histone deacetylase inhibitor trichostatin A elevated G1 and G2/M activity to that of the S phase, indicating that the failure to recruit sufficient levels of active histone acetyltransferase is the primary defect in PR-mediated transactivation.
Sample-efficient adaptive text-to-speech (2018)

We present a meta-learning approach for adaptive text-to-speech (TTS) with few data. During training, we learn a multi-speaker model using a shared conditional WaveNet core and independent learned embeddings for each speaker. The aim of training is not to produce a neural network with fixed weights, which is then deployed as a TTS system. Instead, the aim is to produce a network that requires few data at deployment time to rapidly adapt to new speakers. We introduce and benchmark three strategies: (i) learning the speaker embedding while keeping the WaveNet core fixed, (ii) fine-tuning the entire architecture with stochastic gradient descent, and (iii) predicting the speaker embedding with a trained neural network encoder. The experiments show that these approaches are successful at adapting the multi-speaker neural network to new speakers, obtaining state-of-the-art results in both sample naturalness and voice similarity with merely a few minutes of audio data from new speakers.
Site-Specific Binding of Quinones to Proteins through Thiol Addition and Addition−Elimination Reactions (2005)

Ubiquinone-0, menaquinone-0, and 2,3,5-trimethyl-1,4-benzoquinone were site-specifically bound to free cysteine of proteins (yeast iso-1 cytochrome c as a model protein) through thioether bond formation. Model thioether quinone conjugates showed unexpected reactivity to cysteine of proteins as their parent quinones by thiol addition-elimination reaction. Cyclic voltammetry studies of the model compounds showed only minor differences in their redox potentials as compared to their parent quinones. Thioether ligation provides a general, simple, and fast method to construct model quinone protein systems. In addition, these studies also contribute to the understanding of biological activities, toxicity, and anti-cancer mechanism of quinones and thioether quinone adducts.
Affinity Extraction into Carbon Dioxide. 1. Extraction of Avidin Using a Biotin-Functional Fluoroether Surfactant (1997)

Carbon dioxide is a naturally abundant, environmentally benign solvent whose use, like water, in a process is not regulated by either EPA or FDA. As such, CO2 would be an ideal medium to use in a liquid−liquid extraction process involving cell culture broth, in that contamination of the aqueous phase with residual organic would not be an issue. Unfortunately, amino acids and proteins are essentially insoluble in carbon dioxide. Further, alkyl-functional surfactants, which have been shown to allow extraction of proteins into conventional organic solvents, exhibit very poor or negligible solubility in CO2 at pressures below 50 MPa. Fortunately, recent work has shown that replacement of the alkyl hydrophobic portion of a surfactant with either fluorinated or siloxane-functional oligomers allows for high solubility in carbon dioxide and micelle formation. Consequently, biotinyl-fluoroether-functional surfactants have been generated and used to extract avidin into carbon dioxide. We extracted avidin into carbon dioxide via inverse and three-phase emulsions. We observed that the amount of avidin extracted via three-phase emulsion is twice as great as the protein extracted using an inverse emulsion.
Total synthesis and further characterization of the .gamma.-carboxyglutamate-containing "sleeper" peptide from Conus geographus venom (1987)

The total synthesis of the Gla-containing "sleeper" peptide (Gly-Glu-Gla-Gla-Leu-Gln-Gla-Asn-Gln-Gla-Leu-Ile-Arg-Gla-Lys-Ser-Asn-NH2 ) from Conus geographus is described. A new strategy for the synthesis of acid-sensitive peptide amides was developed, which allowed complete deprotection and cleavage of the L-gamma-carboxyglutamate-containing peptide from the 2,4-dimethoxybenzhydrylamine resin. Synthetic sleeper peptide, after preparative high-performance liquid chromatography (HPLC) purification, was shown to be identical with the native peptide by all criteria (coelution experiments of HPLC, sequence analysis, and biological activity). In addition, a developmental switch in the behavioral symptoms induced by the peptide after intracerebral administration in mice was documented. At low doses of the peptide (4-30 pmol/g), a sleeplike state was induced in mice under 2 weeks old; in contrast, older mice became markedly hyperactive. It is proposed that, in the presence of Ca2+, the sleeper peptide assumes an alpha-helical configuration in which all the gamma-carboxyglutamate residues are located on the same side of the alpha-helix.
Signal-to-noise ratio study of full-field Fourier-domain optical coherence tomography (2005)

