gebhart/patrepeval huggingface dataset:
The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille (2003)

Here we describe the discovery of a group I intron in the DNA polymerase gene of Bacillus thuringiensis phage Bastille. Although the intron insertion site is identical to that of the Bacillus subtilis phages SPO1 and SP82 introns, the Bastille intron differs from them substantially in primary and secondary structure. Like the SPO1 and SP82 introns, the Bastille intron encodes a nicking DNA endonuclease of the H-N-H family, I-BasI, with a cleavage site identical to that of the SPO1-encoded enzyme I-HmuI. Unlike I-HmuI, which nicks both intron-minus and intron-plus DNA, I-BasI cleaves only intron-minus alleles, which is a characteristic of typical homing endonucleases. Interestingly, the C-terminal portions of these H-N-H phage endonucleases contain a conserved sequence motif, the intron-encoded endonuclease repeat motif (IENR1) that also has been found in endonucleases of the GIY-YIG family, and which likely comprises a small DNA-binding module with a globular betabetaalphaalphabeta fold, suggestive of module shuffling between different homing endonuclease families.
Vaccination of adult and newborn mice of a resistant strain (C57BL/6J) against challenge with leukemias induced by Moloney murine leukemia virus. (1985)

Adult or newborn C57BL/6J mice were immunized with isogenic Moloney strain MuLV-induced leukemia cells irradiated with 10,000 rads or treated with low concentrations of formalin. Groups of immunized and control mice were challenged with a range of doses of viable leukemia cells, and tumor deaths were recorded for 90 days after challenge. Then, the doses of challenge cells which produced 50% tumor deaths were calculated for immunized and control mice. The logarithm of their ratio quantified the degree of protection provided by immunization. For adult C57BL/6J mice, a single immunization with MuLV-induced leukemia cells was not effective; either cells plus Bacillus Calmette-Guérin or Corynebacterium parvum, or else two immunizations with irradiated leukemia cells were needed to produce statistically significant increases in the values of the doses of challenge cells which produced 50% tumor deaths. Cross-protection was obtained by immunization with other isogenic MuLV-induced leukemias, but not by immunization with isogenic carcinogen-induced tumors or with an isogenic spontaneous leukemia. For newborn mice, a single injection of irradiated leukemia cells provided 1.3 to 1.5 logs of protection, and admixture of B. Calmette-Guérin or C. parvum increased this protection to 2.4 to 2.7 logs. Since irradiated and frozen-thawed MuLV-induced leukemia cells contained viable MuLV, leukemia cells treated with 0.5 or 1.0% formalin were tested as an alternative. A single injection of formalin-treated isogenic leukemia cells admixed with C. parvum provided between 1.7 and 2.8 logs of protection. These results demonstrate that a single vaccination of newborn animals against a highly antigenic virally induced leukemia produces strong protection against a subsequent challenge with viable leukemia cells.
Hidrolizados de proteína: procesos y aplicaciones (2008)

En la hidrólisis enzimática de proteínas hasta péptidos o aminoácidos, por&#13;\nacción de enzimas proteolíticas, la composición final y, por tanto, el uso de&#13;\nlos hidrolizados dependerá principalmente de la fuente proteica, del tipo de&#13;\nproteasa usada, de las condiciones de hidrólisis y del grado de hidrólisis alcanzado&#13;\nen la reacción. Los hidrolizados se utilizan ampliamente en la tecnología&#13;\nalimentaria por sus propiedades nutricionales o funcionales (solubilidad,&#13;\npoder emulsificante, capacidad espumante). En este trabajo se&#13;\nmuestra la tendencia actual en las técnicas empleadas para la obtención&#13;\nde hidrolizados mediante enzimas y los diferentes métodos usados para el&#13;\ncontrol de estos preparados; se indican además sus posibles aplicaciones.
Robust and fine-grained prosody control of end-to-end speech synthesis (2018)