We report a new approach in optical coherence tomography (OCT) called full-field Fourier-domain OCT (3F-OCT). A three-dimensional image of a sample is obtained by digital reconstruction of a three-dimensional data cube, acquired with a Fourier holography recording system, illuminated with a swept source. We present a theoretical and experimental study of the signal-to-noise ratio of the 3F-OCT approach versus serial image acquisition (flying-spot OCT) approach.
High‐yield method for immobilization of enzymes (1980)

Two types of polyethylenimine-coated glass microbeads (13-44 micrometer) were synthesized and used for the immobilization of glucose oxidase from Aspergillus niger and catalase from A. niger and beef liver. The two types of beads were distinguishable by differences in their surface topography. Immobilizations were performed by adsorption followed by treatment with glutaraldehyde. The immobilized-enzyme activities per unit support of all of the enzymes tested were compared with and found to be superior to the immobilized activities attainable on aminopropyl-activated glass microbeads. When enzyme was present in less than saturating amounts, the coated beads were able to remove 100% of the glucose oxidase activity initially present in the immobilization solution, with 78-87% of that activity expressed on the support surface. Bound glucose oxidase was more stable to thermal inactivation than native enzyme.
Erythrocytes and the regulation of human skeletal muscle blood flow and oxygen delivery: role of erythrocyte count and oxygenation state of haemoglobin (2006)

Blood flow to dynamically contracting myocytes is regulated to match O(2) delivery to metabolic demand. The red blood cell (RBC) itself functions as an O(2) sensor, contributing to the control of O(2) delivery by releasing the vasodilators ATP and S-nitrosohaemoglobin with the offloading of O(2) from the haemoglobin molecule. Whether RBC number is sensed remains unknown. To investigate the role of RBC number, in isolation and in combination with alterations in blood oxygenation, on muscle and systemic perfusion, we measured local and central haemodynamics during one-legged knee-extensor exercise ( approximately 50% peak power) in 10 healthy males under conditions of normocythaemia (control), anaemia, anaemia + plasma volume expansion (PVX), anaemia + PVX + hypoxia, polycythaemia, polycythaemia + hyperoxia and polycythaemia + hypoxia, which changed either RBC count alone or both RBC count and oxyhaemoglobin. Leg blood flow (LBF), cardiac output (Q) and vascular conductance did not change with either anaemia or polycythaemia alone. However, LBF increased with anaemia + PVX (28 +/- 4%) and anaemia + PVX + hypoxia (46 +/- 6%) and decreased with polycythaemia + hyperoxia (18 +/- 5%). LBF and Q with anaemia + PVX + hypoxia (8.0 +/- 0.5 and 15.8 +/- 0.7 l min(-1), respectively) equalled those during maximal knee-extensor exercise. Collectively, LBF and vascular conductance were intimately related to leg arterial-venous (a-v) O(2) difference (r(2)= 0.89-0.93; P < 0.001), suggesting a pivotal role of blood O(2) gradients in muscle microcirculatory control. The systemic circulation accommodated to the changes in muscle perfusion. Our results indicate that, when coping with severe haematological challenges, local regulation of skeletal muscle blood flow and O(2) delivery primarily senses alterations in the oxygenation state of haemoglobin and, to a lesser extent, alterations in the number of RBCs and haemoglobin molecules.
cDNA Libraries (1988)

This unit provides a basic description of issues that require careful consideration before undertaking construction of cDNA libraries. Topics include: generating a double-stranded DNA copy of the mRNA, the quality of the mRNA, the relative abundance of the clone of interest, the choice of screening method, the size of the library that will be necessary to include the clone of interest, and choices of linkers or adaptors for insertion into the vector.
Pyrrolnitrin, a New Antibiotic Substance, Produced byPseudomonas (1964)

Journal Article Pyrrolnitrin, a New Antibiotic Substance, Produced by Pseudomonas Get access Kei Arima, Kei Arima Department of Agricultural Chemistry, The University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Hiroshi Imanaka, Hiroshi Imanaka Department of Agricultural Chemistry, The University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Masanobu Kousaka, Masanobu Kousaka Department of Agricultural Chemistry, The University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Akio Fukuta, Akio Fukuta Research Laboratory of Fujisawa Pharmaceutical Industries Co. Ltd. Search for other works by this author on: Oxford Academic Google Scholar Gakuzo Tamura Gakuzo Tamura Department of Agricultural Chemistry, The University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 28, Issue 8, 1 August 1964, Pages 575–576, https://doi.org/10.1080/00021369.1964.10858275 Published: 01 August 1964 Article history Received: 18 June 1964 Published: 01 August 1964
Adhesion Properties of Plasma Sprayed Hydroxylapatite Coatings for Orthopaedic Prostheses (1993)