We propose prosody embeddings for emotional and expressive speech synthesis networks. The proposed methods introduce temporal structures in the embedding networks, thus enabling fine-grained control of the speaking style of the synthesized speech. The temporal structures can be designed either on the speech side or the text side, leading to different control resolutions in time. The prosody embedding networks are plugged into end-to-end speech synthesis networks and trained without any other supervision except for the target speech for synthesizing. It is demonstrated that the prosody embedding networks learned to extract prosodic features. By adjusting the learned prosody features, we could change the pitch and amplitude of the synthesized speech both at the frame level and the phoneme level. We also introduce the temporal normalization of prosody embeddings, which shows better robustness against speaker perturbations during prosody transfer tasks.
Adhesion of Pseudomonas aeruginosa to human buccal epithelial cells: evidence for two classes of receptors (1985)

The adhesion of Pseudomonas aeruginosa strain 492c to trypsinized and untrypsinized buccal epithelial cells (BECs) was studied. Kinetic analysis of the adhesion data, employing a Langmuir absorption isotherm, indicated the presence of two classes of binding sites on untrypsinized BECs: a high affinity - low copy number site (apparent association constant (Ka) approximately equal to 1.57 X 10(-8) mL/cell with ca. 29 binding sites/cell) and a low affinity - high copy number class of binding sites (Ka approximately equal to 4.78 X 10(-10) mL/cell with ca. 264 binding sites/cell). The low affinity - high copy number class of sites was found to be trypsin sensitive. A single class of binding sites was found on trypsinized BECs exhibiting a high affinity - low copy number (Ka approximately equal to 3.70 X 10(-7) mL/cell with ca. 31 binding sites/cell). Positive cooperativity in binding of P. aeruginosa strain 492c to the low affinity - high copy number class site on untrypsinized BECs was demonstrated by analysis of Hill plots of the adhesion data. Sugar inhibition data using a preincubation methodology showed an inhibition of adhesion to trypsinized BECs in the presence of N-acetylneuraminic acid and D-arabinose, while these same two sugars enhanced adhesion to untrypsinized BECs. D-Galactose and N-acetylglucosamine enhanced adhesion to both types of BECs though the latter did to different extents. D-Fucose only inhibited adhesion to untrypsinized BECs.(ABSTRACT TRUNCATED AT 250 WORDS)
Glycopeptide and Lipoglycopeptide Antibiotics (2005)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGlycopeptide and Lipoglycopeptide AntibioticsDan Kahne, Catherine Leimkuhler, Wei Lu, and Christopher WalshView Author Information The Department of Chemistry, Princeton University, Princeton, New Jersey 08544, and the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115 Cite this: Chem. Rev. 2005, 105, 2, 425–448Publication Date (Web):January 22, 2005Publication History Received12 May 2004Published online22 January 2005Published inissue 1 February 2005https://pubs.acs.org/doi/10.1021/cr030103ahttps://doi.org/10.1021/cr030103aresearch-articleACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views7361Altmetric-Citations528LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Antimicrobial agents,Carbohydrates,Monomers,Peptides and proteins,Scaffolds Get e-Alerts
Autonomic diseases: clinical features and laboratory evaluation (2003)

The autonomic nervous system has a craniosacral parasympathetic and a thoracolumbar sympathetic pathway (fig 1) and supplies every organ in the body. It influences localised organ function and also integrated processes that control vital functions such as arterial blood pressure and body temperature. There are specific neurotransmitters in each system that influence ganglionic and post-ganglionic function (fig 2). Figure 1 The autonomic nervous system supply to various organs. Sweat glands (not included) are supplied by cholinergic fibres Reproduced from Jänig W. In: Schmidt RF, Thews G, eds. Physiologie des menschen , 26th ed. Heidelberg: Springer-Verlag, 1995:340–69. Figure 2 Neurotransmitters involved in the parasympathetic and sympathetic pathways that influence ganglionic and post-ganglionic function. ACh, acetylcholine; NA, noradrenaline. Reproduced from Mathias CJ. Autonomic dysfunction. Br J Hosp Med 1987;38:238–43. [OpenUrl][1][PubMed][2] The symptoms and signs of autonomic disease cover a wide spectrum (table 1) that vary depending upon the aetiology (tables 2 and 3). In some they are localised (table 4). Autonomic disease can result in underactivity or overactivity. Sympathetic adrenergic failure causes orthostatic (postural) hypotension and in the male ejaculatory failure, while sympathetic cholinergic failure results in anhidrosis; parasympathetic failure causes dilated pupils, a fixed heart rate, a sluggish urinary bladder, an atonic large bowel and, in the male, erectile failure. With autonomic hyperactivity, the reverse occurs. In some disorders, particularly in neurally mediated syncope, there may be a combination of effects, with bradycardia caused by parasympathetic activity and hypotension resulting from withdrawal of sympathetic activity. The history is of particular importance in the consideration and recognition of autonomic disease, and in separating dysfunction that may result from non-autonomic disorders. View this table: Table 1 Some clinical manifestations of autonomic dysfunction View this table: Table 2 Outline classification of autonomic diseases View this table: Table 3 Drugs, chemicals, poisons, and toxins causing autonomic dysfunction View this table: Table 4 Examples of localised autonomic disorders ### General aspects Autonomic disease may present at any age … [1]: {openurl}?query=rft.jtitle%253DBritish%2Bjournal%2Bof%2Bhospital%2Bmedicine%26rft.stitle%253DBr%2BJ%2BHosp%2BMed%26rft.aulast%253DMathias%26rft.auinit1%253DC.%2BJ.%26rft.volume%253D38%26rft.issue%253D3%26rft.spage%253D238%26rft.epage%253D243%26rft.atitle%253DAutonomic%2Bdysfunction.%26rft_id%253Dinfo%253Apmid%252F2823944%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [2]: /lookup/external-ref?access_num=2823944&link_type=MED&atom=%2Fjnnp%2F74%2Fsuppl_3%2Fiii31.atom
Quality Characteristics of Yellow-Seeded Brassica Seed Meals: Protein, Carbohydrate, and Dietary Fiber Components (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuality Characteristics of Yellow-Seeded Brassica Seed Meals: Protein, Carbohydrate, and Dietary Fiber ComponentsJoseph Simbaya, Bogdan A. Slominski, Gerhard Rakow, Lloyd D. Campbell, R. Keith Downey, and J. Milton BellCite this: J. Agric. Food Chem. 1995, 43, 8, 2062–2066Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/jf00056a020https://doi.org/10.1021/jf00056a020research-articleACS PublicationsRequest reuse permissionsArticle Views747Altmetric-Citations106LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Agarose droplet microfluidics for highly parallel and efficient single molecule emulsion PCR (2010)

An agarose droplet method was developed for highly parallel and efficient single molecule emulsion PCR. The method capitalizes on the unique thermoresponsive sol-gel switching property of agarose for highly efficient DNA amplification and amplicon trapping. Uniform agarose solution droplets generated via a microfluidic chip serve as robust and inert nanolitre PCR reactors for single copy DNA molecule amplification. After PCR, agarose droplets are gelated to form agarose beads, trapping all amplicons in each reactor to maintain the monoclonality of each droplet. This method does not require cocapsulation of primer labeled microbeads, allows high throughput generation of uniform droplets and enables high PCR efficiency, making it a promising platform for many single copy genetic studies.
Signal Transduction by the Platelet-derived Growth Factor Receptor (1988)