Using Air Plasma Spraying (APS) and Vacuum Plasma Spraying (VPS) techniques, hydroxylapatite (HA) and mixtures of HA and titanium (Ti) were deposited on a Ti6A14V alloy (and on an AISI 316L steel) subjected to different surface treatments. The deposits were investigated for their crystallinity, thickness, and adhesion properties. Higher adhesion values were obtained with VPS rather than with APS. By utilising VPS, the deposition conditions were selected in order to achieve crystallinity values between 70 and 90%. The adhesion results depend on the crystallinity (increasing with its decrease), on the thickness (decreasing slightly with its increase) and especially on the surface finish of the metallic substrate. A porous Ti precoat was more effective than either chemical etching in HCl or sandblasting; sandblasting being the least effective. In particular, the double deposits consisting of a porous Ti precoat and a successive layer of HA proved to be most interesting for their higher adhesion properties and for their capability of providing primary stability due to the presence of the HA and secondary stability, in the case of its reabsorption, due to the porous metal.
Development of a Real-Time Reverse-Transcription PCR for Detection of Newcastle Disease Virus RNA in Clinical Samples (2004)

A real-time reverse-transcription PCR (RRT-PCR) was developed to detect avian paramyxovirus 1 (APMV-1) RNA, also referred to as Newcastle disease virus (NDV), in clinical samples from birds. The assay uses a single-tube protocol with fluorogenic hydrolysis probes. Oligonucleotide primers and probes were designed to detect sequences from a conserved region of the matrix protein (M) gene that recognized a diverse set (n = 44) of APMV-1 isolates. A second primer-probe set was targeted to sequences in the fusion protein (F) gene that code for the cleavage site and detect potentially virulent NDV isolates. A third set, also directed against the M gene, was specific for the North American (N.A.) pre-1960 genotype that includes the common vaccine strains used in commercial poultry in the United States. The APMV-1 M gene, N.A. pre-1960 M gene, and F gene probe sets were capable of detecting approximately 10(3), 10(2), and 10(4) genome copies, respectively, with in vitro-transcribed RNA. Both M gene assays could detect approximately 10(1) 50% egg infective doses (EID(50)), and the F gene assay could detect approximately 10(3) EID(50). The RRT-PCR test was used to examine clinical samples from chickens experimentally infected with the NDV strain responsible for a recent epizootic in the southwestern United States. Overall, a positive correlation was obtained between the RRT-PCR results and virus isolation for NDV from clinical samples.
Universal Encrypted Deniable Authentication Protocol. (2009)

The notion of deniable authentication protocol was introduced in 1998 by Dwork et al. [11] and Aumann and Rabin [1, 2] independently. As a new cryptographic authentication protocol, a deniable authentication protocol enables an intended receiver to identify the source of a given message without being able to prove the identity of the sender to a third party. Over the past years, many deniable authentication protocols have been proposed. In this paper, we would like to present a universal encrypted deniable authentication protocol from any public key encryption scheme. Provided that the public key encryption scheme is secure, a secure deniable authentication protocol can be directly derived.
Herpes Simplex Virus and Human Cytomegalovirus Replication in WI-38 Cells I. Sequence of Viral Replication (1973)

A comparison, under standardized conditions, of herpes simplex virus (HSV) and human cytomegalovirus (CMV) revealed differences in viral morphology, in the timing of their infectious cycles, and in several morphological events during those cycles. Structural distinctions between the two viruses included the coating of unenveloped cytoplasmic CMV capsids, but not those of HSV, and a variation in the structure of their cores. Since the two cycles were carried out in the same host cell strain under conditions of one-step growth (input multiplicity = 10 PFU/cell), it was possible to construct time scales locating the major events of each cycle. Comparison of the two showed that HSV replicated and released progeny within 8 h postinfection, whereas CMV required 4 days. These results correlated well with those of concurrent plaque assays. Within the longer CMV cycle, most of the major events appeared retarded to a similar degree, and no obvious limiting step in particle production could be identified. Distinctions between the two cycles included the following: condensation of the chromatin in HSV- but not CMV-infected cells; the greater tendency of HSV to produce membrane alterations; and the appearance of cytoplasmic dense bodies in CMV- but not HSV-infected cells. Identification of these differences even under identical conditions of culture and infection strongly implies that they result from intrinsic differences in the nature of the viruses, and are not caused by variations in experimental conditions.