When platelet-derived growth factor (PDGF) binds to its receptor on the surface of a mesenchymal cell, it stimulates almost every known type of hormone-activated signal transduction pathway. Within seconds, tyrosine kinase activity is stimulated (Nishimura et al. 1982; Ek et al. 1983; Frackelton et al. 1984), phosphatidylinositol (PtdIns) is hydrolyzed (Habenicht et al. 1981), the cellular pH changes (L'Allemain et al. 1984), and cytosolic calcium increases (Escobedo et al. 1988a). Other rapid responses include dramatic changes in the cytoskeleton, enhanced expression of a group of genes (Kelly et al. 1983; Greenberg and Ziff 1984), elevation in the level of cellular cAMP (Rozengurt et al. 1983), and internalization of the receptor. How these events culminate in DNA synthesis is still unknown. However, recent progress in understanding the structure and function of the PDGF receptor is providing mechanistic insight into the interrelationships among the pathways and their roles in mitogenesis.
Power adjustable visible supercontinuum generation using amplified nanosecond gains-witched laser diode (2008)

Supercontinuum (SC) light with a continuous spectrum covering 0.45-1.2 microm is scaled from 250-740 mW by varying the repetition rate of an amplified, frequency doubled, telecom laser diode. Efficient SC generation requires minimal non-linearity in the amplifier and anomalous dispersion pumping close to the fiber zero dispersion wavelength. Based on simulations, we present a 2-stage design that separates pulse break-up from spectral broadening to enhance the SC bandwidth for quasi-CW pumping.
Lymphocyte-specific chemokine receptor CXCR3: regulation, chemokine binding and gene localization (1998)

Expression of CXCR3, the receptor for the CXC chemokines IFN-gamma-inducible 10-kDa protein (IP10) and monokine induced by IFN-gamma (Mig), in human T lymphocytes and their responses to IP10 and Mig were analyzed. About 40 % of resting T lymphocytes (and low numbers of B cells and natural killer cells) stained positive for CXCR3 but these cells did not express CXCR3 transcripts and did not respond to these chemokines. However, treatment with IL-2 with or without addition of phytohemagglutinin for 10 or more days resulted in cultures of fully responsive, CXCR3-positive T lymphocytes. Treatment with anti-CD3 antibodies in the presence or absence of soluble anti-CD28 antibodies was inhibitory. Addition of chondroitin sulfate C to CXCR3-expressing murine pre-B cells allowed the determination of high-affinity binding for Mig and IP10 with Kd of 0.9-1.2 nM and 0.2-0.3 nM, respectively, and 1.3 x 10(4) binding sites per cell. The gene for CXCR3 was localized on human chromosome Xq13 which is in clear contrast to all other chemokine receptor genes, suggesting unique function(s) for this receptor and its ligands that may lie beyond their established role in T cell-dependent immunity.
Information storage in neural networks with low levels of activity (1987)

The Hopfield model of a neural network is extended to allow for the storage and retrieval of biased patterns, {${\ensuremath{\xi}}_{i}^{\ensuremath{\mu}}$}, where ${N}^{\mathrm{\ensuremath{-}}1}$${\mathcal{J}}_{i}^{N}$${\ensuremath{\xi}}_{i}^{\ensuremath{\mu}}$=a is arbitrary. Such patterns represent levels of activity (i.e., percentage of firing neurons) equal to (1/2)(1+a), -1&lt;a&lt;1. If the coupling constants (synaptic efficacies) are constructed as in the original Hopfield model, the system can retrieve at most a very small number of patterns (p1+${a}^{\mathrm{\ensuremath{-}}2}$). This is due to the finite correlations (overlaps) between the patterns. The model is modified by subtracting the bias a from each pattern as it enters into the couplings. This modification restores the ability of the model to store a macroscopic number of patterns. Yet spurious states are found to plague the dynamics. It is then argued that the dynamics of the network should be consistent with the levels of activity of the stored patterns. This is implemented by adding a global constraint, which restricts the configuration space to states whose mean activity is in the neighborhood of (1/2)(1+a). The consequences of the restricted dynamics are analyzed in the replica symmetric mean-field theory. The global constraint suppresses spurious states and leads to the unexpected result that the storage capacity is higher than that of the unbiased network, up to very high values of the bias (\ensuremath{\Vert}a\ensuremath{\Vert}\ensuremath{\simeq}0.99). However, the information content of such networks is shown to be a monotonically decreasing function of a.
Physics of Oil Entrapment in Water-Wet Rock (1987)

Summary Displacement of oil from an initially oil-filled porous rock by water consists of advancement of menisci and rupture of oil connections. In displacements controlled by capillarity, which are typical of oil reservoir floods, these pore-level events are governed by the local pore geometry, pore topology, and fluid properties, but the pressure field initiates these pore-level events and integrates them with the externally imposed Darcy flow. This paper reports the physics of the pore-level events and their integration on a computationally simple model of rock: a square network of pores. The novelty of the approach lies in keeping track of the evolution of the displacement front and in constructing an approximation of the entire pressure field that carries the information essential for predicting the evolution. The result gives insight into the state of the residual oil saturation and its dependence on pore geometry and the capillary number, Nca, of displacement. As the capillary number increases, the residual oil saturation decreases and the residual oil blobs tend to be smaller. As the pore size distribution becomes wider, the decrease of residual oil saturation with capillary number becomes smoother.
Nickel Hexacyanoferrate Nanoparticle Electrodes For Aqueous Sodium and Potassium Ion Batteries (2011)

The electrical power grid faces a growing need for large-scale energy storage over a wide range of time scales due to costly short-term transients, frequency regulation, and load balancing. The durability, high power, energy efficiency, and low cost needed for grid-scale storage pose substantial challenges for conventional battery technology. (1, 2) Here, we demonstrate insertion/extraction of sodium and potassium ions in a low-strain nickel hexacyanoferrate electrode material for at least five thousand deep cycles at high current densities in inexpensive aqueous electrolytes. Its open-framework structure allows retention of 66% of the initial capacity even at a very high (41.7C) rate. At low current densities, its round trip energy efficiency reaches 99%. This low-cost material is readily synthesized in bulk quantities. The long cycle life, high power, good energy efficiency, safety, and inexpensive production method make nickel hexacyanoferrate an attractive candidate for use in large-scale batteries to support the electrical grid.
Analysis of the peripheral T‐cell repertoire in kidney transplant patients (2010)

The long-term stability of renal grafts depends on the absence of chronic rejection. As T cells play a key role in rejection processes, analyzing the T-cell repertoire may be useful for understanding graft function outcomes. We have therefore investigated the power of a new statistical tool, used to analyze the peripheral blood TCR repertoire, for determining immunological differences in a group of 229 stable renal transplant patients undergoing immunosuppression. Despite selecting the patients according to stringent criteria, the patients displayed heterogeneous T-cell repertoire usage, ranging from unbiased to highly selected TCR repertoires; a skewed TCR repertoire correlating with an increase in the CD8(+) /CD4(+) T-cell ratio. T-cell repertoire patterns were compared in patients with clinically opposing outcomes i.e. stable drug-free operationally tolerant recipients and patients with the "suspicious" form of humoral chronic rejection and were found significantly different, from polyclonal to highly selected TCR repertoires, respectively. Moreover, a selected TCR repertoire was found to positively correlate with the Banff score grade. Collectively, these data suggest that TCR repertoire categorization might be included in the calculation of a composite score for the follow-up of patients after kidney transplantation.
Fluorescent Ion-Selective Nanosensors for Intracellular Analysis with Improved Lifetime and Size (2007)

We describe the synthesis and characterization of sodium-selective polymeric nanosensors that improves upon the lifetime and size of previous fiberless nanosensors. Sonication is used to form the polymer nanospheres that contain all the components needed for ion sensing. Even though the size is small (approximately 120 nm), the lifetime of these sensors in solution is on the order of a week. The surface coating has also been optimized for stability, biocompatibility, and ease of chemical modification.